-- dump date 20140620_023156 -- class Genbank::misc_feature -- table misc_feature_note -- id note 428406000001 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 428406000002 HAMP domain; Region: HAMP; pfam00672 428406000003 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 428406000004 dimer interface [polypeptide binding]; other site 428406000005 phosphorylation site [posttranslational modification] 428406000006 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406000007 ATP binding site [chemical binding]; other site 428406000008 Mg2+ binding site [ion binding]; other site 428406000009 G-X-G motif; other site 428406000010 DNA-binding transcriptional activator CusR; Provisional; Region: PRK09836 428406000011 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406000012 active site 428406000013 phosphorylation site [posttranslational modification] 428406000014 intermolecular recognition site; other site 428406000015 dimerization interface [polypeptide binding]; other site 428406000016 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 428406000017 DNA binding site [nucleotide binding] 428406000018 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 428406000019 Multicopper oxidase; Region: Cu-oxidase; pfam00394 428406000020 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 428406000021 Copper resistance protein B precursor (CopB); Region: CopB; cl01476 428406000022 Copper resistance protein B precursor (CopB); Region: CopB; pfam05275 428406000023 CopC domain; Region: CopC; pfam04234 428406000024 Putative copper export protein [Inorganic ion transport and metabolism]; Region: PcoD; COG1276 428406000025 Protein of unknown function, DUF; Region: DUF411; cl01142 428406000026 Uncharacterized copper-binding protein [Inorganic ion transport and metabolism]; Region: COG4454 428406000027 nitrogen assimilation transcriptional regulator; Provisional; Region: PRK11233 428406000028 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406000029 The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold; Region: PBP2_LysR_opines_like; cd08415 428406000030 putative dimerization interface [polypeptide binding]; other site 428406000031 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 428406000032 cystathionine beta-lyase; Provisional; Region: PRK09028 428406000033 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 428406000034 catalytic residue [active] 428406000035 glutamate and aspartate transporter subunit; Provisional; Region: PRK10797 428406000036 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 428406000037 substrate binding pocket [chemical binding]; other site 428406000038 membrane-bound complex binding site; other site 428406000039 hinge residues; other site 428406000040 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406000041 dimer interface [polypeptide binding]; other site 428406000042 conserved gate region; other site 428406000043 putative PBP binding loops; other site 428406000044 ABC-ATPase subunit interface; other site 428406000045 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406000046 dimer interface [polypeptide binding]; other site 428406000047 conserved gate region; other site 428406000048 putative PBP binding loops; other site 428406000049 ABC-ATPase subunit interface; other site 428406000050 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 428406000051 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 428406000052 Walker A/P-loop; other site 428406000053 ATP binding site [chemical binding]; other site 428406000054 Q-loop/lid; other site 428406000055 ABC transporter signature motif; other site 428406000056 Walker B; other site 428406000057 D-loop; other site 428406000058 H-loop/switch region; other site 428406000059 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 428406000060 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 428406000061 trimer interface [polypeptide binding]; other site 428406000062 eyelet of channel; other site 428406000063 CopC domain; Region: CopC; pfam04234 428406000064 heavy metal efflux pump, CzcA family; Region: 2A0601; TIGR00914 428406000065 PemK-like protein; Region: PemK; cl00995 428406000066 Antidote-toxin recognition MazE; Region: Antitoxin-MazE; cl00877 428406000067 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 428406000068 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 428406000069 catalytic residues [active] 428406000070 catalytic nucleophile [active] 428406000071 Presynaptic Site I dimer interface [polypeptide binding]; other site 428406000072 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 428406000073 Synaptic Flat tetramer interface [polypeptide binding]; other site 428406000074 Synaptic Site I dimer interface [polypeptide binding]; other site 428406000075 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 428406000076 DNA-binding interface [nucleotide binding]; DNA binding site 428406000077 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor...; Region: Ribosomal_L24e_L24; cl00909 428406000078 MgtC family; Region: MgtC; pfam02308 428406000079 Predicted membrane protein [Function unknown]; Region: COG3174 428406000080 Domain of unknown function (DUF4010); Region: DUF4010; pfam13194 428406000081 Outer membrane efflux protein; Region: OEP; pfam02321 428406000082 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 428406000083 HlyD family secretion protein; Region: HlyD_3; pfam13437 428406000084 heavy metal efflux pump, CzcA family; Region: 2A0601; TIGR00914 428406000085 Solute carrier families 5 and 6-like; solute binding domain; Region: SLC5-6-like_sbd; cl00456 428406000086 HupE / UreJ protein; Region: HupE_UreJ_2; pfam13795 428406000087 H+ Antiporter protein; Region: 2A0121; TIGR00900 428406000088 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406000089 Protein of unknown function (DUF3240); Region: DUF3240; pfam11582 428406000090 Domain of unknown function (DUF4158); Region: DUF4158; pfam13700 428406000091 Domain of unknown function (DUF4158); Region: DUF4158; pfam13700 428406000092 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; pfam01526 428406000093 Outer membrane efflux protein; Region: OEP; pfam02321 428406000094 Transcriptional regulators RcnR and FrmR, and related domains; this domain family was previously known as part of DUF156; Region: RcnR-FrmR-like_DUF156; cd10153 428406000095 putative metal binding site [ion binding]; other site 428406000096 putative homodimer interface [polypeptide binding]; other site 428406000097 putative homotetramer interface [polypeptide binding]; other site 428406000098 putative homodimer-homodimer interface [polypeptide binding]; other site 428406000099 putative allosteric switch controlling residues; other site 428406000100 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 428406000101 Cation efflux family; Region: Cation_efflux; cl00316 428406000102 Plasmid replication region DNA-binding N-term; Region: KfrA_N; pfam11740 428406000103 2'-5' RNA ligase [Translation, ribosomal structure and biogenesis]; Region: LigT; COG1514 428406000104 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 428406000105 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 428406000106 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 428406000107 active site 428406000108 Int/Topo IB signature motif; other site 428406000109 catalytic residues [active] 428406000110 DNA binding site [nucleotide binding] 428406000111 H-NS histone family; Region: Histone_HNS; pfam00816 428406000112 Domain in histone-like proteins of HNS family; Region: HNS; smart00528 428406000113 H-NS histone family; Region: Histone_HNS; pfam00816 428406000114 Domain in histone-like proteins of HNS family; Region: HNS; smart00528 428406000115 Protein of unknown function (DUF3800); Region: DUF3800; pfam12686 428406000116 Protein of unknown function (DUF3800); Region: DUF3800; pfam12686 428406000117 Plasmid replication region DNA-binding N-term; Region: KfrA_N; pfam11740 428406000118 TraB family; Region: TraB; pfam01963 428406000119 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cl00257 428406000120 IHF - DNA interface [nucleotide binding]; other site 428406000121 IHF dimer interface [polypeptide binding]; other site 428406000122 Restriction endonuclease; Region: Mrr_cat; pfam04471 428406000123 Phage integrase protein; Region: DUF3701; pfam12482 428406000124 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 428406000125 Phage integrase, N-terminal SAM-like domain; Region: Phage_integr_N2; pfam13495 428406000126 INT_SG1, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 1, C-terminal catalytic domain. The CD contains mainly predicted integrase/recombinase and site-specific XerD recombinases. The members of this CD are found predominantly in...; Region: INT_SG1_C; cd01183 428406000127 Int/Topo IB signature motif; other site 428406000128 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 428406000129 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 428406000130 P-loop; other site 428406000131 Magnesium ion binding site [ion binding]; other site 428406000132 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 428406000133 ParB-like nuclease domain; Region: ParBc; pfam02195 428406000134 Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; Region: PI-PLCc_GDPD_SF; cl14615 428406000135 Initiator Replication protein; Region: Rep_3; pfam01051 428406000136 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 428406000137 Family description; Region: UvrD_C_2; pfam13538 428406000138 Flagellar transcriptional activator (FlhD); Region: FlhD; cl05012 428406000139 Domain of unknown function (DUF4400); Region: DUF4400; pfam14348 428406000140 conjugative coupling factor TraD, SXT/TOL subfamily; Region: SXT_TraD; TIGR03743 428406000141 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 428406000142 integrating conjugative element relaxase, PFL_4751 family; Region: ICE_TraI_Pfluor; TIGR03760 428406000143 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; pfam04610 428406000144 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 428406000145 Transposase; Region: HTH_Tnp_1; pfam01527 428406000146 putative transposase OrfB; Reviewed; Region: PHA02517 428406000147 HTH-like domain; Region: HTH_21; pfam13276 428406000148 Integrase core domain; Region: rve; pfam00665 428406000149 Integrase core domain; Region: rve_3; pfam13683 428406000150 P-type DNA transfer ATPase VirB11; Region: VirB11; TIGR02788 428406000151 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 428406000152 Walker A motif; other site 428406000153 hexamer interface [polypeptide binding]; other site 428406000154 ATP binding site [chemical binding]; other site 428406000155 Walker B motif; other site 428406000156 VirB8 protein; Region: VirB8; pfam04335 428406000157 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 428406000158 VirB7 interaction site; other site 428406000159 Bacterial conjugation TrbI-like protein; Region: TrbI; pfam03743 428406000160 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 428406000161 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cl11423 428406000162 VirB7 interaction site; other site 428406000163 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 428406000164 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 428406000165 N-acetyl-D-glucosamine binding site [chemical binding]; other site 428406000166 catalytic residue [active] 428406000167 Toxin co-regulated pilus biosynthesis protein Q; Region: TcpQ; pfam10671 428406000168 type IVB pilus formation outer membrane protein, R64 PilN family; Region: pilus_B_mal_scr; TIGR02520 428406000169 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 428406000170 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 428406000171 type IV pilus biogenesis protein PilP; Region: pilP_fam; TIGR03021 428406000172 Pilin accessory protein (PilO); Region: PAP_PilO; pfam06864 428406000173 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 428406000174 Walker A motif; other site 428406000175 ATP binding site [chemical binding]; other site 428406000176 Walker B motif; other site 428406000177 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 428406000178 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 428406000179 Bacterial shufflon protein, N-terminal constant region; Region: Shufflon_N; pfam04917 428406000180 SCP_bacterial: SCP-like extracellular protein domain, as found in bacteria and archaea. The wider family of SCP containing proteins includes plant pathogenesis-related protein 1 (PR-1), CRISPs, mammalian cysteine-rich secretory proteins, and allergen 5...; Region: SCP_bacterial; cd05379 428406000181 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 428406000182 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 428406000183 SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date...; Region: SSB_OBF; cd04496 428406000184 dimer interface [polypeptide binding]; other site 428406000185 ssDNA binding site [nucleotide binding]; other site 428406000186 tetramer (dimer of dimers) interface [polypeptide binding]; other site 428406000187 Zinc-binding domain of primase-helicase; Region: Prim_Zn_Ribbon; smart00778 428406000188 Toprim domain; Region: Toprim_3; pfam13362 428406000189 Plasmid segregation protein ParM and similar proteins; Region: ParM_like; cd10227 428406000190 PRTRC system protein D; Region: PRTRC_D; TIGR03739 428406000191 Mg binding site [ion binding]; other site 428406000192 nucleotide binding site [chemical binding]; other site 428406000193 putative protofilament interface [polypeptide binding]; other site 428406000194 Phage integrase, N-terminal; Region: Integrase_l_N; pfam12834 428406000195 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 428406000196 active site 428406000197 catalytic residues [active] 428406000198 Int/Topo IB signature motif; other site 428406000199 DNA binding site [nucleotide binding] 428406000200 DNA/RNA endonuclease G, NUC1 [Nucleotide transport and metabolism]; Region: NUC1; COG1864 428406000201 DNA/RNA non-specific endonuclease; Region: Endonuclease_NS; smart00892 428406000202 active site 428406000203 substrate binding site [chemical binding]; other site 428406000204 Mg2+ binding site [ion binding]; other site 428406000205 Protein of unknown function (DUF1173); Region: DUF1173; pfam06666 428406000206 Ylxr homologs; group of conserved hypothetical bacterial proteins of unknown function; structure revealed putative RNA binding cleft; proteins are encoded by an operon that includes other proteins involved in transcription and/or translation; Region: YlxR; cl00189 428406000207 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 428406000208 Family description; Region: UvrD_C_2; pfam13538 428406000209 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 428406000210 ParB-like nuclease domain; Region: ParBc; pfam02195 428406000211 PRTRC system ParB family protein; Region: PRTRC_parB; TIGR03734 428406000212 PRTRC system protein E; Region: PRTRC_E; TIGR03741 428406000213 PRTRC system protein C; Region: PRTRC_C; TIGR03738 428406000214 PRTRC system protein F; Region: PRTRC_F; TIGR03742 428406000215 Alpha-helical domain 2; Region: alpha-hel2; pfam14456 428406000216 PRTRC system protein B; Region: PRTRC_B; TIGR03737 428406000217 Domain of unknown function (DUF2016); Region: DUF2016; pfam09436 428406000218 PRTRC system protein A; Region: PRTRC_A; TIGR03735 428406000219 Prokaryotic homologs of the JAB domain; Region: Prok-JAB; pfam14464 428406000220 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2268 428406000221 SPFH domain / Band 7 family; Region: Band_7; pfam01145 428406000222 Glycine zipper 2TM domain; Region: Rick_17kDa_Anti; cl10470 428406000223 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406000224 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 428406000225 Walker A motif; other site 428406000226 ATP binding site [chemical binding]; other site 428406000227 Walker B motif; other site 428406000228 arginine finger; other site 428406000229 Putative metallopeptidase domain; Region: DUF2201_N; pfam13203 428406000230 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 428406000231 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 428406000232 DNA repair exonuclease [DNA replication, recombination, and repair]; Region: SbcD; COG0420 428406000233 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 428406000234 active site 428406000235 metal binding site [ion binding]; metal-binding site 428406000236 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: SbcC; COG0419 428406000237 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 428406000238 Walker A/P-loop; other site 428406000239 ATP binding site [chemical binding]; other site 428406000240 Domain of unknown function (DUF4158); Region: DUF4158; pfam13700 428406000241 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; cl14901 428406000242 Cre recombinase, C-terminal catalytic domain. Cre-like recombinases belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The bacteriophage P1 Cre...; Region: INT_Cre; cd00799 428406000243 DNA binding site [nucleotide binding] 428406000244 dimer interface [polypeptide binding]; other site 428406000245 active site 428406000246 Int/Topo IB signature motif; other site 428406000247 Cytochrome c; Region: Cytochrom_C; pfam00034 428406000248 High-affinity Fe2+/Pb2+ permease [Inorganic ion transport and metabolism]; Region: FTR1; COG0672 428406000249 Cd(II)/Pb(II)-responsive transcriptional regulator; Region: CadR-PbrR; TIGR02047 428406000250 Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; Region: HTH_CadR-PbrR; cd04784 428406000251 DNA binding residues [nucleotide binding] 428406000252 dimer interface [polypeptide binding]; other site 428406000253 putative metal binding site [ion binding]; other site 428406000254 Heavy-metal-associated domain; Region: HMA; pfam00403 428406000255 metal-binding site [ion binding] 428406000256 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 428406000257 Heavy-metal-associated domain; Region: HMA; pfam00403 428406000258 metal-binding site [ion binding] 428406000259 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 428406000260 Soluble P-type ATPase [General function prediction only]; Region: COG4087 428406000261 PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid...; Region: PAP2_like; cd01610 428406000262 active site 428406000263 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 428406000264 Uncharacterized conserved protein [Function unknown]; Region: COG5569 428406000265 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 428406000266 copper/silver efflux system membrane fusion protein CusB; Provisional; Region: PRK09783 428406000267 HlyD family secretion protein; Region: HlyD_3; pfam13437 428406000268 Copper binding periplasmic protein CusF; Region: CusF_Ec; pfam11604 428406000269 Outer membrane efflux protein; Region: OEP; pfam02321 428406000270 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor...; Region: Ribosomal_L24e_L24; cl00909 428406000271 Uncharacterized conserved protein [Function unknown]; Region: COG3350 428406000272 copper-(or silver)-translocating P-type ATPase; Region: ATPase-IB1_Cu; TIGR01511 428406000273 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 428406000274 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 428406000275 motif II; other site 428406000276 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor...; Region: Ribosomal_L24e_L24; cl00909 428406000277 Protein of unknown function (DUF2933); Region: DUF2933; pfam11666 428406000278 Putative protein-S-isoprenylcysteine methyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: STE14; COG2020 428406000279 Protein of unknown function (DUF3141); Region: DUF3141; pfam11339 428406000280 Outer membrane lipoprotein-sorting protein [Cell envelope biogenesis, outer membrane]; Region: LolA; COG2834 428406000281 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 428406000282 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 428406000283 Walker A/P-loop; other site 428406000284 ATP binding site [chemical binding]; other site 428406000285 Q-loop/lid; other site 428406000286 ABC transporter signature motif; other site 428406000287 Walker B; other site 428406000288 D-loop; other site 428406000289 H-loop/switch region; other site 428406000290 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 428406000291 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 428406000292 FtsX-like permease family; Region: FtsX; pfam02687 428406000293 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 428406000294 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 428406000295 FtsX-like permease family; Region: FtsX; pfam02687 428406000296 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 428406000297 ABC1 family; Region: ABC1; cl17513 428406000298 S-adenosylmethionine synthetase (AdoMet synthetase); Region: AdoMet_Synthase; pfam01941 428406000299 Uncharacterized conserved protein [Function unknown]; Region: LemA; COG1704 428406000300 Beta-propeller domains of methanol dehydrogenase type [General function prediction only]; Region: COG1512 428406000301 Repair protein; Region: Repair_PSII; pfam04536 428406000302 Repair protein; Region: Repair_PSII; cl01535 428406000303 polyphosphate kinase 2, PA0141 family; Region: PPK2_P_aer; TIGR03707 428406000304 FtsH Extracellular; Region: FtsH_ext; pfam06480 428406000305 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 428406000306 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406000307 Walker A motif; other site 428406000308 ATP binding site [chemical binding]; other site 428406000309 Walker B motif; other site 428406000310 arginine finger; other site 428406000311 Peptidase family M41; Region: Peptidase_M41; pfam01434 428406000312 putative transposase OrfB; Reviewed; Region: PHA02517 428406000313 HTH-like domain; Region: HTH_21; pfam13276 428406000314 Integrase core domain; Region: rve; pfam00665 428406000315 Integrase core domain; Region: rve_3; pfam13683 428406000316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 428406000317 Transposase; Region: HTH_Tnp_1; cl17663 428406000318 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 428406000319 metal-binding site [ion binding] 428406000320 Putative protein-S-isoprenylcysteine methyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: STE14; COG2020 428406000321 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 428406000322 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 428406000323 Beta-Casp domain; Region: Beta-Casp; smart01027 428406000324 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 428406000325 thymidine phosphorylase; Provisional; Region: PRK04350 428406000326 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 428406000327 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 428406000328 Pyrimidine nucleoside phosphorylase C-terminal domain; Region: PYNP_C; smart00941 428406000329 phosphoribosylpyrophosphate synthetase; Provisional; Region: PRK07199 428406000330 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 428406000331 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 428406000332 active site 428406000333 putative transposase OrfB; Reviewed; Region: PHA02517 428406000334 HTH-like domain; Region: HTH_21; pfam13276 428406000335 Integrase core domain; Region: rve; pfam00665 428406000336 Integrase core domain; Region: rve_3; pfam13683 428406000337 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 428406000338 Transposase; Region: HTH_Tnp_1; pfam01527 428406000339 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 428406000340 metal-binding site [ion binding] 428406000341 copper-(or silver)-translocating P-type ATPase; Region: ATPase-IB1_Cu; TIGR01511 428406000342 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 428406000343 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 428406000344 motif II; other site 428406000345 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406000346 Major Facilitator Superfamily; Region: MFS_1; pfam07690 428406000347 CopC domain; Region: CopC; pfam04234 428406000348 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 428406000349 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 428406000350 dimerization interface [polypeptide binding]; other site 428406000351 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 428406000352 dimer interface [polypeptide binding]; other site 428406000353 phosphorylation site [posttranslational modification] 428406000354 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406000355 ATP binding site [chemical binding]; other site 428406000356 Mg2+ binding site [ion binding]; other site 428406000357 G-X-G motif; other site 428406000358 DNA-binding transcriptional activator CusR; Provisional; Region: PRK09836 428406000359 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406000360 active site 428406000361 phosphorylation site [posttranslational modification] 428406000362 intermolecular recognition site; other site 428406000363 dimerization interface [polypeptide binding]; other site 428406000364 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 428406000365 DNA binding site [nucleotide binding] 428406000366 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 428406000367 Multicopper oxidase; Region: Cu-oxidase; pfam00394 428406000368 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 428406000369 Copper resistance protein B precursor (CopB); Region: CopB; pfam05275 428406000370 CopC domain; Region: CopC; pfam04234 428406000371 Putative copper export protein [Inorganic ion transport and metabolism]; Region: PcoD; COG1276 428406000372 Protein of unknown function, DUF; Region: DUF411; cl01142 428406000373 Cre recombinase, C-terminal catalytic domain. Cre-like recombinases belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The bacteriophage P1 Cre...; Region: INT_Cre; cd00799 428406000374 DNA binding site [nucleotide binding] 428406000375 dimer interface [polypeptide binding]; other site 428406000376 active site 428406000377 Int/Topo IB signature motif; other site 428406000378 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 428406000379 putative DNA binding site [nucleotide binding]; other site 428406000380 putative Zn2+ binding site [ion binding]; other site 428406000381 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_20; cd07254 428406000382 putative metal binding site [ion binding]; other site 428406000383 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 428406000384 Low molecular weight phosphatase family; Region: LMWPc; cd00115 428406000385 active site 428406000386 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 428406000387 Low molecular weight phosphatase family; Region: LMWPc; cd00115 428406000388 active site 428406000389 Glycerol uptake facilitator and related permeases (Major Intrinsic Protein Family) [Carbohydrate transport and metabolism]; Region: GlpF; COG0580 428406000390 amphipathic channel; other site 428406000391 Asn-Pro-Ala signature motifs; other site 428406000392 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 428406000393 Coenzyme A binding pocket [chemical binding]; other site 428406000394 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406000395 Major Facilitator Superfamily; Region: MFS_1; pfam07690 428406000396 putative substrate translocation pore; other site 428406000397 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 428406000398 Cytochrome c; Region: Cytochrom_C; pfam00034 428406000399 High-affinity Fe2+/Pb2+ permease [Inorganic ion transport and metabolism]; Region: FTR1; COG0672 428406000400 Cd(II)/Pb(II)-responsive transcriptional regulator; Region: CadR-PbrR; TIGR02047 428406000401 Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; Region: HTH_CadR-PbrR; cd04784 428406000402 DNA binding residues [nucleotide binding] 428406000403 dimer interface [polypeptide binding]; other site 428406000404 putative metal binding site [ion binding]; other site 428406000405 Heavy-metal-associated domain; Region: HMA; pfam00403 428406000406 metal-binding site [ion binding] 428406000407 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 428406000408 Heavy-metal-associated domain; Region: HMA; pfam00403 428406000409 metal-binding site [ion binding] 428406000410 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 428406000411 Soluble P-type ATPase [General function prediction only]; Region: COG4087 428406000412 PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid...; Region: PAP2_like; cd01610 428406000413 active site 428406000414 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 428406000415 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 428406000416 lipoprotein signal peptidase; Provisional; Region: PRK14787 428406000417 Uncharacterized conserved protein [Function unknown]; Region: COG5569 428406000418 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 428406000419 copper/silver efflux system membrane fusion protein CusB; Provisional; Region: PRK09783 428406000420 HlyD family secretion protein; Region: HlyD_3; pfam13437 428406000421 Copper binding periplasmic protein CusF; Region: CusF_Ec; pfam11604 428406000422 Outer membrane efflux protein; Region: OEP; pfam02321 428406000423 Outer membrane efflux protein; Region: OEP; pfam02321 428406000424 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 428406000425 Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Region: HTH_CueR; cd01108 428406000426 DNA binding residues [nucleotide binding] 428406000427 dimer interface [polypeptide binding]; other site 428406000428 copper binding site [ion binding]; other site 428406000429 YHS domain; Region: YHS; pfam04945 428406000430 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 428406000431 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 428406000432 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 428406000433 motif II; other site 428406000434 Protein of unknown function (DUF2933); Region: DUF2933; pfam11666 428406000435 Putative protein-S-isoprenylcysteine methyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: STE14; COG2020 428406000436 Nitrogen regulatory protein P-II; Region: P-II; cl00412 428406000437 Nitrogen regulatory protein P-II; Region: P-II; smart00938 428406000438 thiol:disulfide interchange protein precursor; Provisional; Region: dipZ; PRK00293 428406000439 Disulphide bond corrector protein DsbC; Region: DsbC; pfam11412 428406000440 DsbD gamma family; DsbD gamma is the C-terminal periplasmic domain of the bacterial protein DsbD. It contains a CXXC motif in a TRX fold and shuttles the reducing potential from the membrane domain (DsbD beta) to the N-terminal periplasmic domain (DsbD...; Region: DsbDgamma; cd02953 428406000441 DsbD alpha interface [polypeptide binding]; other site 428406000442 catalytic residues [active] 428406000443 Cytochrome c2 [Energy production and conversion]; Region: COG3474 428406000444 Secreted repeat of unknown function; Region: Lipoprotein_15; pfam03640 428406000445 Secreted repeat of unknown function; Region: Lipoprotein_15; pfam03640 428406000446 Methyltransferase domain; Region: Methyltransf_23; pfam13489 428406000447 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 428406000448 S-adenosylmethionine binding site [chemical binding]; other site 428406000449 Predicted membrane protein [Function unknown]; Region: COG2246 428406000450 GtrA-like protein; Region: GtrA; pfam04138 428406000451 Nicotinamide mononucleotide transporter; Region: NMN_transporter; cl01256 428406000452 Copper resistance protein B precursor (CopB); Region: CopB; pfam05275 428406000453 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 428406000454 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 428406000455 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 428406000456 motif II; other site 428406000457 FMN-binding domain; Region: FMN_bind; pfam04205 428406000458 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 428406000459 ApbE family; Region: ApbE; pfam02424 428406000460 Cysteine-rich 4 helical bundle widely conserved in bacteria; Region: DUF326; cd08026 428406000461 dimerization interface [polypeptide binding]; other site 428406000462 RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner; Region: RNase_H; cl14782 428406000463 ParG; Region: ParG; pfam09274 428406000464 ParA-like protein; Provisional; Region: PHA02518 428406000465 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 428406000466 P-loop; other site 428406000467 Magnesium ion binding site [ion binding]; other site 428406000468 Initiator Replication protein; Region: Rep_3; pfam01051 428406000469 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 428406000470 AAA-like domain; Region: AAA_10; pfam12846 428406000471 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 428406000472 Walker B motif; other site 428406000473 Methyltransferase domain; Region: Methyltransf_27; pfam13708 428406000474 ParB-like nuclease domain; Region: ParBc; pfam02195 428406000475 Domain of unknown function (DUF932); Region: DUF932; pfam06067 428406000476 Protein of unknown function (DUF3717); Region: DUF3717; pfam12512 428406000477 Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar proteins; Region: PLDc_Nuc; cd09170 428406000478 PLD-like domain; Region: PLDc_2; pfam13091 428406000479 putative active site [active] 428406000480 catalytic site [active] 428406000481 Protein of unknown function (DUF2274); Region: DUF2274; cl02406 428406000482 conjugal transfer protein TraB; Provisional; Region: PRK13825 428406000483 active site 428406000484 catalytic triad [active] 428406000485 dimer interface [polypeptide binding]; other site 428406000486 Bacterial conjugation TrbI-like protein; Region: TrbI; pfam03743 428406000487 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cl11423 428406000488 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 428406000489 VirB7 interaction site; other site 428406000490 VirB8 protein; Region: VirB8; pfam04335 428406000491 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; pfam04610 428406000492 Conjugal transfer/entry exclusion protein [Intracellular trafficking and secretion]; Region: COG5314 428406000493 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 428406000494 Type IV secretory pathway, VirB3-like protein; Region: VirB3; cl01501 428406000495 P-type DNA transfer ATPase VirB11; Region: VirB11; TIGR02788 428406000496 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 428406000497 Walker A motif; other site 428406000498 hexamer interface [polypeptide binding]; other site 428406000499 ATP binding site [chemical binding]; other site 428406000500 Walker B motif; other site 428406000501 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 428406000502 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 428406000503 N-acetyl-D-glucosamine binding site [chemical binding]; other site 428406000504 catalytic residue [active] 428406000505 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 428406000506 SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date...; Region: SSB_OBF; cd04496 428406000507 dimer interface [polypeptide binding]; other site 428406000508 ssDNA binding site [nucleotide binding]; other site 428406000509 tetramer (dimer of dimers) interface [polypeptide binding]; other site 428406000510 SCP_bacterial: SCP-like extracellular protein domain, as found in bacteria and archaea. The wider family of SCP containing proteins includes plant pathogenesis-related protein 1 (PR-1), CRISPs, mammalian cysteine-rich secretory proteins, and allergen 5...; Region: SCP_bacterial; cd05379 428406000511 Bacterial shufflon protein, N-terminal constant region; Region: Shufflon_N; pfam04917 428406000512 PilS N terminal; Region: PilS; pfam08805 428406000513 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 428406000514 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 428406000515 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 428406000516 Walker A motif; other site 428406000517 ATP binding site [chemical binding]; other site 428406000518 Walker B motif; other site 428406000519 type IV pilus biogenesis protein PilP; Region: pilP_fam; TIGR03021 428406000520 type IVB pilus formation outer membrane protein, R64 PilN family; Region: pilus_B_mal_scr; TIGR02520 428406000521 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 428406000522 Toxin co-regulated pilus biosynthesis protein Q; Region: TcpQ; pfam10671 428406000523 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 428406000524 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 428406000525 N-acetyl-D-glucosamine binding site [chemical binding]; other site 428406000526 catalytic residue [active] 428406000527 Pleckstrin homology-like domain; Region: PH-like; cl17171 428406000528 PemK-like protein; Region: PemK; pfam02452 428406000529 Phage integrase protein; Region: DUF3701; pfam12482 428406000530 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 428406000531 active site 428406000532 catalytic residues [active] 428406000533 DNA binding site [nucleotide binding] 428406000534 Int/Topo IB signature motif; other site 428406000535 cobaltochelatase, CobS subunit; Region: PD_CobS; TIGR01650 428406000536 AAA domain (dynein-related subfamily); Region: AAA_5; pfam07728 428406000537 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 428406000538 SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date...; Region: SSB_OBF; cd04496 428406000539 dimer interface [polypeptide binding]; other site 428406000540 ssDNA binding site [nucleotide binding]; other site 428406000541 tetramer (dimer of dimers) interface [polypeptide binding]; other site 428406000542 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK07207 428406000543 ATP cone domain; Region: ATP-cone; pfam03477 428406000544 Class I ribonucleotide reductase; Region: RNR_I; cd01679 428406000545 active site 428406000546 dimer interface [polypeptide binding]; other site 428406000547 catalytic residues [active] 428406000548 effector binding site; other site 428406000549 R2 peptide binding site; other site 428406000550 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 428406000551 dimer interface [polypeptide binding]; other site 428406000552 putative radical transfer pathway; other site 428406000553 diiron center [ion binding]; other site 428406000554 tyrosyl radical; other site 428406000555 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 428406000556 non-specific DNA binding site [nucleotide binding]; other site 428406000557 salt bridge; other site 428406000558 sequence-specific DNA binding site [nucleotide binding]; other site 428406000559 Domain of unknown function (DUF955); Region: DUF955; cl01076 428406000560 Caseinolytic protease (ClpP) is an ATP-dependent protease; Region: Clp_protease_like; cl15763 428406000561 active site 428406000562 Transposase; Region: HTH_Tnp_1; cl17663 428406000563 putative transposase OrfB; Reviewed; Region: PHA02517 428406000564 HTH-like domain; Region: HTH_21; pfam13276 428406000565 Integrase core domain; Region: rve; pfam00665 428406000566 Integrase core domain; Region: rve_3; pfam13683 428406000567 transposase/IS protein; Provisional; Region: PRK09183 428406000568 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406000569 Walker A motif; other site 428406000570 ATP binding site [chemical binding]; other site 428406000571 Walker B motif; other site 428406000572 arginine finger; other site 428406000573 Winged helix-turn-helix DNA-binding; Region: HTH_24; pfam13412 428406000574 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG4584 428406000575 Integrase core domain; Region: rve; pfam00665 428406000576 H-NS histone family; Region: Histone_HNS; pfam00816 428406000577 Domain in histone-like proteins of HNS family; Region: HNS; smart00528 428406000578 Thiolase domain associated with sterol carrier protein (SCP)-x isoform and related proteins; SCP-2 has multiple roles in intracellular lipid circulation and metabolism. The N-terminal presequence in the SCP-x isoform represents a peroxisomal...; Region: SCP-x_thiolase; cd00829 428406000579 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK06187 428406000580 Bacterial Bile acid CoA ligases and similar proteins; Region: BACL_like; cd05929 428406000581 acyl-activating enzyme (AAE) consensus motif; other site 428406000582 putative AMP binding site [chemical binding]; other site 428406000583 putative active site [active] 428406000584 putative CoA binding site [chemical binding]; other site 428406000585 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 428406000586 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 428406000587 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 428406000588 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 428406000589 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 428406000590 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 428406000591 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 428406000592 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 428406000593 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 428406000594 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 428406000595 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 428406000596 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 428406000597 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 428406000598 probable polyamine oxidase; Region: PLN02268 428406000599 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 428406000600 CLC voltage-gated chloride channel. The ClC chloride channels catalyse the selective flow of Cl- ions across cell membranes, thereby regulating electrical excitation in skeletal muscle and the flow of salt and water across epithelial barriers. This...; Region: Voltage_gated_ClC; cd00400 428406000601 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 428406000602 Cl- selectivity filter; other site 428406000603 Cl- binding residues [ion binding]; other site 428406000604 pore gating glutamate residue; other site 428406000605 dimer interface [polypeptide binding]; other site 428406000606 Protein of unknown function (DUF3604); Region: DUF3604; pfam12228 428406000607 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 428406000608 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 428406000609 tetramerization interface [polypeptide binding]; other site 428406000610 NAD(P) binding site [chemical binding]; other site 428406000611 catalytic residues [active] 428406000612 choline dehydrogenase; Validated; Region: PRK02106 428406000613 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 428406000614 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406000615 D-galactonate transporter; Region: 2A0114; TIGR00893 428406000616 putative substrate translocation pore; other site 428406000617 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406000618 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406000619 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 428406000620 dimerization interface [polypeptide binding]; other site 428406000621 Putative glycosyl hydrolase of unknown function (DUF1680); Region: DUF1680; pfam07944 428406000622 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 428406000623 probable polyamine oxidase; Region: PLN02268 428406000624 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK06945 428406000625 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 428406000626 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 428406000627 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 428406000628 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 428406000629 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 428406000630 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 428406000631 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 428406000632 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 428406000633 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 428406000634 flagellin; Provisional; Region: PRK12802 428406000635 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 428406000636 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 428406000637 probable polyamine oxidase; Region: PLN02268 428406000638 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 428406000639 Uncharacterized ACR, COG2135; Region: DUF159; pfam02586 428406000640 TnsA endonuclease N terminal; Region: Tn7_Tnp_TnsA_N; pfam08722 428406000641 Integrase core domain; Region: rve; pfam00665 428406000642 AAA domain; Region: AAA_22; pfam13401 428406000643 TniQ; Region: TniQ; pfam06527 428406000644 Helix-turn-helix domain; Region: HTH_17; pfam12728 428406000645 hypothetical protein; Provisional; Region: PRK06153 428406000646 Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common...; Region: E1_enzyme_family; cd01483 428406000647 ATP binding site [chemical binding]; other site 428406000648 substrate interface [chemical binding]; other site 428406000649 Bacterial multiubiquitin; Region: Bac_multiUb; pfam14452 428406000650 TIGR04255 family protein; Region: sporadTIGR04255 428406000651 AAA domain; Region: AAA_33; pfam13671 428406000652 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4185 428406000653 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 428406000654 Protein of unknown function (DUF3150); Region: DUF3150; pfam11348 428406000655 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 428406000656 metal ion-dependent adhesion site (MIDAS); other site 428406000657 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4643 428406000658 Zinc-binding domain of primase-helicase; Region: Prim_Zn_Ribbon; smart00778 428406000659 Toprim domain; Region: Toprim_3; pfam13362 428406000660 Flagellar transcriptional activator (FlhC); Region: FlhC; cl05036 428406000661 Putative helicase; Region: TraI_2; pfam07514 428406000662 integrating conjugative element relaxase, PFL_4751 family; Region: ICE_TraI_Pfluor; TIGR03760 428406000663 conjugative coupling factor TraD, SXT/TOL subfamily; Region: SXT_TraD; TIGR03743 428406000664 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 428406000665 Domain of unknown function (DUF4400); Region: DUF4400; pfam14348 428406000666 Type II/IV secretion system protein; Region: T2SE; pfam00437 428406000667 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 428406000668 ATP binding site [chemical binding]; other site 428406000669 Walker A motif; other site 428406000670 hexamer interface [polypeptide binding]; other site 428406000671 Walker B motif; other site 428406000672 TrbC/VIRB2 family; Region: TrbC; pfam04956 428406000673 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 428406000674 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 428406000675 conjugal transfer protein TrbJ; Provisional; Region: PRK13874; cl02193 428406000676 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; pfam04610 428406000677 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406000678 ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]; Region: SpoVK; COG0464 428406000679 Walker A motif; other site 428406000680 ATP binding site [chemical binding]; other site 428406000681 Walker B motif; other site 428406000682 arginine finger; other site 428406000683 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406000684 Walker A motif; other site 428406000685 ATP binding site [chemical binding]; other site 428406000686 Walker B motif; other site 428406000687 arginine finger; other site 428406000688 VirB8 protein; Region: VirB8; pfam04335 428406000689 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cl11423 428406000690 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 428406000691 VirB7 interaction site; other site 428406000692 Bacterial conjugation TrbI-like protein; Region: TrbI; pfam03743 428406000693 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 428406000694 VirB7 interaction site; other site 428406000695 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cl02931 428406000696 ligand binding site [chemical binding]; other site 428406000697 Toxin co-regulated pilus biosynthesis protein Q; Region: TcpQ; pfam10671 428406000698 type IVB pilus formation outer membrane protein, R64 PilN family; Region: pilus_B_mal_scr; TIGR02520 428406000699 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 428406000700 Type II/IV secretion system protein; Region: T2SE; pfam00437 428406000701 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 428406000702 Walker A motif; other site 428406000703 ATP binding site [chemical binding]; other site 428406000704 Walker B motif; other site 428406000705 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 428406000706 PilS N terminal; Region: PilS; pfam08805 428406000707 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 428406000708 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 428406000709 N-acetyl-D-glucosamine binding site [chemical binding]; other site 428406000710 catalytic residue [active] 428406000711 alpha-ketoglutarate decarboxylase; Reviewed; Region: kgd; PRK12270 428406000712 PRTRC system protein D; Region: PRTRC_D; TIGR03739 428406000713 Plasmid segregation protein ParM and similar proteins; Region: ParM_like; cd10227 428406000714 Mg binding site [ion binding]; other site 428406000715 nucleotide binding site [chemical binding]; other site 428406000716 putative protofilament interface [polypeptide binding]; other site 428406000717 Phage integrase, N-terminal; Region: Integrase_l_N; pfam12834 428406000718 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 428406000719 DNA binding site [nucleotide binding] 428406000720 Int/Topo IB signature motif; other site 428406000721 active site 428406000722 catalytic residues [active] 428406000723 Protein of unknown function DUF262; Region: DUF262; pfam03235 428406000724 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cl11423 428406000725 CobN subunit of cobaltochelatase, bchH and chlH subunits of magnesium chelatases, and similar proteins; Region: CobN_like; cd10150 428406000726 DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]; Region: DnaQ; COG0847 428406000727 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 428406000728 active site 428406000729 catalytic site [active] 428406000730 substrate binding site [chemical binding]; other site 428406000731 HipA N-terminal domain; Region: Couple_hipA; pfam13657 428406000732 Toxin module HipA, protein kinase of phosphatidylinositol 3/4-kinase superfamily [General function prediction only]; Region: HipA; COG3550 428406000733 HipA-like N-terminal domain; Region: HipA_N; pfam07805 428406000734 HipA-like C-terminal domain; Region: HipA_C; pfam07804 428406000735 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 428406000736 sequence-specific DNA binding site [nucleotide binding]; other site 428406000737 salt bridge; other site 428406000738 Domain of unknown function (DUF1768); Region: DUF1768; pfam08719 428406000739 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 428406000740 non-specific DNA binding site [nucleotide binding]; other site 428406000741 salt bridge; other site 428406000742 sequence-specific DNA binding site [nucleotide binding]; other site 428406000743 Phosphoribosylformylglycinamidine (FGAM) synthase, synthetase domain [Nucleotide transport and metabolism]; Region: PurL; COG0046 428406000744 A circularly permuted ATPgrasp; Region: CP_ATPgrasp_1; cl17448 428406000745 The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Region: NR_LBD; cl11397 428406000746 Predicted transcriptional regulator [Transcription]; Region: COG2944 428406000747 Uncharacterized protein family (UPF0182); Region: UPF0182; pfam03699 428406000748 Toxin co-regulated pilus biosynthesis protein Q; Region: TcpQ; pfam10671 428406000749 tellurium resistance terB-like protein; Region: terB_like; cl11965 428406000750 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 428406000751 Protein of unknown function (DUF2491); Region: DUF2491; pfam10679 428406000752 Uncharacterized protein conserved in bacteria (DUF2186); Region: DUF2186; pfam09952 428406000753 Methyltransferase domain; Region: Methyltransf_26; pfam13659 428406000754 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 428406000755 homocitrate synthase; Region: LysS_fung_arch; TIGR02146 428406000756 Uncharacterized ACR, COG2135; Region: DUF159; pfam02586 428406000757 Predicted periplasmic protein [Function unknown]; Region: COG3904 428406000758 Peptidase family M50; Region: Peptidase_M50; pfam02163 428406000759 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic...; Region: S2P-M50; cl10020 428406000760 active site 428406000761 Acetyltransferase (isoleucine patch superfamily) [General function prediction only]; Region: WbbJ; COG0110 428406000762 Maltose O-acetyltransferase (MAT) and Galactoside O-acetyltransferase (GAT): MAT and GAT catalyze the CoA-dependent acetylation of the 6-hydroxyl group of their respective sugar substrates. MAT acetylates maltose and glucose exclusively at the C6...; Region: LbH_MAT_GAT; cd03357 428406000763 active site 428406000764 substrate binding site [chemical binding]; other site 428406000765 trimer interface [polypeptide binding]; other site 428406000766 CoA binding site [chemical binding]; other site 428406000767 Domain of unknown function (DUF4343); Region: DUF4343; pfam14243 428406000768 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 428406000769 ASC-1 homology or ASCH domain, a small beta-barrel domain found in all three kingdoms of life. ASCH resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation; Region: ASCH; cl01020 428406000770 DNA repair protein RadA; Provisional; Region: PRK11823 428406000771 Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of...; Region: Sms; cd01121 428406000772 Walker A motif/ATP binding site; other site 428406000773 ATP binding site [chemical binding]; other site 428406000774 Walker B motif; other site 428406000775 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 428406000776 H-NS histone family; Region: Histone_HNS; pfam00816 428406000777 Domain in histone-like proteins of HNS family; Region: HNS; smart00528 428406000778 Protein of unknown function (DUF1294); Region: DUF1294; pfam06961 428406000779 sugar transferase, PEP-CTERM system associated; Region: EpsB_2; TIGR03013 428406000780 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 428406000781 active site 428406000782 catalytic residues [active] 428406000783 DNA binding site [nucleotide binding] 428406000784 Int/Topo IB signature motif; other site 428406000785 Rieske non-heme iron oxygenase (RO) family, Phthalate 4,5-dioxygenase (PhDO)-like subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; composed of the oxygenase alpha subunits of PhDO and similar proteins including 3-chlorobenzoate 3; Region: Rieske_RO_Alpha_PhDO_like; cd03479 428406000786 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 428406000787 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 428406000788 hydrophobic ligand binding site; other site 428406000789 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 428406000790 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 428406000791 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 428406000792 nicotinate-nucleotide pyrophosphorylase; Provisional; Region: PRK06978 428406000793 Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase), also called nicotinate-nucleotide pyrophosphorylase, is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid (QA) with...; Region: QPRTase; cd01572 428406000794 dimerization interface [polypeptide binding]; other site 428406000795 active site 428406000796 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 428406000797 MarR family; Region: MarR_2; cl17246 428406000798 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 428406000799 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 428406000800 trimer interface [polypeptide binding]; other site 428406000801 eyelet of channel; other site 428406000802 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cl17432 428406000803 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406000804 D-galactonate transporter; Region: 2A0114; TIGR00893 428406000805 putative substrate translocation pore; other site 428406000806 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 428406000807 Phthalate dioxygenase reductase (PDR) is an FMN-dependent reductase that mediates electron transfer from NADH to FMN to an iron sulfur cluster. PDR has an an N-terminal ferrredoxin reductase (FNR)-like NAD(H) binding domain and a C-terminal iron-sulfur; Region: PDR_like; cd06185 428406000808 FMN-binding pocket [chemical binding]; other site 428406000809 flavin binding motif; other site 428406000810 phosphate binding motif [ion binding]; other site 428406000811 beta-alpha-beta structure motif; other site 428406000812 NAD binding pocket [chemical binding]; other site 428406000813 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 428406000814 catalytic loop [active] 428406000815 iron binding site [ion binding]; other site 428406000816 Hemerythrin; Region: Hemerythrin; cd12107 428406000817 Fe binding site [ion binding]; other site 428406000818 Superinfection exclusion protein B; Region: SieB; pfam14163 428406000819 TOPRIM_OLD: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in bacterial and archaeal nucleases of the OLD (overcome lysogenization defect) family. The bacteriophage P2 OLD protein, which has DNase as well as...; Region: TOPRIM_OLD; cd01026 428406000820 putative active site [active] 428406000821 putative metal-binding site [ion binding]; other site 428406000822 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 428406000823 Part of AAA domain; Region: AAA_19; pfam13245 428406000824 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 428406000825 Ligand Binding Site [chemical binding]; other site 428406000826 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cl00075 428406000827 ATP binding site [chemical binding]; other site 428406000828 Mg2+ binding site [ion binding]; other site 428406000829 G-X-G motif; other site 428406000830 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 428406000831 PLD-like domain; Region: PLDc_2; pfam13091 428406000832 putative active site [active] 428406000833 catalytic site [active] 428406000834 Mrr N-terminal domain; Region: Mrr_N; pfam14338 428406000835 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 428406000836 DNA methylase; Region: N6_N4_Mtase; pfam01555 428406000837 MHYT domain (predicted integral membrane sensor domain) [Signal transduction mechanisms]; Region: COG3300 428406000838 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 428406000839 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 428406000840 metal binding site [ion binding]; metal-binding site 428406000841 active site 428406000842 I-site; other site 428406000843 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 428406000844 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 428406000845 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 428406000846 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 428406000847 Walker A/P-loop; other site 428406000848 ATP binding site [chemical binding]; other site 428406000849 Family description; Region: UvrD_C_2; pfam13538 428406000850 Phage protein Gp37/Gp68; Region: Gp37_Gp68; cl15384 428406000851 Protein of unknown function (DUF1643); Region: DUF1643; cl01787 428406000852 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 428406000853 ParB-like nuclease domain; Region: ParBc; pfam02195 428406000854 Glycine zipper 2TM domain; Region: Rick_17kDa_Anti; cl10470 428406000855 Glutathione synthase/Ribosomal protein S6 modification enzyme (glutaminyl transferase) [Coenzyme metabolism / Translation, ribosomal structure and biogenesis]; Region: RimK; COG0189 428406000856 Domain of unknown function (DUF1768); Region: DUF1768; pfam08719 428406000857 This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. A highly...; Region: PAPS_reductase; cd01713 428406000858 Active Sites [active] 428406000859 Methyltransferase domain; Region: Methyltransf_26; pfam13659 428406000860 Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]; Region: HepA; COG0553 428406000861 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 428406000862 nucleotide binding region [chemical binding]; other site 428406000863 ATP-binding site [chemical binding]; other site 428406000864 Type II secretory pathway, prepilin signal peptidase PulO and related peptidases [Cell motility and secretion / Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: PulO; COG1989 428406000865 Type IV leader peptidase family; Region: Peptidase_A24; pfam01478 428406000866 PRTRC system ParB family protein; Region: PRTRC_parB; TIGR03734 428406000867 ParB-like nuclease domain; Region: ParB; smart00470 428406000868 PRTRC system protein E; Region: PRTRC_E; TIGR03741 428406000869 Prokaryotic Ubiquitin; Region: Prok_Ub; cl14020 428406000870 PRTRC system protein F; Region: PRTRC_F; TIGR03742 428406000871 Prokaryotic E2 family D; Region: Prok-E2_D; cl14019 428406000872 Domain of unknown function (DUF2016); Region: DUF2016; pfam09436 428406000873 PRTRC system protein A; Region: PRTRC_A; TIGR03735 428406000874 Prokaryotic homologs of the JAB domain; Region: Prok-JAB; pfam14464 428406000875 PRTRC system ThiF family protein; Region: PRTRC_ThiF; TIGR03736 428406000876 Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common...; Region: E1_enzyme_family; cd01483 428406000877 ATP binding site [chemical binding]; other site 428406000878 substrate interface [chemical binding]; other site 428406000879 Protein of unknown function (DUF1173); Region: DUF1173; pfam06666 428406000880 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 428406000881 IHF dimer interface [polypeptide binding]; other site 428406000882 IHF - DNA interface [nucleotide binding]; other site 428406000883 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 428406000884 active site 428406000885 Int/Topo IB signature motif; other site 428406000886 catalytic residues [active] 428406000887 DNA binding site [nucleotide binding] 428406000888 T5orf172 domain; Region: T5orf172; pfam10544 428406000889 Plasmid replication region DNA-binding N-term; Region: KfrA_N; pfam11740 428406000890 Protein of unknown function (DUF2807); Region: DUF2807; pfam10988 428406000891 Domain of unknown function (DUF4098); Region: DUF4098; pfam13345 428406000892 Predicted transcriptional regulator [Transcription]; Region: COG3905 428406000893 Plasmid stabilisation system protein; Region: Plasmid_stabil; pfam05016 428406000894 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 428406000895 INT_SG1, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 1, C-terminal catalytic domain. The CD contains mainly predicted integrase/recombinase and site-specific XerD recombinases. The members of this CD are found predominantly in...; Region: INT_SG1_C; cd01183 428406000896 Int/Topo IB signature motif; other site 428406000897 Domain of unknown function (DUF4158); Region: DUF4158; pfam13700 428406000898 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; pfam01526 428406000899 Plasmid replication region DNA-binding N-term; Region: KfrA_N; pfam11740 428406000900 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3677 428406000901 Domain of Unknown Function (DUF746); Region: DUF746; pfam05344 428406000902 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3677 428406000903 Domain of Unknown Function (DUF746); Region: DUF746; pfam05344 428406000904 peptidylprolyl isomerase; Provisional; Region: prsA; PRK04405 428406000905 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 428406000906 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 428406000907 POTRA domain, ShlB-type; Region: POTRA_2; pfam08479 428406000908 Haemolysin secretion/activation protein ShlB/FhaC/HecB; Region: ShlB; pfam03865 428406000909 haemagglutination activity domain; Region: Haemagg_act; pfam05860 428406000910 Initiator Replication protein; Region: Rep_3; cl17676 428406000911 haemagglutination activity domain; Region: Haemagg_act; pfam05860 428406000912 Possible hemagglutinin (DUF637); Region: DUF637; pfam04830 428406000913 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 428406000914 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406000915 ATP binding site [chemical binding]; other site 428406000916 Mg2+ binding site [ion binding]; other site 428406000917 G-X-G motif; other site 428406000918 Response regulator receiver domain; Region: Response_reg; pfam00072 428406000919 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406000920 active site 428406000921 phosphorylation site [posttranslational modification] 428406000922 intermolecular recognition site; other site 428406000923 dimerization interface [polypeptide binding]; other site 428406000924 Response regulator receiver domain; Region: Response_reg; pfam00072 428406000925 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406000926 active site 428406000927 phosphorylation site [posttranslational modification] 428406000928 intermolecular recognition site; other site 428406000929 dimerization interface [polypeptide binding]; other site 428406000930 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cl00086 428406000931 TENA/THI-4/PQQC family; Region: TENA_THI-4; cl15243 428406000932 DNA-binding protein H-NS [General function prediction only]; Region: Hns; COG2916 428406000933 Domain in histone-like proteins of HNS family; Region: HNS; smart00528 428406000934 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 428406000935 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406000936 active site 428406000937 phosphorylation site [posttranslational modification] 428406000938 intermolecular recognition site; other site 428406000939 Bacterial DNA-binding protein; Region: Bac_DNA_binding; pfam00216 428406000940 IHF - DNA interface [nucleotide binding]; other site 428406000941 IHF dimer interface [polypeptide binding]; other site 428406000942 PAAR motif; Region: PAAR_motif; pfam05488 428406000943 Domain of unknown function (DUF4123); Region: DUF4123; pfam13503 428406000944 Phage integrase protein; Region: DUF3701; pfam12482 428406000945 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 428406000946 active site 428406000947 DNA binding site [nucleotide binding] 428406000948 Int/Topo IB signature motif; other site 428406000949 Plasmid encoded RepA protein; Region: RepA_C; pfam04796 428406000950 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 428406000951 ParB-like nuclease domain; Region: ParB; smart00470 428406000952 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 428406000953 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 428406000954 P-loop; other site 428406000955 Magnesium ion binding site [ion binding]; other site 428406000956 Initiator Replication protein; Region: Rep_3; pfam01051 428406000957 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3108 428406000958 Peptidase M15; Region: Peptidase_M15_3; cl01194 428406000959 PDDEXK-like domain of unknown function (DUF3799); Region: DUF3799; pfam12684 428406000960 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 428406000961 conjugal transfer protein TraB; Provisional; Region: PRK13825 428406000962 active site 428406000963 catalytic triad [active] 428406000964 dimer interface [polypeptide binding]; other site 428406000965 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 428406000966 Family description; Region: UvrD_C_2; pfam13538 428406000967 DnaA N-terminal domain; Region: DnaA_N; pfam11638 428406000968 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 428406000969 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406000970 Walker A motif; other site 428406000971 ATP binding site [chemical binding]; other site 428406000972 Walker B motif; other site 428406000973 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 428406000974 arginine finger; other site 428406000975 C-terminal domain of bacterial DnaA proteins. The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple...; Region: Bac_DnaA_C; cd06571 428406000976 DnaA box-binding interface [nucleotide binding]; other site 428406000977 DNA polymerase III subunit beta; Validated; Region: PRK05643 428406000978 Beta clamp domain. The beta subunit (processivity factor) of DNA polymerase III holoenzyme, refered to as the beta clamp, forms a ring shaped dimer that encircles dsDNA (sliding clamp) in bacteria. The beta-clamp is structurally similar to the trimeric...; Region: beta_clamp; cd00140 428406000979 putative DNA binding surface [nucleotide binding]; other site 428406000980 dimer interface [polypeptide binding]; other site 428406000981 beta-clamp/clamp loader binding surface; other site 428406000982 beta-clamp/translesion DNA polymerase binding surface; other site 428406000983 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 428406000984 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406000985 ATP binding site [chemical binding]; other site 428406000986 Mg2+ binding site [ion binding]; other site 428406000987 G-X-G motif; other site 428406000988 TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIA family of DNA topoisomerases similar to the B subunits of E. coli DNA gyrase and E. coli Topoisomerase IV which are; Region: TopoII_Trans_DNA_gyrase; cd00822 428406000989 anchoring element; other site 428406000990 dimer interface [polypeptide binding]; other site 428406000991 ATP binding site [chemical binding]; other site 428406000992 TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to the Escherichia coli GyrB subunit. TopoIIA enzymes cut both strands of the...; Region: TOPRIM_TopoIIA_GyrB; cd03366 428406000993 active site 428406000994 putative metal-binding site [ion binding]; other site 428406000995 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 428406000996 Protein of unknown function (DUF3800); Region: DUF3800; pfam12686 428406000997 Transposase, Mutator family; Region: Transposase_mut; pfam00872 428406000998 MULE transposase domain; Region: MULE; pfam10551 428406000999 P pilus assembly protein, pilin FimA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimA; COG3539 428406001000 Transcriptional regulators [Transcription]; Region: FadR; COG2186 428406001001 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 428406001002 DNA-binding site [nucleotide binding]; DNA binding site 428406001003 FCD domain; Region: FCD; pfam07729 428406001004 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 428406001005 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 428406001006 substrate binding pocket [chemical binding]; other site 428406001007 membrane-bound complex binding site; other site 428406001008 hinge residues; other site 428406001009 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406001010 dimer interface [polypeptide binding]; other site 428406001011 conserved gate region; other site 428406001012 putative PBP binding loops; other site 428406001013 ABC-ATPase subunit interface; other site 428406001014 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406001015 dimer interface [polypeptide binding]; other site 428406001016 conserved gate region; other site 428406001017 putative PBP binding loops; other site 428406001018 ABC-ATPase subunit interface; other site 428406001019 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 428406001020 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 428406001021 Walker A/P-loop; other site 428406001022 ATP binding site [chemical binding]; other site 428406001023 Q-loop/lid; other site 428406001024 ABC transporter signature motif; other site 428406001025 Walker B; other site 428406001026 D-loop; other site 428406001027 H-loop/switch region; other site 428406001028 Predicted membrane protein [Function unknown]; Region: COG3781 428406001029 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 428406001030 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 428406001031 ligand binding site [chemical binding]; other site 428406001032 flexible hinge region; other site 428406001033 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 428406001034 non-specific DNA interactions [nucleotide binding]; other site 428406001035 DNA binding site [nucleotide binding] 428406001036 sequence specific DNA binding site [nucleotide binding]; other site 428406001037 putative cAMP binding site [chemical binding]; other site 428406001038 acyl-CoA synthetase; Validated; Region: PRK08162 428406001039 Fatty acyl-CoA synthetases similar to LC-FACS from Thermus thermophiles and Arabidopsis; Region: ttLC_FACS_AEE21_like; cd12118 428406001040 acyl-activating enzyme (AAE) consensus motif; other site 428406001041 putative active site [active] 428406001042 AMP binding site [chemical binding]; other site 428406001043 putative CoA binding site [chemical binding]; other site 428406001044 Lactonase, 7-bladed beta-propeller; Region: Lactonase; pfam10282 428406001045 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 428406001046 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 428406001047 Uncharacterized conserved protein [Function unknown]; Region: COG2128 428406001048 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 428406001049 RNA polymerase sigma-70 factor, TIGR02957 family; Region: SigX4 428406001050 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 428406001051 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 428406001052 DNA binding residues [nucleotide binding] 428406001053 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 428406001054 dimer interface [polypeptide binding]; other site 428406001055 phosphorylation site [posttranslational modification] 428406001056 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406001057 ATP binding site [chemical binding]; other site 428406001058 G-X-G motif; other site 428406001059 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 428406001060 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406001061 active site 428406001062 phosphorylation site [posttranslational modification] 428406001063 intermolecular recognition site; other site 428406001064 dimerization interface [polypeptide binding]; other site 428406001065 Response regulator receiver domain; Region: Response_reg; pfam00072 428406001066 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406001067 active site 428406001068 phosphorylation site [posttranslational modification] 428406001069 intermolecular recognition site; other site 428406001070 dimerization interface [polypeptide binding]; other site 428406001071 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 428406001072 Glutathione S-transferase (GST) family, N-terminal domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic...; Region: GST_N_family; cd00570 428406001073 C-terminal domain interface [polypeptide binding]; other site 428406001074 GSH binding site (G-site) [chemical binding]; other site 428406001075 dimer interface [polypeptide binding]; other site 428406001076 C-terminal, alpha helical domain of an unknown subfamily 6 of Glutathione S-transferases; Region: GST_C_6; cd03205 428406001077 dimer interface [polypeptide binding]; other site 428406001078 N-terminal domain interface [polypeptide binding]; other site 428406001079 putative substrate binding pocket (H-site) [chemical binding]; other site 428406001080 CBS-domain-containing membrane protein [Signal transduction mechanisms]; Region: COG3448 428406001081 HPP family; Region: HPP; pfam04982 428406001082 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cl15354 428406001083 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the HPP motif domain. These proteins are integral membrane proteins with four transmembrane spanning helices. The function of these proteins is...; Region: CBS_pair_HPP_assoc; cd04600 428406001084 PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid...; Region: PAP2_like; cl00474 428406001085 active site 428406001086 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 428406001087 Autotransporter-associated beta strand repeat; Region: Autotrns_rpt; pfam12951 428406001088 Helix-turn-helix domain; Region: HTH_18; pfam12833 428406001089 DNA gyrase inhibitor [DNA replication, recombination, and repair]; Region: COG3449 428406001090 GYD domain; Region: GYD; cl01743 428406001091 S-adenosylmethionine synthetase; Validated; Region: PRK05250 428406001092 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 428406001093 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 428406001094 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 428406001095 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 428406001096 putative acyl-acceptor binding pocket; other site 428406001097 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 428406001098 putative acyl-acceptor binding pocket; other site 428406001099 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 428406001100 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 428406001101 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 428406001102 polyphosphate:nucleotide phosphotransferase, PPK2 family; Region: PPK2_rel_1; TIGR03709 428406001103 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 428406001104 active site 428406001105 Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Nape_like_AP-endo; cd10281 428406001106 putative active site [active] 428406001107 putative catalytic site [active] 428406001108 putative DNA binding site [nucleotide binding]; other site 428406001109 putative phosphate binding site [ion binding]; other site 428406001110 metal binding site A [ion binding]; metal-binding site 428406001111 putative AP binding site [nucleotide binding]; other site 428406001112 putative metal binding site B [ion binding]; other site 428406001113 N-acetyl-gamma-glutamyl-phosphate reductase; Provisional; Region: PRK11863 428406001114 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 428406001115 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 428406001116 The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. Many of these band 7 domain-containing proteins are lipid raft-associated. Individual proteins of this...; Region: Band_7; cd02106 428406001117 Uncharacterized conserved protein [Function unknown]; Region: COG1434 428406001118 YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been...; Region: YdcF-like; cd06259 428406001119 putative active site [active] 428406001120 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 428406001121 MarR family; Region: MarR; pfam01047 428406001122 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 428406001123 EamA-like transporter family; Region: EamA; pfam00892 428406001124 Peptidase family M48; Region: Peptidase_M48; cl12018 428406001125 muropeptide transporter; Reviewed; Region: ampG; PRK11902 428406001126 Acetyl-coenzyme A transporter 1; Region: Acatn; pfam13000 428406001127 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406001128 Uncharacterized conserved protein [Function unknown]; Region: COG1565 428406001129 short chain dehydrogenase; Provisional; Region: PRK09134 428406001130 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 428406001131 NAD(P) binding site [chemical binding]; other site 428406001132 active site 428406001133 Dihydroneopterin aldolase; Region: FolB; smart00905 428406001134 active site 428406001135 Arginase family; Region: Arginase; cd09989 428406001136 active site 428406001137 Mn binding site [ion binding]; other site 428406001138 oligomer interface [polypeptide binding]; other site 428406001139 ornithine--oxo-acid transaminase; Reviewed; Region: rocD; PRK00854 428406001140 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 428406001141 inhibitor-cofactor binding pocket; inhibition site 428406001142 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406001143 catalytic residue [active] 428406001144 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406001145 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406001146 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 428406001147 dimerization interface [polypeptide binding]; other site 428406001148 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 428406001149 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 428406001150 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 428406001151 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 428406001152 HlyD family secretion protein; Region: HlyD_3; pfam13437 428406001153 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 428406001154 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 428406001155 Walker A/P-loop; other site 428406001156 ATP binding site [chemical binding]; other site 428406001157 Q-loop/lid; other site 428406001158 ABC transporter signature motif; other site 428406001159 Walker B; other site 428406001160 D-loop; other site 428406001161 H-loop/switch region; other site 428406001162 ABC-type Na+ efflux pump, permease component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatB; COG1668 428406001163 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 428406001164 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 428406001165 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 428406001166 PAAR motif; Region: PAAR_motif; pfam05488 428406001167 PNGase/UBA or UBX (PUB) domain of p97 adaptor proteins; Region: PUB; cl15262 428406001168 peptide binding site [polypeptide binding]; other site 428406001169 Domain of unknown function (DUF4123); Region: DUF4123; pfam13503 428406001170 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 428406001171 Phage late control gene D protein (GPD); Region: Phage_GPD; pfam05954 428406001172 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 428406001173 Putative type VI secretion system Rhs element Vgr; Region: T6SS_Vgr; pfam13296 428406001174 Uncharacterized protein conserved in bacteria (DUF2345); Region: DUF2345; pfam10106 428406001175 2-dehydropantoate 2-reductase; Provisional; Region: PRK12921 428406001176 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 428406001177 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 428406001178 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 428406001179 This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This subfamily; Region: Alpha_ANH_like_II; cd01993 428406001180 Ligand Binding Site [chemical binding]; other site 428406001181 N-acetylglucosamine-1-phosphate uridyltransferase (contains nucleotidyltransferase and I-patch acetyltransferase domains) [Cell envelope biogenesis, outer membrane]; Region: GlmU; COG1207 428406001182 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 428406001183 Substrate binding site; other site 428406001184 Mg++ binding site; other site 428406001185 N-acetyl-glucosamine-1-phosphate uridyltransferase (GlmU), C-terminal left-handed beta-helix (LbH) acetyltransferase domain: GlmU is also known as UDP-N-acetylglucosamine pyrophosphorylase. It is a bifunctional bacterial enzyme that catalyzes two...; Region: LbH_GlmU_C; cd03353 428406001186 active site 428406001187 substrate binding site [chemical binding]; other site 428406001188 CoA binding site [chemical binding]; other site 428406001189 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 428406001190 Glutamine amidotransferases class-II (Gn-AT)_GFAT-type. This domain is found at the N-terminus of glucosamine-6P synthase (GlmS, or GFAT in humans). The glutaminase domain catalyzes amide nitrogen transfer from glutamine to the appropriate substrate. In...; Region: GFAT; cd00714 428406001191 glutaminase active site [active] 428406001192 SIS (Sugar ISomerase) domain repeat 1 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal...; Region: SIS_GlmS_GlmD_1; cd05008 428406001193 dimer interface [polypeptide binding]; other site 428406001194 active site 428406001195 SIS (Sugar ISomerase) domain repeat 2 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal...; Region: SIS_GlmS_GlmD_2; cd05009 428406001196 dimer interface [polypeptide binding]; other site 428406001197 active site 428406001198 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 428406001199 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 428406001200 active site 428406001201 nucleophile elbow; other site 428406001202 Arginate lyase and other MDR family members; Region: AL_MDR; cd08252 428406001203 zinc-binding alcohol dehydrogenase family protein; Region: adh_fam_1; TIGR02817 428406001204 putative NAD(P) binding site [chemical binding]; other site 428406001205 dimer interface [polypeptide binding]; other site 428406001206 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406001207 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406001208 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 428406001209 putative effector binding pocket; other site 428406001210 dimerization interface [polypeptide binding]; other site 428406001211 thiamine pyrophosphate protein; Provisional; Region: PRK08273 428406001212 Pyrimidine (PYR) binding domain of POX; Region: TPP_PYR_POX; cd07039 428406001213 PYR/PP interface [polypeptide binding]; other site 428406001214 dimer interface [polypeptide binding]; other site 428406001215 tetramer interface [polypeptide binding]; other site 428406001216 TPP binding site [chemical binding]; other site 428406001217 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 428406001218 Thiamine pyrophosphate (TPP) family, Pyruvate oxidase (POX) subfamily, TPP-binding module; composed of proteins similar to Lactobacillus plantarum POX, which plays a key role in controlling acetate production under aerobic conditions. POX decarboxylates...; Region: TPP_POX; cd02014 428406001219 TPP-binding site [chemical binding]; other site 428406001220 Hemerythrin-like domain; Region: Hr-like; cd12108 428406001221 Fe binding site [ion binding]; other site 428406001222 PRC-barrel domain; Region: PRC; pfam05239 428406001223 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_5; cd07238 428406001224 dimer interface [polypeptide binding]; other site 428406001225 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 428406001226 Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]; Region: COG0436 428406001227 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 428406001228 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406001229 homodimer interface [polypeptide binding]; other site 428406001230 catalytic residue [active] 428406001231 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 428406001232 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 428406001233 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 428406001234 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 428406001235 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_16; cd07263 428406001236 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406001237 Major Facilitator Superfamily; Region: MFS_1; pfam07690 428406001238 putative substrate translocation pore; other site 428406001239 C-terminal, alpha helical domain of Escherichia coli YfcG Glutathione S-transferases and related uncharacterized proteins; Region: GST_C_YfcG_like; cd10291 428406001240 putative dimer interface [polypeptide binding]; other site 428406001241 N-terminal domain interface [polypeptide binding]; other site 428406001242 active site 428406001243 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 428406001244 Transposase, Mutator family; Region: Transposase_mut; pfam00872 428406001245 MULE transposase domain; Region: MULE; pfam10551 428406001246 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 428406001247 EamA-like transporter family; Region: EamA; pfam00892 428406001248 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 428406001249 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 428406001250 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 428406001251 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2343 428406001252 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 428406001253 methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom...; Region: MM_CoA_mut_B12_BD; cd02071 428406001254 B12 binding site [chemical binding]; other site 428406001255 cobalt ligand [ion binding]; other site 428406001256 The function of this protein family is unkown. The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and...; Region: ArgK-like; cd03114 428406001257 Walker A; other site 428406001258 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM)-like family; contains proteins similar to MCM, and the large subunit of Streptomyces coenzyme B12-dependent isobutyryl-CoA mutase (ICM). MCM catalyzes the isomerization of...; Region: MM_CoA_mutase; cl00817 428406001259 3-hydroxybutyryl-CoA dehydrogenase; Validated; Region: PRK05808 428406001260 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 428406001261 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 428406001262 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]; Region: COG0384 428406001263 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 428406001264 Coenzyme A binding pocket [chemical binding]; other site 428406001265 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 428406001266 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 428406001267 non-specific DNA binding site [nucleotide binding]; other site 428406001268 salt bridge; other site 428406001269 sequence-specific DNA binding site [nucleotide binding]; other site 428406001270 Cupin domain; Region: Cupin_2; pfam07883 428406001271 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 428406001272 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406001273 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 428406001274 dimerization interface [polypeptide binding]; other site 428406001275 Uncharacterized conserved protein [Function unknown]; Region: COG5361 428406001276 Protein of unknown function (DUF1254); Region: DUF1254; pfam06863 428406001277 Protein of unknown function (DUF1214); Region: DUF1214; pfam06742 428406001278 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 428406001279 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase...; Region: NPD_like; cd04730 428406001280 FMN binding site [chemical binding]; other site 428406001281 substrate binding site [chemical binding]; other site 428406001282 putative catalytic residue [active] 428406001283 A type 1 glutamine amidotransferase (GATase1)-like domain found in PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_like; cd03134 428406001284 intracellular protease, PfpI family; Region: PfpI; TIGR01382 428406001285 proposed catalytic triad [active] 428406001286 conserved cys residue [active] 428406001287 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 428406001288 Fe(II)-dependent oxygenase superfamily protein; Provisional; Region: PRK05467 428406001289 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 428406001290 Sel1-like repeats; Region: SEL1; smart00671 428406001291 Sel1-like repeats; Region: SEL1; smart00671 428406001292 Outer membrane receptor for monomeric catechols [Inorganic ion transport and metabolism]; Region: Fiu; COG4774 428406001293 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 428406001294 N-terminal plug; other site 428406001295 ligand-binding site [chemical binding]; other site 428406001296 enoyl-CoA hydratase; Provisional; Region: PRK05995 428406001297 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 428406001298 substrate binding site [chemical binding]; other site 428406001299 oxyanion hole (OAH) forming residues; other site 428406001300 trimer interface [polypeptide binding]; other site 428406001301 Protein of unknown function (DUF1446); Region: DUF1446; pfam07287 428406001302 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 428406001303 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 428406001304 active site 428406001305 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 428406001306 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 428406001307 NAD(P) binding site [chemical binding]; other site 428406001308 active site 428406001309 3-methylcrotonyl-CoA carboxylase, beta chain; Region: PLN02820 428406001310 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 428406001311 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 428406001312 active site 428406001313 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 428406001314 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 428406001315 ATP-grasp domain; Region: ATP-grasp_4; cl17255 428406001316 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; pfam02785 428406001317 The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase; Region: biotinyl_domain; cd06850 428406001318 carboxyltransferase (CT) interaction site; other site 428406001319 biotinylation site [posttranslational modification]; other site 428406001320 acyl-CoA synthetase; Validated; Region: PRK08316 428406001321 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 428406001322 acyl-activating enzyme (AAE) consensus motif; other site 428406001323 AMP binding site [chemical binding]; other site 428406001324 active site 428406001325 CoA binding site [chemical binding]; other site 428406001326 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 428406001327 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 428406001328 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 428406001329 Protein of unknown function (DUF1289); Region: DUF1289; pfam06945 428406001330 This CD, composed mainly of bacterial single-domain proteins, includes the Thermus thermophilus (Tt) YbaK-like protein, a homolog of the trans-acting Escherichia coli YbaK Cys-tRNA(Pro) deacylase and the Agrobacterium tumefaciens ProX Ala-tRNA(Pro)...; Region: ProX_deacylase; cd04333 428406001331 putative deacylase active site [active] 428406001332 Isopropylmalate/homocitrate/citramalate synthases [Amino acid transport and metabolism]; Region: LeuA; COG0119 428406001333 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 428406001334 active site 428406001335 catalytic residues [active] 428406001336 metal binding site [ion binding]; metal-binding site 428406001337 bifunctional glyoxylate/hydroxypyruvate reductase A; Provisional; Region: ghrA; PRK15469 428406001338 Putative glycerate dehydrogenase and related proteins of the D-specific 2-hydroxy dehydrogenase family; Region: GDH_like_2; cd12164 428406001339 putative ligand binding site [chemical binding]; other site 428406001340 NAD binding site [chemical binding]; other site 428406001341 dimerization interface [polypeptide binding]; other site 428406001342 catalytic site [active] 428406001343 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 428406001344 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 428406001345 ATP-grasp domain; Region: ATP-grasp_4; cl17255 428406001346 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 428406001347 The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase; Region: biotinyl_domain; cd06850 428406001348 carboxyltransferase (CT) interaction site; other site 428406001349 biotinylation site [posttranslational modification]; other site 428406001350 biotin synthase; Region: bioB; TIGR00433 428406001351 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 428406001352 FeS/SAM binding site; other site 428406001353 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 428406001354 enoyl-CoA hydratase; Provisional; Region: PRK05995 428406001355 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 428406001356 substrate binding site [chemical binding]; other site 428406001357 oxyanion hole (OAH) forming residues; other site 428406001358 trimer interface [polypeptide binding]; other site 428406001359 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 428406001360 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 428406001361 3-methylcrotonyl-CoA carboxylase, beta chain; Region: PLN02820 428406001362 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 428406001363 hypothetical protein; Provisional; Region: PRK01842 428406001364 SEC-C motif; Region: SEC-C; pfam02810 428406001365 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 428406001366 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 428406001367 motif II; other site 428406001368 2-hydroxychromene-2-carboxylate isomerase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: NahD; COG3917 428406001369 DsbA family, 2-hydroxychromene-2-carboxylate (HCCA) isomerase subfamily; HCCA isomerase is a glutathione (GSH) dependent enzyme involved in the naphthalene catabolic pathway. It converts HCCA, a hemiketal formed spontaneously after ring cleavage of 1; Region: DsbA_HCCA_Iso; cd03022 428406001370 putative catalytic residue [active] 428406001371 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 428406001372 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 428406001373 active site 428406001374 carbonyl reductase sniffer-like, classical (c) SDRs; Region: carb_red_sniffer_like_SDR_c; cd05325 428406001375 C factor cell-cell signaling protein; Provisional; Region: PRK09009 428406001376 NADP binding site [chemical binding]; other site 428406001377 homodimer interface [polypeptide binding]; other site 428406001378 active site 428406001379 acetyl-CoA acetyltransferase; Provisional; Region: PRK06954 428406001380 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 428406001381 dimer interface [polypeptide binding]; other site 428406001382 active site 428406001383 Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an...; Region: beta_CA_cladeA; cd00883 428406001384 active site clefts [active] 428406001385 zinc binding site [ion binding]; other site 428406001386 dimer interface [polypeptide binding]; other site 428406001387 Isocitrate dehydrogenase kinase/phosphatase [Signal transduction mechanisms]; Region: COG4579 428406001388 bifunctional isocitrate dehydrogenase kinase/phosphatase protein; Validated; Region: aceK; PRK02946 428406001389 isovaleryl-CoA dehydrogenase; Region: PLN02519 428406001390 Isovaleryl-CoA dehydrogenase; Region: IVD; cd01156 428406001391 substrate binding site [chemical binding]; other site 428406001392 FAD binding site [chemical binding]; other site 428406001393 catalytic base [active] 428406001394 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 428406001395 Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Region: HTH_GnyR; cd04776 428406001396 DNA binding residues [nucleotide binding] 428406001397 putative dimer interface [polypeptide binding]; other site 428406001398 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 428406001399 Uncharacterized enzyme involved in biosynthesis of extracellular polysaccharides [General function prediction only]; Region: COG2329 428406001400 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 428406001401 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between...; Region: TroA-like; cl00262 428406001402 intersubunit interface [polypeptide binding]; other site 428406001403 short chain dehydrogenase; Provisional; Region: PRK07024 428406001404 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 428406001405 NAD(P) binding site [chemical binding]; other site 428406001406 active site 428406001407 DsbA family, DsbA subfamily; DsbA is a monomeric thiol disulfide oxidoreductase protein containing a redox active CXXC motif imbedded in a TRX fold. It is involved in the oxidative protein folding pathway in prokaryotes, and is the strongest thiol...; Region: DsbA_DsbA; cd03019 428406001408 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 428406001409 catalytic residues [active] 428406001410 hinge region; other site 428406001411 alpha helical domain; other site 428406001412 Cell division protein [Cell division and chromosome partitioning]; Region: FtsN; COG3087 428406001413 Sporulation related domain; Region: SPOR; pfam05036 428406001414 arginyl-tRNA synthetase; Reviewed; Region: argS; PRK01611 428406001415 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 428406001416 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 428406001417 active site 428406001418 HIGH motif; other site 428406001419 KMSK motif region; other site 428406001420 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 428406001421 tRNA binding surface [nucleotide binding]; other site 428406001422 anticodon binding site; other site 428406001423 Domain of unknown function (DUF1840); Region: DUF1840; pfam08895 428406001424 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 428406001425 Ferritin-like domain; Region: Ferritin; pfam00210 428406001426 dinuclear metal binding motif [ion binding]; other site 428406001427 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]; Region: COG5278 428406001428 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 428406001429 Histidine kinase; Region: HisKA_3; pfam07730 428406001430 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406001431 ATP binding site [chemical binding]; other site 428406001432 Mg2+ binding site [ion binding]; other site 428406001433 G-X-G motif; other site 428406001434 Predicted small secreted protein [Function unknown]; Region: COG5510 428406001435 Response regulator receiver domain; Region: Response_reg; pfam00072 428406001436 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406001437 active site 428406001438 phosphorylation site [posttranslational modification] 428406001439 intermolecular recognition site; other site 428406001440 dimerization interface [polypeptide binding]; other site 428406001441 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 428406001442 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406001443 active site 428406001444 phosphorylation site [posttranslational modification] 428406001445 intermolecular recognition site; other site 428406001446 dimerization interface [polypeptide binding]; other site 428406001447 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 428406001448 DNA binding residues [nucleotide binding] 428406001449 dimerization interface [polypeptide binding]; other site 428406001450 Methionine synthase I, cobalamin-binding domain [Amino acid transport and metabolism]; Region: MetH; COG1410 428406001451 MeTr subgroup of pterin binding enzymes. This family includes cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). Cobalamin-dependent...; Region: MeTr; cd00740 428406001452 substrate binding pocket [chemical binding]; other site 428406001453 B12 binding domain of methionine synthase. This domain binds methylcobalamin, which it uses as an intermediate methyl carrier from methyltetrahydrofolate (CH3H4folate) to homocysteine (Hcy); Region: methionine_synthase_B12_BD; cd02069 428406001454 B12 binding site [chemical binding]; other site 428406001455 cobalt ligand [ion binding]; other site 428406001456 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 428406001457 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; COG0646 428406001458 Homocysteine S-methyltransferase; Region: S-methyl_trans; pfam02574 428406001459 Member of the Rhodanese Homology Domain superfamily, subgroup 1. This CD includes the putative rhodanese-related sulfurtransferases of several uncharacterized proteins; Region: RHOD_1; cd01522 428406001460 active site residue [active] 428406001461 Protein of unknown function (DUF3567); Region: DUF3567; pfam12091 428406001462 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 428406001463 3-oxoadipate enol-lactonase; Region: protocat_pcaD; TIGR02427 428406001464 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 428406001465 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 428406001466 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 428406001467 Transcriptional regulator [Transcription]; Region: IclR; COG1414 428406001468 Bacterial transcriptional regulator; Region: IclR; pfam01614 428406001469 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]; Region: MhpD; COG0179 428406001470 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 428406001471 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 428406001472 Transcriptional regulator [Transcription]; Region: IclR; COG1414 428406001473 Bacterial transcriptional regulator; Region: IclR; pfam01614 428406001474 Luciferase-like monooxygenase; Region: Bac_luciferase; pfam00296 428406001475 probable oxidoreductase, LLM family; Region: LLM_2I7G; TIGR03858 428406001476 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 428406001477 Type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids; Region: PBP1_ABC-type_HAAT_like; cd06333 428406001478 putative ligand binding site [chemical binding]; other site 428406001479 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 428406001480 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 428406001481 substrate binding site [chemical binding]; other site 428406001482 oxyanion hole (OAH) forming residues; other site 428406001483 trimer interface [polypeptide binding]; other site 428406001484 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cl15762 428406001485 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 428406001486 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 428406001487 nucleophile elbow; other site 428406001488 Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue per...; Region: GSH_Peroxidase; cd00340 428406001489 catalytic residues [active] 428406001490 dimer interface [polypeptide binding]; other site 428406001491 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 428406001492 dinuclear metal binding motif [ion binding]; other site 428406001493 rfaE bifunctional protein, domain II; Region: rfaE_dom_II; TIGR02199 428406001494 Cytidylyltransferase; Region: CTP_transf_2; pfam01467 428406001495 active site 428406001496 nucleotide binding site [chemical binding]; other site 428406001497 HIGH motif; other site 428406001498 KMSKS motif; other site 428406001499 Sporulation related domain; Region: SPOR; pfam05036 428406001500 pantothenate kinase; Reviewed; Region: PRK13328 428406001501 biotin--protein ligase; Provisional; Region: PRK06955 428406001502 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 428406001503 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 428406001504 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 428406001505 Permease; Region: Permease; pfam02405 428406001506 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 428406001507 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 428406001508 Walker A/P-loop; other site 428406001509 ATP binding site [chemical binding]; other site 428406001510 Q-loop/lid; other site 428406001511 ABC transporter signature motif; other site 428406001512 Walker B; other site 428406001513 D-loop; other site 428406001514 H-loop/switch region; other site 428406001515 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 428406001516 mce related protein; Region: MCE; pfam02470 428406001517 Predicted integral membrane protein [Function unknown]; Region: COG5652 428406001518 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406001519 Major Facilitator Superfamily; Region: MFS_1; pfam07690 428406001520 putative substrate translocation pore; other site 428406001521 Siderophore synthetase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: RhbC; COG4264 428406001522 IucA / IucC family; Region: IucA_IucC; pfam04183 428406001523 Ferric iron reductase FhuF-like transporter; Region: FhuF; pfam06276 428406001524 phospholipase C, phosphocholine-specific, Pseudomonas-type; Region: PC_PLC; TIGR03396 428406001525 Phosphoesterase family; Region: Phosphoesterase; pfam04185 428406001526 Domain of unknown function (DUF756); Region: DUF756; pfam05506 428406001527 Domain of unknown function (DUF756); Region: DUF756; pfam05506 428406001528 Predicted secreted protein (DUF2300); Region: DUF2300; pfam10062 428406001529 lipoyl synthase; Provisional; Region: PRK05481 428406001530 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 428406001531 FeS/SAM binding site; other site 428406001532 lipoate-protein ligase B; Provisional; Region: PRK14343 428406001533 Protein of unknown function (DUF2917); Region: DUF2917; pfam11142 428406001534 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 428406001535 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406001536 The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 428406001537 dimerization interface [polypeptide binding]; other site 428406001538 substrate binding pocket [chemical binding]; other site 428406001539 hypothetical protein; Provisional; Region: PRK02047 428406001540 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 428406001541 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 428406001542 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; pfam07943 428406001543 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 428406001544 Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:...; Region: TRX_Fd_family; cd02980 428406001545 dimer interface [polypeptide binding]; other site 428406001546 [2Fe-2S] cluster binding site [ion binding]; other site 428406001547 C4-dicarboxylate transporter DctA; Reviewed; Region: PRK01663 428406001548 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 428406001549 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 428406001550 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 428406001551 dimer interface [polypeptide binding]; other site 428406001552 phosphorylation site [posttranslational modification] 428406001553 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406001554 ATP binding site [chemical binding]; other site 428406001555 Mg2+ binding site [ion binding]; other site 428406001556 G-X-G motif; other site 428406001557 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 428406001558 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406001559 active site 428406001560 phosphorylation site [posttranslational modification] 428406001561 intermolecular recognition site; other site 428406001562 dimerization interface [polypeptide binding]; other site 428406001563 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406001564 Walker A motif; other site 428406001565 ATP binding site [chemical binding]; other site 428406001566 Walker B motif; other site 428406001567 arginine finger; other site 428406001568 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 428406001569 Uncharacterized conserved protein (DUF2278); Region: DUF2278; pfam10042 428406001570 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a...; Region: TlpA_like_family; cd02966 428406001571 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 428406001572 catalytic residues [active] 428406001573 Macro domain, Appr-1"-pase_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly...; Region: Macro_Appr_pase_like; cd02908 428406001574 putative ADP-ribose binding site [chemical binding]; other site 428406001575 putative active site [active] 428406001576 LysE type translocator; Region: LysE; cl00565 428406001577 TnsA endonuclease N terminal; Region: Tn7_Tnp_TnsA_N; pfam08722 428406001578 TnsA endonuclease C terminal; Region: Tn7_Tnp_TnsA_C; pfam08721 428406001579 Helix-turn-helix domain; Region: HTH_28; pfam13518 428406001580 Winged helix-turn helix; Region: HTH_29; pfam13551 428406001581 Homeodomain-like domain; Region: HTH_32; pfam13565 428406001582 Integrase core domain; Region: rve; pfam00665 428406001583 Mu transposase, C-terminal; Region: Mu-transpos_C; pfam09299 428406001584 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406001585 AAA domain; Region: AAA_22; pfam13401 428406001586 Walker A motif; other site 428406001587 ATP binding site [chemical binding]; other site 428406001588 Walker B motif; other site 428406001589 arginine finger; other site 428406001590 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 428406001591 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 428406001592 cofactor binding site; other site 428406001593 DNA binding site [nucleotide binding] 428406001594 substrate interaction site [chemical binding]; other site 428406001595 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 428406001596 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 428406001597 Part of AAA domain; Region: AAA_19; pfam13245 428406001598 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 428406001599 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 428406001600 Very Short Patch Repair (Vsr) Endonuclease. Endonucleases in DNA repair that recognize damaged DNA and cleave the phosphodiester backbone. Vsr endonucleases have a common endonuclease topology that has been tailored for recognition of TG mismatches; Region: Vsr; cd00221 428406001601 mismatch recognition site; other site 428406001602 additional DNA contacts [nucleotide binding]; other site 428406001603 active site 428406001604 zinc binding site [ion binding]; other site 428406001605 DNA intercalation site [nucleotide binding]; other site 428406001606 HNH endonuclease; Region: HNH_2; pfam13391 428406001607 AAA domain; Region: AAA_23; pfam13476 428406001608 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 428406001609 Walker A/P-loop; other site 428406001610 ATP binding site [chemical binding]; other site 428406001611 AAA domain; Region: AAA_21; pfam13304 428406001612 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cd00267 428406001613 Walker B; other site 428406001614 D-loop; other site 428406001615 H-loop/switch region; other site 428406001616 Membrane fusogenic activity; Region: BMFP; pfam04380 428406001617 conserved hypothetical protein, proteobacterial; Region: gcw_chp; TIGR02001 428406001618 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 428406001619 Nitrogen regulatory protein P-II; Region: P-II; smart00938 428406001620 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 428406001621 Glutamate-cysteine ligase; Region: GshA; pfam08886 428406001622 glutamate--cysteine ligase, T. ferrooxidans family; Region: gshA_ferroox; TIGR02049 428406001623 glutathione synthetase; Provisional; Region: PRK05246 428406001624 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 428406001625 Prokaryotic glutathione synthetase, ATP-grasp domain; Region: GSH-S_ATP; pfam02955 428406001626 PTS_IIA, PTS system, mannose/sorbose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIA_man; cd00006 428406001627 active pocket/dimerization site; other site 428406001628 active site 428406001629 phosphorylation site [posttranslational modification] 428406001630 Histidine-containing phosphocarrier protein (HPr)-like proteins. HPr is a central component of the bacterial phosphoenolpyruvate sugar phosphotransferase system (PTS). The PTS catalyses the phosphorylation of sugar substrates during their translocation...; Region: PTS-HPr_like; cd00367 428406001631 dimerization domain swap beta strand [polypeptide binding]; other site 428406001632 regulatory protein interface [polypeptide binding]; other site 428406001633 active site 428406001634 regulatory phosphorylation site [posttranslational modification]; other site 428406001635 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 428406001636 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 428406001637 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 428406001638 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 428406001639 Bacterioferritin-associated ferredoxin [Inorganic ion transport and metabolism]; Region: Bfd; COG2906 428406001640 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 428406001641 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 428406001642 heme binding site [chemical binding]; other site 428406001643 ferroxidase pore; other site 428406001644 ferroxidase diiron center [ion binding]; other site 428406001645 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 428406001646 ThiF_MoeB_HesA. Family of E1-like enzymes involved in molybdopterin and thiamine biosynthesis family. The common reaction mechanism catalyzed by MoeB and ThiF, like other E1 enzymes, begins with a nucleophilic attack of the C-terminal carboxylate of MoaD...; Region: ThiF_MoeB_HesA_family; cd00757 428406001647 ATP binding site [chemical binding]; other site 428406001648 substrate interface [chemical binding]; other site 428406001649 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 428406001650 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 428406001651 PDZ domain of C-terminal processing-, tail-specific-, and tricorn proteases, which function in posttranslational protein processing, maturation, and disassembly or degradation, in Bacteria, Archaea, and plant chloroplasts. May be responsible for...; Region: PDZ_CTP_protease; cd00988 428406001652 protein binding site [polypeptide binding]; other site 428406001653 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 428406001654 Catalytic dyad [active] 428406001655 Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP_PGM_like; cd07067 428406001656 catalytic core [active] 428406001657 Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP_PGM_like; cd07067 428406001658 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cd00158 428406001659 active site residue [active] 428406001660 Glutaredoxin (GRX) family, GRX bacterial class 1 and 3 (b_1_3)-like subfamily; composed of bacterial GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the...; Region: GRX_GRXb_1_3_like; cd03418 428406001661 GSH binding site [chemical binding]; other site 428406001662 catalytic residues [active] 428406001663 preprotein translocase subunit SecB; Validated; Region: PRK05751 428406001664 SecA binding site; other site 428406001665 Preprotein binding site; other site 428406001666 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 428406001667 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 428406001668 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 428406001669 Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]; Region: CspR; COG0219 428406001670 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 428406001671 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 428406001672 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 428406001673 S-adenosylmethionine binding site [chemical binding]; other site 428406001674 Integral membrane protein (DUF2244); Region: DUF2244; cl02302 428406001675 Heme/copper-type cytochrome/quinol oxidases, subunit 2 [Energy production and conversion]; Region: CyoA; COG1622 428406001676 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 428406001677 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 428406001678 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 428406001679 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 428406001680 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 428406001681 Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of...; Region: Cyt_c_Oxidase_I; cd01663 428406001682 Subunit I/III interface [polypeptide binding]; other site 428406001683 D-pathway; other site 428406001684 Subunit I/VIIc interface [polypeptide binding]; other site 428406001685 Subunit I/IV interface [polypeptide binding]; other site 428406001686 Subunit I/II interface [polypeptide binding]; other site 428406001687 Low-spin heme (heme a) binding site [chemical binding]; other site 428406001688 Subunit I/VIIa interface [polypeptide binding]; other site 428406001689 Subunit I/VIa interface [polypeptide binding]; other site 428406001690 Dimer interface; other site 428406001691 Putative water exit pathway; other site 428406001692 Binuclear center (heme a3/CuB) [ion binding]; other site 428406001693 K-pathway; other site 428406001694 Subunit I/Vb interface [polypeptide binding]; other site 428406001695 Putative proton exit pathway; other site 428406001696 Subunit I/VIb interface; other site 428406001697 Subunit I/VIc interface [polypeptide binding]; other site 428406001698 Electron transfer pathway; other site 428406001699 Subunit I/VIIIb interface [polypeptide binding]; other site 428406001700 Subunit I/VIIb interface [polypeptide binding]; other site 428406001701 cytochrome C oxidase assembly protein; Provisional; Region: PRK05089 428406001702 Protein of unknown function (DUF2970); Region: DUF2970; pfam11174 428406001703 Cytochrome c oxidase subunit III. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of...; Region: Cyt_c_Oxidase_III; cd01665 428406001704 Subunit III/VIIa interface [polypeptide binding]; other site 428406001705 Phospholipid binding site [chemical binding]; other site 428406001706 Subunit I/III interface [polypeptide binding]; other site 428406001707 Subunit III/VIb interface [polypeptide binding]; other site 428406001708 Subunit III/VIa interface; other site 428406001709 Subunit III/Vb interface [polypeptide binding]; other site 428406001710 Protein of unknown function (DUF2909); Region: DUF2909; pfam11137 428406001711 SURF1 superfamily. Surf1/Shy1 has been implicated in the posttranslational steps of the biogenesis of the mitochondrially-encoded Cox1 subunit of cytochrome c oxidase (complex IV). Cytochrome c oxidase (complex IV), the terminal electron-transferring...; Region: SURF1; cd06662 428406001712 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 428406001713 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 428406001714 Cytochrome oxidase assembly protein; Region: COX15-CtaA; pfam02628 428406001715 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 428406001716 UbiA prenyltransferase family; Region: UbiA; pfam01040 428406001717 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 428406001718 SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c...; Region: SCO; cd02968 428406001719 Cu(I) binding site [ion binding]; other site 428406001720 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 428406001721 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 428406001722 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 428406001723 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 428406001724 DNA binding residues [nucleotide binding] 428406001725 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 428406001726 PAS domain; Region: PAS_9; pfam13426 428406001727 putative active site [active] 428406001728 heme pocket [chemical binding]; other site 428406001729 PAS fold; Region: PAS_4; pfam08448 428406001730 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 428406001731 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 428406001732 metal binding site [ion binding]; metal-binding site 428406001733 active site 428406001734 I-site; other site 428406001735 Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]; Region: COG1765 428406001736 Pirin-related protein [General function prediction only]; Region: COG1741 428406001737 Pirin; Region: Pirin; pfam02678 428406001738 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 428406001739 glycosyl transferase family protein; Provisional; Region: PRK08136 428406001740 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 428406001741 Transposase, Mutator family; Region: Transposase_mut; pfam00872 428406001742 MULE transposase domain; Region: MULE; pfam10551 428406001743 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 428406001744 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 428406001745 Walker A/P-loop; other site 428406001746 ATP binding site [chemical binding]; other site 428406001747 Q-loop/lid; other site 428406001748 ABC transporter signature motif; other site 428406001749 Walker B; other site 428406001750 D-loop; other site 428406001751 H-loop/switch region; other site 428406001752 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 428406001753 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406001754 dimer interface [polypeptide binding]; other site 428406001755 conserved gate region; other site 428406001756 putative PBP binding loops; other site 428406001757 ABC-ATPase subunit interface; other site 428406001758 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 428406001759 NMT1-like family; Region: NMT1_2; pfam13379 428406001760 Response regulator with putative antiterminator output domain [Signal transduction mechanisms]; Region: AmiR; COG3707 428406001761 ANTAR domain; Region: ANTAR; pfam03861 428406001762 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]; Region: MhpD; COG0179 428406001763 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 428406001764 GST_N family, Class Zeta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens; Region: GST_N_Zeta; cd03042 428406001765 maleylacetoacetate isomerase; Region: maiA; TIGR01262 428406001766 C-terminal domain interface [polypeptide binding]; other site 428406001767 GSH binding site (G-site) [chemical binding]; other site 428406001768 putative dimer interface [polypeptide binding]; other site 428406001769 C-terminal, alpha helical domain of Class Zeta Glutathione S-transferases; Region: GST_C_Zeta; cd03191 428406001770 dimer interface [polypeptide binding]; other site 428406001771 maleylacetoacetate (MAA) substrate binding site (H site) [chemical binding]; other site 428406001772 N-terminal domain interface [polypeptide binding]; other site 428406001773 PAAR motif; Region: PAAR_motif; pfam05488 428406001774 PAAR motif; Region: PAAR_motif; pfam05488 428406001775 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 428406001776 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 428406001777 The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes. SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The...; Region: SRP; cd03115 428406001778 P loop; other site 428406001779 GTP binding site [chemical binding]; other site 428406001780 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 428406001781 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 428406001782 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 428406001783 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 428406001784 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 428406001785 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 428406001786 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 428406001787 S-adenosylmethionine binding site [chemical binding]; other site 428406001788 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 428406001789 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 428406001790 active site 428406001791 (T/H)XGH motif; other site 428406001792 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 428406001793 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 428406001794 Peptidyl-tRNA hydrolase (PTH) is a monomeric protein that cleaves the ester bond linking the nascent peptide and tRNA when peptidyl-tRNA is released prematurely from the ribosome. This ensures the recycling of peptidyl-tRNAs into tRNAs produced through...; Region: PTH; cd00462 428406001795 putative active site [active] 428406001796 catalytic residue [active] 428406001797 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 428406001798 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 428406001799 5S rRNA interface [nucleotide binding]; other site 428406001800 CTC domain interface [polypeptide binding]; other site 428406001801 L16 interface [polypeptide binding]; other site 428406001802 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 428406001803 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 428406001804 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 428406001805 active site 428406001806 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00343 428406001807 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 428406001808 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 428406001809 outer membrane lipoprotein LolB; Provisional; Region: lolB; PRK00022 428406001810 Outer membrane lipoprotein LolB; Region: LolB; pfam03550 428406001811 heme biosynthesis-associated TPR protein; Region: TPR_hemY_coli; TIGR00540 428406001812 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 428406001813 TPR motif; other site 428406001814 binding surface 428406001815 FOG: TPR repeat [General function prediction only]; Region: NrfG; COG0457 428406001816 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 428406001817 binding surface 428406001818 TPR motif; other site 428406001819 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 428406001820 binding surface 428406001821 TPR motif; other site 428406001822 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 428406001823 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 428406001824 DNA binding site [nucleotide binding] 428406001825 catalytic residue [active] 428406001826 H2TH interface [polypeptide binding]; other site 428406001827 putative catalytic residues [active] 428406001828 turnover-facilitating residue; other site 428406001829 intercalation triad [nucleotide binding]; other site 428406001830 8OG recognition residue [nucleotide binding]; other site 428406001831 putative reading head residues; other site 428406001832 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 428406001833 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 428406001834 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 428406001835 G1 box; other site 428406001836 GTP/Mg2+ binding site [chemical binding]; other site 428406001837 Predicted GTPases (dynamin-related) [General function prediction only]; Region: COG0699 428406001838 G2 box; other site 428406001839 Switch I region; other site 428406001840 Dynamin-like protein including dynamins, mitofusins, and guanylate-binding proteins; Region: DLP_2; cd09912 428406001841 G3 box; other site 428406001842 Switch II region; other site 428406001843 GTP/Mg2+ binding site [chemical binding]; other site 428406001844 G4 box; other site 428406001845 G5 box; other site 428406001846 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 428406001847 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 428406001848 minor groove reading motif; other site 428406001849 helix-hairpin-helix signature motif; other site 428406001850 substrate binding pocket [chemical binding]; other site 428406001851 active site 428406001852 DNA glycosylase (MutY in bacteria and hMYH in humans) is responsible for repairing misread A*oxoG residues to C*G by removing the inappropriately paired adenine base from the DNA backbone. It belongs to the Nudix hydrolase superfamily and is important...; Region: DNA_Glycosylase_C; cd03431 428406001853 DNA binding and oxoG recognition site [nucleotide binding] 428406001854 ATP-dependent protease La (LON) domain; Region: LON; pfam02190 428406001855 glmZ(sRNA)-inactivating NTPase; Provisional; Region: PRK05416 428406001856 AAA domain; Region: AAA_18; pfam13238 428406001857 psiF repeat; Region: PsiF_repeat; pfam07769 428406001858 hypothetical protein; Provisional; Region: PRK11505 428406001859 HPr kinase/phosphorylase; Provisional; Region: PRK05428 428406001860 HPr Serine kinase N terminus; Region: Hpr_kinase_N; pfam02603 428406001861 HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent...; Region: HprK_C; cd01918 428406001862 Hpr binding site; other site 428406001863 active site 428406001864 homohexamer subunit interaction site [polypeptide binding]; other site 428406001865 PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_fru; cd00211 428406001866 active site 428406001867 phosphorylation site [posttranslational modification] 428406001868 RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal...; Region: RaiA; cd00552 428406001869 30S subunit binding site; other site 428406001870 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 428406001871 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 428406001872 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 428406001873 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 428406001874 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 428406001875 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 428406001876 Walker A/P-loop; other site 428406001877 ATP binding site [chemical binding]; other site 428406001878 Q-loop/lid; other site 428406001879 ABC transporter signature motif; other site 428406001880 Walker B; other site 428406001881 D-loop; other site 428406001882 H-loop/switch region; other site 428406001883 lipopolysaccharide transport periplasmic protein LptA; Region: outer_YhbN_LptA; TIGR03002 428406001884 OstA-like protein; Region: OstA; pfam03968 428406001885 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3117 428406001886 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 428406001887 Low specificity phosphatase (HAD superfamily) [General function prediction only]; Region: COG1778 428406001888 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 428406001889 KpsF-like protein. KpsF is an arabinose-5-phosphate isomerase which contains SIS (Sugar ISomerase) domains. SIS domains are found in many phosphosugar isomerases and phosphosugar binding proteins. KpsF catalyzes the reversible reaction of ribulose...; Region: SIS_Kpsf; cd05014 428406001890 putative active site [active] 428406001891 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with KpsF/GutQ domains in the API [A5P (D-arabinose 5-phosphate) isomerase] protein. These APIs catalyze the conversion of the pentose pathway...; Region: CBS_pair_KpsF_GutQ_assoc; cd04604 428406001892 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 428406001893 putative cation:proton antiport protein; Provisional; Region: PRK10669 428406001894 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 428406001895 TrkA-N domain; Region: TrkA_N; pfam02254 428406001896 TrkA-C domain; Region: TrkA_C; pfam02080 428406001897 Uncharacterized protein related to arylsulfate sulfotransferase involved in siderophore biosynthesis [General function prediction only]; Region: COG4321 428406001898 intracellular protease, PfpI family; Region: PfpI; TIGR01382 428406001899 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_1; cd03169 428406001900 conserved cys residue [active] 428406001901 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 428406001902 active site 428406001903 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 428406001904 Adenosine specific kinase; Region: Adenosine_kin; pfam04008 428406001905 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 428406001906 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 428406001907 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 428406001908 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 428406001909 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406001910 Major Facilitator Superfamily; Region: MFS_1; pfam07690 428406001911 putative substrate translocation pore; other site 428406001912 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 428406001913 SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date...; Region: SSB_OBF; cd04496 428406001914 dimer interface [polypeptide binding]; other site 428406001915 ssDNA binding site [nucleotide binding]; other site 428406001916 tetramer (dimer of dimers) interface [polypeptide binding]; other site 428406001917 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 428406001918 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 428406001919 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 428406001920 dimer interface [polypeptide binding]; other site 428406001921 phosphorylation site [posttranslational modification] 428406001922 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406001923 ATP binding site [chemical binding]; other site 428406001924 Mg2+ binding site [ion binding]; other site 428406001925 G-X-G motif; other site 428406001926 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 428406001927 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406001928 active site 428406001929 phosphorylation site [posttranslational modification] 428406001930 intermolecular recognition site; other site 428406001931 dimerization interface [polypeptide binding]; other site 428406001932 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 428406001933 DNA binding site [nucleotide binding] 428406001934 Cytochrome b(N-terminal)/b6/petB; Region: Cytochrom_B_N; pfam00033 428406001935 Sulfite oxidase and related enzymes [General function prediction only]; Region: COG2041 428406001936 Sulfite oxidase (SO) family, molybdopterin binding domain. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate reductase (NR) and sulfite oxidase (SO). SO catalyzes the...; Region: SO_family_Moco; cl00199 428406001937 Moco binding site; other site 428406001938 metal coordination site [ion binding]; other site 428406001939 Cytochrome c biogenesis protein [Posttranslational modification, protein turnover, chaperones]; Region: CcdA; COG0785 428406001940 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 428406001941 TlpA-like family, DipZ-like subfamily; composed uncharacterized proteins containing a TlpA-like TRX domain. Some members show domain architectures similar to that of E. coli DipZ protein (also known as DsbD). The only eukaryotic members of the TlpA...; Region: TlpA_like_DipZ_like; cd03012 428406001942 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 428406001943 catalytic residues [active] 428406001944 Domain of unknown function, appears to be related to a diverse group of beta-hydroxydecanoyl ACP dehydratases (FabA) and beta-hydroxyacyl ACP dehydratases (FabZ). This group appears to lack the conserved active site histidine of FabA and FabZ; Region: FabA_like; cd01289 428406001945 putative active site 1 [active] 428406001946 Beta-ketoacyl synthase, N-terminal domain; Region: Ketoacyl-synt_2; pfam13723 428406001947 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK09185 428406001948 Beta-ketoacyl-acyl carrier protein (ACP) synthase (KAS), type I and II. KASs are responsible for the elongation steps in fatty acid biosynthesis. KASIII catalyses the initial condensation and KAS I and II catalyze further elongation steps by Claisen...; Region: KAS_I_II; cd00834 428406001949 dimer interface [polypeptide binding]; other site 428406001950 active site 428406001951 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 428406001952 Catalytic NodB homology domain of rhizobial NodB-like proteins; Region: CE4_NodB_like_6s_7s; cd10917 428406001953 NodB motif; other site 428406001954 active site 428406001955 metal binding site [ion binding]; metal-binding site 428406001956 Predicted exporter [General function prediction only]; Region: COG4258 428406001957 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 428406001958 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 428406001959 putative acyl-acceptor binding pocket; other site 428406001960 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 428406001961 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 428406001962 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 428406001963 acyl-activating enzyme (AAE) consensus motif; other site 428406001964 acyl-activating enzyme (AAE) consensus motif; other site 428406001965 AMP binding site [chemical binding]; other site 428406001966 active site 428406001967 CoA binding site [chemical binding]; other site 428406001968 FabA/Z, beta-hydroxyacyl-acyl carrier protein (ACP)-dehydratases: One of several distinct enzyme types of the dissociative, type II, fatty acid synthase system (found in bacteria and plants) required to complete successive cycles of fatty acid elongation; Region: FabA_FabZ; cd00493 428406001969 active site 2 [active] 428406001970 dimer interface [polypeptide binding]; other site 428406001971 active site 1 [active] 428406001972 Predicted membrane protein [Function unknown]; Region: COG4648 428406001973 acyl carrier protein; Provisional; Region: PRK09184 428406001974 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 428406001975 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 428406001976 Ligand binding site; other site 428406001977 Putative Catalytic site; other site 428406001978 DXD motif; other site 428406001979 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 428406001980 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 428406001981 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 428406001982 Sel1-like repeats; Region: SEL1; smart00671 428406001983 Protein of unknown function (DUF3897); Region: DUF3897; cl17494 428406001984 Cytochrome c [Energy production and conversion]; Region: COG3258 428406001985 Cytochrome c; Region: Cytochrom_C; pfam00034 428406001986 Predicted transporter component [General function prediction only]; Region: COG2391 428406001987 Sulphur transport; Region: Sulf_transp; pfam04143 428406001988 Domain of unknown function (DUF4341); Region: DUF4341; pfam14241 428406001989 Predicted transporter component [General function prediction only]; Region: COG2391 428406001990 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 428406001991 Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate. The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits; Region: GntK; cd02021 428406001992 ATP-binding site [chemical binding]; other site 428406001993 Gluconate-6-phosphate binding site [chemical binding]; other site 428406001994 Shikimate kinase; Region: SKI; pfam01202 428406001995 AMP-binding domain protein; Validated; Region: PRK08315 428406001996 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 428406001997 Uncharacterized subfamily of fatty acid CoA ligase (FACL); Region: FACL_like_2; cd05917 428406001998 acyl-activating enzyme (AAE) consensus motif; other site 428406001999 putative AMP binding site [chemical binding]; other site 428406002000 putative active site [active] 428406002001 putative CoA binding site [chemical binding]; other site 428406002002 A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various...; Region: Peptidase_C39G; cd02423 428406002003 putative active site [active] 428406002004 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2904 428406002005 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 428406002006 Enzyme related to GTP cyclohydrolase I [General function prediction only]; Region: COG0780 428406002007 threonine dehydratase; Reviewed; Region: PRK09224 428406002008 Threonine dehydratase: The first step in amino acid degradation is the removal of nitrogen. Although the nitrogen atoms of most amino acids are transferred to alpha-ketoglutarate before removal, the alpha-amino group of threonine can be directly...; Region: Thr-dehyd; cd01562 428406002009 tetramer interface [polypeptide binding]; other site 428406002010 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406002011 catalytic residue [active] 428406002012 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_1; cd04906 428406002013 putative Ile/Val binding site [chemical binding]; other site 428406002014 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_2; cd04907 428406002015 putative Ile/Val binding site [chemical binding]; other site 428406002016 Inward rectifier potassium channel; Region: IRK; pfam01007 428406002017 Uncharacterized membrane protein, required for spore maturation in B.subtilis. [General function prediction only]; Region: SpmA; COG2715 428406002018 Uncharacterized membrane protein [Function unknown]; Region: SpmB; COG0700 428406002019 Predicted membrane protein [Function unknown]; Region: COG1238 428406002020 Protein of unknown function (DUF3683); Region: DUF3683; pfam12447 428406002021 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 428406002022 FAD binding domain; Region: FAD_binding_4; pfam01565 428406002023 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 428406002024 4Fe-4S dicluster domain; Region: Fer4_8; pfam13183 428406002025 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 428406002026 Cysteine-rich domain; Region: CCG; pfam02754 428406002027 Domain of unknown function (DUF3400); Region: DUF3400; pfam11880 428406002028 Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases [Nucleotide transport and metabolism / Carbohydrate transport and metabolism / General function prediction only]; Region: Hit; COG0537 428406002029 HIT family signature motif; other site 428406002030 catalytic residue [active] 428406002031 ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]; Region: COG4178 428406002032 ABC transporter transmembrane region 2; Region: ABC_membrane_2; cl00549 428406002033 ATP-binding cassette domain of peroxisomal transporter, subfamily D; Region: ABCD_peroxisomal_ALDP; cd03223 428406002034 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3536 428406002035 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 428406002036 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 428406002037 S-adenosylmethionine binding site [chemical binding]; other site 428406002038 Tim44-like domain; Region: Tim44; cl09208 428406002039 Tim44 is an essential component of the machinery that mediates the translocation of nuclear-encoded proteins across the mitochondrial inner membrane; Region: Tim44; smart00978 428406002040 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3165 428406002041 SCP-2 sterol transfer family; Region: SCP2; pfam02036 428406002042 putative ubiquinone biosynthesis protein UbiB; Reviewed; Region: ubiB; PRK04750 428406002043 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 428406002044 Thiopurine S-methyltransferase (TPMT); Region: TPMT; pfam05724 428406002045 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 428406002046 Na(+)- and Cl(-)-dependent choline cotransporter CHT and related proteins; solute-binding domain; Region: SLC5sbd_CHT; cd11474 428406002047 Na binding site [ion binding]; other site 428406002048 putative glycosylation site [posttranslational modification]; other site 428406002049 putative glycosylation site [posttranslational modification]; other site 428406002050 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2331 428406002051 Uncharacterized conserved protein [Function unknown]; Region: COG2928 428406002052 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 428406002053 EcAspRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli aspartyl-tRNA synthetase (AspRS), the human mitochondrial (mt) AspRS-2, the discriminating (D) Thermus thermophilus AspRS-1, and the nondiscriminating (ND)...; Region: EcAspRS_like_N; cd04317 428406002054 dimer interface [polypeptide binding]; other site 428406002055 anticodon binding site; other site 428406002056 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of...; Region: AspRS_core; cd00777 428406002057 homodimer interface [polypeptide binding]; other site 428406002058 motif 1; other site 428406002059 active site 428406002060 motif 2; other site 428406002061 GAD domain; Region: GAD; pfam02938 428406002062 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of...; Region: AspRS_core; cd00777 428406002063 motif 3; other site 428406002064 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_7; cd04664 428406002065 nudix motif; other site 428406002066 Metal-dependent hydrolase [General function prediction only]; Region: ElsH; COG3568 428406002067 putative catalytic site [active] 428406002068 putative metal binding site [ion binding]; other site 428406002069 putative phosphate binding site [ion binding]; other site 428406002070 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 428406002071 PLD-like domain; Region: PLDc_2; pfam13091 428406002072 putative active site [active] 428406002073 catalytic site [active] 428406002074 Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; Region: PLDc_ybhO_like_2; cd09159 428406002075 PLD-like domain; Region: PLDc_2; pfam13091 428406002076 putative active site [active] 428406002077 catalytic site [active] 428406002078 Acyl CoA:acetate/3-ketoacid CoA transferase [Lipid metabolism]; Region: COG4670 428406002079 Coenzyme A transferase; Region: CoA_trans; smart00882 428406002080 Coenzyme A transferase; Region: CoA_trans; cl17247 428406002081 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 428406002082 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 428406002083 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 428406002084 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 428406002085 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 428406002086 active site 428406002087 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 428406002088 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism]; Region: FadB; COG1250 428406002089 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 428406002090 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 428406002091 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 428406002092 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 428406002093 substrate binding site [chemical binding]; other site 428406002094 oxyanion hole (OAH) forming residues; other site 428406002095 acetyl-CoA acetyltransferase; Provisional; Region: PRK09052 428406002096 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 428406002097 dimer interface [polypeptide binding]; other site 428406002098 active site 428406002099 EDD domain protein, DegV family; Region: DegV; TIGR00762 428406002100 Uncharacterized protein, DegV family COG1307; Region: DegV; pfam02645 428406002101 enoyl-CoA hydratase; Provisional; Region: PRK06688 428406002102 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 428406002103 substrate binding site [chemical binding]; other site 428406002104 oxyanion hole (OAH) forming residues; other site 428406002105 trimer interface [polypeptide binding]; other site 428406002106 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis; Region: BFIT_BACH; cd03442 428406002107 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 428406002108 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 428406002109 ATP-binding cassette domain of iron-sulfur clusters transporter, subfamily C; Region: ABCC_ATM1_transporter; cd03253 428406002110 Walker A/P-loop; other site 428406002111 ATP binding site [chemical binding]; other site 428406002112 Q-loop/lid; other site 428406002113 ABC transporter signature motif; other site 428406002114 Walker B; other site 428406002115 D-loop; other site 428406002116 H-loop/switch region; other site 428406002117 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406002118 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 428406002119 dimerization interface [polypeptide binding]; other site 428406002120 Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]; Region: GdhA; COG0334 428406002121 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 428406002122 NAD(P) binding domain of glutamate dehydrogenase, subgroup 1; Region: NAD_bind_1_Glu_DH; cd01076 428406002123 NAD(P) binding site [chemical binding]; other site 428406002124 glutamate and aspartate transporter subunit; Provisional; Region: PRK10797 428406002125 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 428406002126 substrate binding pocket [chemical binding]; other site 428406002127 membrane-bound complex binding site; other site 428406002128 hinge residues; other site 428406002129 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 428406002130 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406002131 dimer interface [polypeptide binding]; other site 428406002132 conserved gate region; other site 428406002133 putative PBP binding loops; other site 428406002134 ABC-ATPase subunit interface; other site 428406002135 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 428406002136 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406002137 dimer interface [polypeptide binding]; other site 428406002138 conserved gate region; other site 428406002139 putative PBP binding loops; other site 428406002140 ABC-ATPase subunit interface; other site 428406002141 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 428406002142 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 428406002143 Walker A/P-loop; other site 428406002144 ATP binding site [chemical binding]; other site 428406002145 Q-loop/lid; other site 428406002146 ABC transporter signature motif; other site 428406002147 Walker B; other site 428406002148 D-loop; other site 428406002149 H-loop/switch region; other site 428406002150 Predicted glutamine amidotransferase [General function prediction only]; Region: COG0121 428406002151 Glutamine amidotransferases class-II (Gn-AT)_YafJ-type. YafJ is a glutamine amidotransferase-like protein of unknown function found in prokaryotes, eukaryotes and archaea. YafJ has a conserved structural fold similar to those of other class II...; Region: YafJ; cd01908 428406002152 putative active site [active] 428406002153 putative dimer interface [polypeptide binding]; other site 428406002154 Putative glycerate kinase [Carbohydrate transport and metabolism]; Region: GckA; COG2379 428406002155 Domain of unknown function (DUF4147); Region: DUF4147; pfam13660 428406002156 MOFRL family; Region: MOFRL; pfam05161 428406002157 Dihydroorotase (DHOase) catalyzes the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in the pyrimidine biosynthesis. In contrast to the large polyfunctional CAD proteins of higher organisms, this group of DHOases is...; Region: DHOase; cd01294 428406002158 active site 428406002159 substrate binding pocket [chemical binding]; other site 428406002160 dimer interface [polypeptide binding]; other site 428406002161 Protein of unknown function (DUF3025); Region: DUF3025; pfam11227 428406002162 OsmC-like protein; Region: OsmC; cl00767 428406002163 Ribosomal protein L13. Protein L13, a large ribosomal subunit protein, is one of five proteins required for an early folding intermediate of 23S rRNA in the assembly of the large subunit. L13 is situated on the bottom of the large subunit, near the...; Region: Ribosomal_L13; cd00392 428406002164 23S rRNA interface [nucleotide binding]; other site 428406002165 L3 interface [polypeptide binding]; other site 428406002166 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 428406002167 Integral membrane protein CcmA involved in cell shape determination [Cell envelope biogenesis, outer membrane]; Region: CcmA; COG1664 428406002168 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 428406002169 iron-sulfur cluster insertion protein ErpA; Provisional; Region: PRK13623 428406002170 anhydro-N-acetylmuramic acid kinase; Reviewed; Region: anmK; PRK09585 428406002171 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 428406002172 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 428406002173 active site 428406002174 HIGH motif; other site 428406002175 dimer interface [polypeptide binding]; other site 428406002176 KMSKS motif; other site 428406002177 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cd00165 428406002178 RNA binding surface [nucleotide binding]; other site 428406002179 D-Tyrosyl-tRNAtyr deacylases; a class of tRNA-dependent hydrolases which are capable of hydrolyzing the ester bond of D-Tyrosyl-tRNA reducing the level of cellular D-Tyrosine while recycling the peptidyl-tRNA; found in bacteria and in eukaryotes but not...; Region: Dtyr_deacylase; cd00563 428406002180 putative active site [active] 428406002181 dimerization interface [polypeptide binding]; other site 428406002182 putative tRNAtyr binding site [nucleotide binding]; other site 428406002183 Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP_PGM_like; cd07067 428406002184 catalytic core [active] 428406002185 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; pfam02592 428406002186 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 428406002187 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406002188 Walker A motif; other site 428406002189 ATP binding site [chemical binding]; other site 428406002190 Walker B motif; other site 428406002191 arginine finger; other site 428406002192 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 428406002193 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 428406002194 RuvA N terminal domain; Region: RuvA_N; pfam01330 428406002195 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 428406002196 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 428406002197 Glycerophosphodiester phosphodiesterase domain of Streptomycin coelicolor (GlpQ1) and similar proteins; Region: GDPD_ScGlpQ1_like; cd08602 428406002198 putative active site [active] 428406002199 catalytic site [active] 428406002200 putative metal binding site [ion binding]; other site 428406002201 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD...; Region: RuvC_resolvase; cd00529 428406002202 active site 428406002203 putative DNA-binding cleft [nucleotide binding]; other site 428406002204 dimer interface [polypeptide binding]; other site 428406002205 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 428406002206 Inosine monophosphate cyclohydrolase domain. This is the N-terminal domain in the purine biosynthesis pathway protein ATIC (purH). The bifunctional ATIC protein contains a C-terminal ATIC formylase domain that formylates...; Region: IMPCH; cd01421 428406002207 purine monophosphate binding site [chemical binding]; other site 428406002208 dimer interface [polypeptide binding]; other site 428406002209 putative catalytic residues [active] 428406002210 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; smart00798 428406002211 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 428406002212 DNA-binding protein Fis; Provisional; Region: PRK01905 428406002213 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 428406002214 Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also...; Region: DUS_like_FMN; cd02801 428406002215 FMN binding site [chemical binding]; other site 428406002216 active site 428406002217 catalytic residues [active] 428406002218 substrate binding site [chemical binding]; other site 428406002219 D-amino acid dehydrogenase small subunit; Validated; Region: PRK00711 428406002220 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 428406002221 hydroxyglutarate oxidase; Provisional; Region: PRK11728 428406002222 hypothetical protein; Provisional; Region: PRK06996 428406002223 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 428406002224 proline aminopeptidase P II; Provisional; Region: PRK10879 428406002225 Aminopeptidase P, N-terminal domain; Region: AMP_N; pfam05195 428406002226 Prolidase. E.C. 3.4.13.9. Also known as Xaa-Pro dipeptidase, X-Pro dipeptidase, proline dipeptidase., imidodipeptidase, peptidase D, gamma-peptidase. Catalyses hydrolysis of Xaa-Pro dipeptides; also acts on aminoacyl-hydroxyproline analogs. No action on...; Region: Prolidase; cd01087 428406002227 active site 428406002228 MHYT domain (predicted integral membrane sensor domain) [Signal transduction mechanisms]; Region: COG3300 428406002229 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 428406002230 Bacterial signalling protein N terminal repeat; Region: MHYT; pfam03707 428406002231 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 428406002232 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 428406002233 metal binding site [ion binding]; metal-binding site 428406002234 active site 428406002235 I-site; other site 428406002236 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 428406002237 Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis/translation initiation factor 2B, gamma/epsilon subunits (eIF-2Bgamma/eIF-2Bepsilon) [Cell envelope biogenesis, outer membrane / Translation, ribosomal structure...; Region: GCD1; COG1208 428406002238 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 428406002239 Substrate binding site; other site 428406002240 metal-binding site 428406002241 Predicted membrane protein [Function unknown]; Region: COG4392 428406002242 Predicted branched-chain amino acid permease (azaleucine resistance) [Amino acid transport and metabolism]; Region: AzlC; COG1296 428406002243 Predicted phosphotransferase related to Ser/Thr protein kinases [General function prediction only]; Region: COG3178 428406002244 Phosphotransferase enzyme family; Region: APH; pfam01636 428406002245 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 428406002246 OstA-like protein; Region: OstA; cl00844 428406002247 Organic solvent tolerance protein; Region: OstA_C; pfam04453 428406002248 SurA N-terminal domain; Region: SurA_N; pfam09312 428406002249 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 428406002250 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 428406002251 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK01909 428406002252 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 428406002253 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 428406002254 Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]; Region: KsgA; COG0030 428406002255 putative DMT superfamily transporter inner membrane protein; Provisional; Region: PRK11272 428406002256 EamA-like transporter family; Region: EamA; pfam00892 428406002257 EamA-like transporter family; Region: EamA; pfam00892 428406002258 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 428406002259 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 428406002260 dimer interface [polypeptide binding]; other site 428406002261 active site 428406002262 metal binding site [ion binding]; metal-binding site 428406002263 glutathione binding site [chemical binding]; other site 428406002264 Protein of unknown function DUF45; Region: DUF45; pfam01863 428406002265 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 428406002266 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 428406002267 putative acyl-acceptor binding pocket; other site 428406002268 D,D-heptose 1,7-bisphosphate phosphatase; Validated; Region: PRK08942 428406002269 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 428406002270 active site 428406002271 motif I; other site 428406002272 motif II; other site 428406002273 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 428406002274 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 428406002275 Class II Glycyl-tRNA synthetase (GlyRS) alpha subunit core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes and in arabidopsis. It is responsible for the...; Region: GlyRS_alpha_core; cd00733 428406002276 dimer interface [polypeptide binding]; other site 428406002277 motif 1; other site 428406002278 active site 428406002279 motif 2; other site 428406002280 motif 3; other site 428406002281 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 428406002282 Uncharacterized membrane protein [Function unknown]; Region: COG5427; cl02250 428406002283 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 428406002284 putative active site [active] 428406002285 catalytic triad [active] 428406002286 putative dimer interface [polypeptide binding]; other site 428406002287 Putative Mg2+ and Co2+ transporter CorC [Inorganic ion transport and metabolism]; Region: CorC; COG4535 428406002288 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the CorC_HlyC domain. CorC_HlyC is a transporter associated domain. This small domain is found in Na+/H+ antiporters, in proteins involved in...; Region: CBS_pair_CorC_HlyC_assoc; cd04590 428406002289 Transporter associated domain; Region: CorC_HlyC; smart01091 428406002290 unkown domain/putative metalloprotease fusion protein; Provisional; Region: PRK13963 428406002291 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 428406002292 PhoH-like protein; Region: PhoH; pfam02562 428406002293 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 428406002294 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 428406002295 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 428406002296 FeS/SAM binding site; other site 428406002297 TRAM domain; Region: TRAM; pfam01938 428406002298 Predicted NAD/FAD-dependent oxidoreductase [General function prediction only]; Region: COG3380 428406002299 Outer membrane protein W [Cell envelope biogenesis, outer membrane]; Region: OmpW; COG3047 428406002300 Protein of unknown function (DUF1571); Region: DUF1571; pfam07608 428406002301 Long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07059 428406002302 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 428406002303 acyl-activating enzyme (AAE) consensus motif; other site 428406002304 putative AMP binding site [chemical binding]; other site 428406002305 putative active site [active] 428406002306 putative CoA binding site [chemical binding]; other site 428406002307 acetyl-CoA acetyltransferase; Provisional; Region: PRK09268 428406002308 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 428406002309 dimer interface [polypeptide binding]; other site 428406002310 active site 428406002311 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 428406002312 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK08261 428406002313 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 428406002314 NAD(P) binding site [chemical binding]; other site 428406002315 active site 428406002316 acyl-CoA dehydrogenase; Reviewed; Region: fadE; PRK09463 428406002317 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 428406002318 active site 428406002319 Domain of unknown function (DUF1974); Region: DUF1974; pfam09317 428406002320 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 428406002321 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 428406002322 DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif; Region: DEADc; cd00268 428406002323 DEAD-like helicases superfamily; Region: DEXDc; smart00487 428406002324 ATP binding site [chemical binding]; other site 428406002325 Mg++ binding site [ion binding]; other site 428406002326 motif III; other site 428406002327 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 428406002328 nucleotide binding region [chemical binding]; other site 428406002329 ATP-binding site [chemical binding]; other site 428406002330 serine/threonine protein kinase; Provisional; Region: PRK11768 428406002331 Putative homoserine kinase type II (protein kinase fold) [General function prediction only]; Region: COG2334 428406002332 Pirin-related protein [General function prediction only]; Region: COG1741 428406002333 Pirin; Region: Pirin; pfam02678 428406002334 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 428406002335 LysR family transcriptional regulator; Provisional; Region: PRK14997 428406002336 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406002337 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 428406002338 putative effector binding pocket; other site 428406002339 dimerization interface [polypeptide binding]; other site 428406002340 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 428406002341 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406002342 active site 428406002343 phosphorylation site [posttranslational modification] 428406002344 intermolecular recognition site; other site 428406002345 dimerization interface [polypeptide binding]; other site 428406002346 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 428406002347 DNA binding site [nucleotide binding] 428406002348 Cupin domain; Region: Cupin_2; pfam07883 428406002349 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases [Coenzyme metabolism / Energy production and conversion]; Region: UbiH; COG0654 428406002350 hypothetical protein; Provisional; Region: PRK07236 428406002351 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406002352 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406002353 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 428406002354 dimerization interface [polypeptide binding]; other site 428406002355 citrate-proton symporter; Provisional; Region: PRK15075 428406002356 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406002357 putative substrate translocation pore; other site 428406002358 Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA)-like; uncharacterized subgroup; Region: M14_ASTE_ASPA_like_7; cd06910 428406002359 putative active site [active] 428406002360 Zn binding site [ion binding]; other site 428406002361 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 428406002362 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 428406002363 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 428406002364 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_3; pfam13738 428406002365 PGAP1-like protein; Region: PGAP1; pfam07819 428406002366 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 428406002367 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406002368 putative substrate translocation pore; other site 428406002369 Protein of unknown function, DUF485; Region: DUF485; pfam04341 428406002370 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 428406002371 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u4; cd11480 428406002372 Na binding site [ion binding]; other site 428406002373 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]; Region: COG2905 428406002374 Cyclic nucleotide-binding domain; Region: cNMP_binding; pfam00027 428406002375 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cl15354 428406002376 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 428406002377 metal binding triad; other site 428406002378 DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]; Region: DnaQ; COG0847 428406002379 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 428406002380 active site 428406002381 catalytic site [active] 428406002382 substrate binding site [chemical binding]; other site 428406002383 Domain of unknown function (DUF4212); Region: DUF4212; cl01781 428406002384 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 428406002385 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 428406002386 HAMP domain; Region: HAMP; pfam00672 428406002387 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 428406002388 dimer interface [polypeptide binding]; other site 428406002389 phosphorylation site [posttranslational modification] 428406002390 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406002391 ATP binding site [chemical binding]; other site 428406002392 Mg2+ binding site [ion binding]; other site 428406002393 G-X-G motif; other site 428406002394 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 428406002395 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406002396 active site 428406002397 phosphorylation site [posttranslational modification] 428406002398 intermolecular recognition site; other site 428406002399 dimerization interface [polypeptide binding]; other site 428406002400 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 428406002401 DNA binding site [nucleotide binding] 428406002402 RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response. RecA couples ATP hydrolysis to DNA strand exchange; Region: recA; cd00983 428406002403 RecA/RadA recombinase [DNA replication, recombination, and repair]; Region: RecA; COG0468 428406002404 hexamer interface [polypeptide binding]; other site 428406002405 Walker A motif; other site 428406002406 ATP binding site [chemical binding]; other site 428406002407 Walker B motif; other site 428406002408 recombination regulator RecX; Reviewed; Region: recX; PRK00117 428406002409 Protein of unknown function (DUF2889); Region: DUF2889; pfam11136 428406002410 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 428406002411 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 428406002412 CoA-ligase; Region: Ligase_CoA; pfam00549 428406002413 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 428406002414 CoA binding domain; Region: CoA_binding; smart00881 428406002415 CoA-ligase; Region: Ligase_CoA; pfam00549 428406002416 integral membrane protein, YjbE family; Region: R_switched_YjbE; TIGR03717 428406002417 Pilin (bacterial filament); Region: Pilin; pfam00114 428406002418 Tfp pilus assembly protein, major pilin PilA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilA; COG4969 428406002419 Pilin (bacterial filament); Region: Pilin; pfam00114 428406002420 O-Antigen ligase; Region: Wzy_C; pfam04932 428406002421 Domain of unknown function (DUF3366); Region: DUF3366; pfam11846 428406002422 O-Antigen ligase; Region: Wzy_C; pfam04932 428406002423 Domain of unknown function (DUF3366); Region: DUF3366; pfam11846 428406002424 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 428406002425 MoaC family, prokaryotic and eukaryotic. Members of this family are involved in molybdenum cofactor (Moco) biosynthesis, an essential cofactor of a diverse group of redox enzymes. MoaC, a small hexameric protein, converts, together with MoaA, a guanosine...; Region: MoaC_PE; cd01420 428406002426 trimer interface [polypeptide binding]; other site 428406002427 dimer interface [polypeptide binding]; other site 428406002428 putative active site [active] 428406002429 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]; Region: COG4783 428406002430 Peptidase family M48; Region: Peptidase_M48; pfam01435 428406002431 Protein of unknown function (DUF2946); Region: DUF2944; pfam11161 428406002432 Predicted hydrolase of the alpha/beta-hydrolase fold [General function prediction only]; Region: COG0429 428406002433 Calcium/calmodulin dependent protein kinase II Association; Region: CaMKII_AD; cl17504 428406002434 SnoaL-like domain; Region: SnoaL_3; pfam13474 428406002435 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 428406002436 Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from...; Region: GT1_LPS_heptosyltransferase; cd03789 428406002437 putative active site [active] 428406002438 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4391 428406002439 AzlC protein; Region: AzlC; pfam03591 428406002440 Predicted membrane protein [Function unknown]; Region: COG4392 428406002441 Predicted permeases [General function prediction only]; Region: RarD; COG2962 428406002442 phosphoglycerate kinase; Provisional; Region: pgk; PRK00073 428406002443 Phosphoglycerate kinase; Region: PGK; pfam00162 428406002444 substrate binding site [chemical binding]; other site 428406002445 hinge regions; other site 428406002446 ADP binding site [chemical binding]; other site 428406002447 catalytic site [active] 428406002448 pyruvate kinase; Provisional; Region: PRK05826 428406002449 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl17342 428406002450 domain interfaces; other site 428406002451 active site 428406002452 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 428406002453 Tagatose-1,6-bisphosphate (TBP) aldolase and related Type B Class II aldolases. TBP aldolase is a tetrameric class II aldolase that catalyzes the reversible condensation of dihydroxyacetone phosphate with glyceraldehyde 3-phsophate to produce tagatose 1; Region: TBP_aldolase_IIB; cd00947 428406002454 intersubunit interface [polypeptide binding]; other site 428406002455 active site 428406002456 zinc binding site [ion binding]; other site 428406002457 Na+ binding site [ion binding]; other site 428406002458 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 428406002459 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 428406002460 ATP binding site [chemical binding]; other site 428406002461 active site 428406002462 substrate binding site [chemical binding]; other site 428406002463 AIR carboxylase; Region: AIRC; pfam00731 428406002464 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 428406002465 ATP-grasp domain; Region: ATP-grasp; pfam02222 428406002466 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 428406002467 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 428406002468 Triacylglycerol lipase-like subfamily of the SGNH hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its...; Region: Triacylglycerol_lipase_like; cd01847 428406002469 active site 428406002470 catalytic triad [active] 428406002471 oxyanion hole [active] 428406002472 Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes. In E. coli, the synthesis of Moco involves genes from several loci: moa; Region: MobB; cd03116 428406002473 D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 4) [Cell envelope biogenesis, outer membrane]; Region: DacB; COG2027 428406002474 ATP-dependent DNA ligase; Reviewed; Region: ligD; PRK05972 428406002475 DNA ligase D, 3'-phosphoesterase domain; Region: LigD_PE_dom; TIGR02777 428406002476 Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases; Region: Adenylation_DNA_ligase_LigD_LigC; cd07906 428406002477 active site 428406002478 DNA binding site [nucleotide binding] 428406002479 The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigD is a DNA-binding module that is part of the catalytic core unit; Region: OBF_DNA_ligase_LigD; cd07971 428406002480 DNA binding site [nucleotide binding] 428406002481 PaeLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for...; Region: PaeLigD_Pol_like; cd04862 428406002482 nucleotide binding site [chemical binding]; other site 428406002483 Ku protein, prokaryotic; Region: Ku_bact; TIGR02772 428406002484 Ku-core domain, Ku-like subfamily; composed of prokaryotic homologs of the eukaryotic DNA binding protein Ku. The alignment includes the core domain shared by the prokaryotic YkoV-like proteins and the eukaryotic Ku70 and Ku80. The prokaryotic Ku...; Region: KU_like; cd00789 428406002485 putative DNA binding site [nucleotide binding]; other site 428406002486 putative homodimer interface [polypeptide binding]; other site 428406002487 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406002488 Major Facilitator Superfamily; Region: MFS_1; pfam07690 428406002489 putative substrate translocation pore; other site 428406002490 putative phosphonate metabolism protein; Region: Phn_opern_protn; TIGR03223 428406002491 phosphonate metabolism protein PhnM; Region: phosphono_phnM; TIGR02318 428406002492 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 428406002493 active site 428406002494 PAS domain S-box; Region: sensory_box; TIGR00229 428406002495 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 428406002496 putative active site [active] 428406002497 heme pocket [chemical binding]; other site 428406002498 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 428406002499 GAF domain; Region: GAF; pfam01590 428406002500 PAS fold; Region: PAS; pfam00989 428406002501 PAS domain; Region: PAS; smart00091 428406002502 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 428406002503 putative active site [active] 428406002504 heme pocket [chemical binding]; other site 428406002505 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 428406002506 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 428406002507 metal binding site [ion binding]; metal-binding site 428406002508 active site 428406002509 I-site; other site 428406002510 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 428406002511 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 428406002512 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 428406002513 dimer interface [polypeptide binding]; other site 428406002514 putative CheW interface [polypeptide binding]; other site 428406002515 4-hydroxyphenylacetate permease; Region: HpaX; TIGR02332 428406002516 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406002517 putative substrate translocation pore; other site 428406002518 amidase; Provisional; Region: PRK07056 428406002519 Amidase; Region: Amidase; cl11426 428406002520 Protein of unknown function (DUF2848); Region: DUF2848; pfam11010 428406002521 Transcriptional regulators [Transcription]; Region: GntR; COG1802 428406002522 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 428406002523 DNA-binding site [nucleotide binding]; DNA binding site 428406002524 FCD domain; Region: FCD; pfam07729 428406002525 hypothetical protein; Provisional; Region: PRK07538 428406002526 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 428406002527 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 428406002528 Type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids; Region: PBP1_ABC-type_HAAT_like; cd06333 428406002529 putative ligand binding site [chemical binding]; other site 428406002530 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 428406002531 MarR family; Region: MarR; pfam01047 428406002532 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 428406002533 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 428406002534 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 428406002535 Zn2+ binding site [ion binding]; other site 428406002536 Mg2+ binding site [ion binding]; other site 428406002537 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 428406002538 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 428406002539 N-terminal plug; other site 428406002540 ligand-binding site [chemical binding]; other site 428406002541 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 428406002542 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 428406002543 DNA-binding site [nucleotide binding]; DNA binding site 428406002544 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 428406002545 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406002546 homodimer interface [polypeptide binding]; other site 428406002547 catalytic residue [active] 428406002548 Protein of unknown function (DUF330); Region: DUF330; pfam03886 428406002549 Paraquat-inducible protein B [General function prediction only]; Region: PqiB; COG3008 428406002550 mce related protein; Region: MCE; pfam02470 428406002551 mce related protein; Region: MCE; pfam02470 428406002552 mce related protein; Region: MCE; pfam02470 428406002553 Paraquat-inducible protein A; Region: PqiA; pfam04403 428406002554 Paraquat-inducible protein A; Region: PqiA; pfam04403 428406002555 S-formylglutathione hydrolase; Region: PLN02442 428406002556 S-formylglutathione hydrolase; Region: fghA_ester_D; TIGR02821 428406002557 Zn-dependent alcohol dehydrogenases, class III [Energy production and conversion]; Region: AdhC; COG1062 428406002558 class III alcohol dehydrogenases; Region: alcohol_DH_class_III; cd08300 428406002559 substrate binding site [chemical binding]; other site 428406002560 catalytic Zn binding site [ion binding]; other site 428406002561 NAD binding site [chemical binding]; other site 428406002562 structural Zn binding site [ion binding]; other site 428406002563 dimer interface [polypeptide binding]; other site 428406002564 Cache domain; Region: Cache_1; pfam02743 428406002565 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 428406002566 dimerization interface [polypeptide binding]; other site 428406002567 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 428406002568 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 428406002569 dimer interface [polypeptide binding]; other site 428406002570 putative CheW interface [polypeptide binding]; other site 428406002571 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 428406002572 GST_N family, Saccharomyces cerevisiae GTT1-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT1, and the Schizosaccharomyces pombe GST-III. GSTs are cytosolic dimeric proteins involved...; Region: GST_N_GTT1_like; cd03046 428406002573 putative C-terminal domain interface [polypeptide binding]; other site 428406002574 putative GSH binding site (G-site) [chemical binding]; other site 428406002575 putative dimer interface [polypeptide binding]; other site 428406002576 C-terminal, alpha helical domain of an unknown subfamily 8 of Glutathione S-transferases; Region: GST_C_8; cd03207 428406002577 dimer interface [polypeptide binding]; other site 428406002578 N-terminal domain interface [polypeptide binding]; other site 428406002579 putative substrate binding pocket (H-site) [chemical binding]; other site 428406002580 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 428406002581 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 428406002582 metal binding site [ion binding]; metal-binding site 428406002583 active site 428406002584 I-site; other site 428406002585 Antibiotic biosynthesis monooxygenase; Region: ABM; pfam03992 428406002586 Uncharacterized conserved protein [Function unknown]; Region: COG3268 428406002587 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 428406002588 Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate...; Region: ICL_PEPM; cd00377 428406002589 tetramer interface [polypeptide binding]; other site 428406002590 active site 428406002591 Mg2+/Mn2+ binding site [ion binding]; other site 428406002592 isocitrate lyase; Region: PLN02892 428406002593 citrate-proton symporter; Provisional; Region: PRK15075 428406002594 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406002595 putative substrate translocation pore; other site 428406002596 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 428406002597 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 428406002598 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406002599 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406002600 TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_4; cd08440 428406002601 putative dimerization interface [polypeptide binding]; other site 428406002602 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 428406002603 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 428406002604 metal binding site [ion binding]; metal-binding site 428406002605 active site 428406002606 I-site; other site 428406002607 Chaperonin 10 Kd subunit (cpn10 or GroES); Cpn10 cooperates with chaperonin 60 (cpn60 or GroEL), an ATPase, to assist the folding and assembly of proteins and is found in eubacterial cytosol, as well as in the matrix of mitochondria and chloroplasts. It...; Region: cpn10; cd00320 428406002608 oligomerisation interface [polypeptide binding]; other site 428406002609 mobile loop; other site 428406002610 roof hairpin; other site 428406002611 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 428406002612 GroEL_like type I chaperonin. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings, each composed of 7-9 subunits. The symmetry of type I is seven-fold and they are found...; Region: GroEL; cd03344 428406002613 ring oligomerisation interface [polypeptide binding]; other site 428406002614 ATP/Mg binding site [chemical binding]; other site 428406002615 stacking interactions; other site 428406002616 hinge regions; other site 428406002617 Bacterial protein of unknown function (DUF898); Region: DUF898; cl01738 428406002618 Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]; Region: HtpX; COG0501 428406002619 Predicted membrane protein [Function unknown]; Region: COG2246 428406002620 GtrA-like protein; Region: GtrA; pfam04138 428406002621 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 428406002622 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 428406002623 Ligand binding site; other site 428406002624 Putative Catalytic site; other site 428406002625 DXD motif; other site 428406002626 Protein of unknown function (DUF2029); Region: DUF2029; pfam09594 428406002627 Putative Flp pilus-assembly TadE/G-like; Region: Tad; pfam13400 428406002628 Putative Tad-like Flp pilus-assembly; Region: Tad_C; pfam09977 428406002629 Flp pilus assembly protein TadG [Intracellular trafficking and secretion]; Region: TadG; COG4961 428406002630 TadE-like protein; Region: TadE; pfam07811 428406002631 Flp pilus assembly protein TadC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: TadC; COG2064 428406002632 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 428406002633 Flp pilus assembly protein TadB [Intracellular trafficking and secretion]; Region: TadB; COG4965 428406002634 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 428406002635 Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]; Region: CpaF; COG4962 428406002636 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 428406002637 ATP binding site [chemical binding]; other site 428406002638 Walker A motif; other site 428406002639 hexamer interface [polypeptide binding]; other site 428406002640 Walker B motif; other site 428406002641 Flp pilus assembly protein, ATPase CpaE [Intracellular trafficking and secretion]; Region: CpaE; COG4963 428406002642 This protein family consists of proteins similar to the cpaE protein of the Caulobacter pilus assembly and the orf4 protein of Actinobacillus pilus formation gene cluster. The function of these proteins are unkown. The Caulobacter pilus assembly contains...; Region: CpaE_like; cd03111 428406002643 This protein family consists of proteins similar to the cpaE protein of the Caulobacter pilus assembly and the orf4 protein of Actinobacillus pilus formation gene cluster. The function of these proteins are unkown. The Caulobacter pilus assembly contains...; Region: CpaE_like; cd03111 428406002644 Pilus formation protein N terminal region; Region: T2SS-T3SS_pil_N; pfam13629 428406002645 Flp pilus assembly protein, secretin CpaC [Intracellular trafficking and secretion]; Region: CpaC; COG4964 428406002646 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 428406002647 Flp pilus assembly protein CpaB [Intracellular trafficking and secretion]; Region: CpaB; COG3745 428406002648 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 428406002649 Flp pilus assembly protein, protease CpaA [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: CpaA; COG4960 428406002650 Flp/Fap pilin component; Region: Flp_Fap; cl01585 428406002651 Repair protein; Region: Repair_PSII; cl01535 428406002652 Beta-propeller domains of methanol dehydrogenase type [General function prediction only]; Region: COG1512 428406002653 Repair protein; Region: Repair_PSII; pfam04536 428406002654 Uncharacterized conserved protein [Function unknown]; Region: LemA; COG1704 428406002655 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 428406002656 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 428406002657 dimer interface [polypeptide binding]; other site 428406002658 active site 428406002659 catalytic residue [active] 428406002660 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 428406002661 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 428406002662 inhibitor-cofactor binding pocket; inhibition site 428406002663 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406002664 catalytic residue [active] 428406002665 Rubredoxin [Energy production and conversion]; Region: COG1773 428406002666 Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are...; Region: rubredoxin; cd00730 428406002667 iron binding site [ion binding]; other site 428406002668 Response regulator receiver domain; Region: Response_reg; pfam00072 428406002669 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406002670 active site 428406002671 phosphorylation site [posttranslational modification] 428406002672 intermolecular recognition site; other site 428406002673 dimerization interface [polypeptide binding]; other site 428406002674 Response regulator receiver domain; Region: Response_reg; pfam00072 428406002675 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406002676 active site 428406002677 phosphorylation site [posttranslational modification] 428406002678 intermolecular recognition site; other site 428406002679 dimerization interface [polypeptide binding]; other site 428406002680 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 428406002681 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 428406002682 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 428406002683 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 428406002684 dimer interface [polypeptide binding]; other site 428406002685 putative CheW interface [polypeptide binding]; other site 428406002686 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cd00088 428406002687 putative binding surface; other site 428406002688 active site 428406002689 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cd00088 428406002690 putative binding surface; other site 428406002691 active site 428406002692 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cd00088 428406002693 putative binding surface; other site 428406002694 active site 428406002695 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 428406002696 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 428406002697 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406002698 ATP binding site [chemical binding]; other site 428406002699 Mg2+ binding site [ion binding]; other site 428406002700 G-X-G motif; other site 428406002701 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 428406002702 Response regulator receiver domain; Region: Response_reg; pfam00072 428406002703 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406002704 active site 428406002705 phosphorylation site [posttranslational modification] 428406002706 intermolecular recognition site; other site 428406002707 dimerization interface [polypeptide binding]; other site 428406002708 Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]; Region: PhrB; COG0415 428406002709 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 428406002710 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 428406002711 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cd00165 428406002712 RNA binding surface [nucleotide binding]; other site 428406002713 Pseudouridine synthase, Escherichia coli RsuA like; Region: PseudoU_synth_RsuA; cd02553 428406002714 active site 428406002715 uracil binding [chemical binding]; other site 428406002716 hypothetical protein; Validated; Region: PRK00228 428406002717 Holliday junction resolvase-like protein; Reviewed; Region: PRK00109 428406002718 Pyrimidine operon attenuation protein/uracil phosphoribosyltransferase [Nucleotide transport and metabolism]; Region: PyrR; COG2065 428406002719 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 428406002720 active site 428406002721 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 428406002722 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 428406002723 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 428406002724 dihydroorotase; Provisional; Region: PRK07627 428406002725 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 428406002726 Dihydroorotase (DHOase), subgroup IIa; DHOases catalyze the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in pyrimidine biosynthesis. This subgroup also contains proteins that lack the active site, like unc-33, a C; Region: DHOase_IIa; cd01317 428406002727 active site 428406002728 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 428406002729 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 428406002730 putative acyl-acceptor binding pocket; other site 428406002731 diadenosine tetraphosphatase; Reviewed; Region: apaH; PRK00166 428406002732 Escherichia coli ApaH and related proteins, metallophosphatase domain; Region: MPP_ApaH; cd07422 428406002733 active site 428406002734 metal binding site [ion binding]; metal-binding site 428406002735 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 428406002736 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 428406002737 NAD binding site [chemical binding]; other site 428406002738 substrate binding site [chemical binding]; other site 428406002739 homodimer interface [polypeptide binding]; other site 428406002740 active site 428406002741 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 428406002742 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 428406002743 NADP binding site [chemical binding]; other site 428406002744 active site 428406002745 putative substrate binding site [chemical binding]; other site 428406002746 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: dTDP_sugar_isom; cl17405 428406002747 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 428406002748 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 428406002749 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 428406002750 NAD(P) binding site [chemical binding]; other site 428406002751 homodimer interface [polypeptide binding]; other site 428406002752 substrate binding site [chemical binding]; other site 428406002753 active site 428406002754 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 428406002755 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 428406002756 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 428406002757 UDP-glucuronate decarboxylase (UGD) and related proteins, extended (e) SDRs; Region: UGD_SDR_e; cd05230 428406002758 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 428406002759 NAD binding site [chemical binding]; other site 428406002760 putative substrate binding site 2 [chemical binding]; other site 428406002761 putative substrate binding site 1 [chemical binding]; other site 428406002762 active site 428406002763 UDP-N-acetylglucosamine 4,6-dehydratase; Region: PseB; TIGR03589 428406002764 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 428406002765 NAD(P) binding site [chemical binding]; other site 428406002766 homodimer interface [polypeptide binding]; other site 428406002767 substrate binding site [chemical binding]; other site 428406002768 active site 428406002769 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 428406002770 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary...; Region: AHBA_syn; cd00616 428406002771 inhibitor-cofactor binding pocket; inhibition site 428406002772 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406002773 catalytic residue [active] 428406002774 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 428406002775 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 428406002776 active site 428406002777 catalytic tetrad [active] 428406002778 SpsF is a glycosyltrnasferase implicated in the synthesis of the spore coat; Region: GT2_SpsF; cd02518 428406002779 ligand binding site; other site 428406002780 glutamate-1-semialdehyde 2,1-aminomutase; Provisional; Region: PRK06209 428406002781 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 428406002782 inhibitor-cofactor binding pocket; inhibition site 428406002783 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406002784 catalytic residue [active] 428406002785 pseudaminic acid biosynthesis-associated protein PseG; Region: PseG; TIGR03590 428406002786 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 428406002787 pseudaminic acid biosynthesis N-acetyl transferase; Region: PseH; TIGR03585 428406002788 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 428406002789 pseudaminic acid synthase; Region: PseI; TIGR03586 428406002790 NeuB family; Region: NeuB; pfam03102 428406002791 C-terminal SAF domain of sialic acid synthetase; Region: SAF_NeuB_like; cd11615 428406002792 NeuB binding interface [polypeptide binding]; other site 428406002793 putative substrate binding site [chemical binding]; other site 428406002794 Capsule polysaccharide biosynthesis protein; Region: Capsule_synth; pfam05159 428406002795 Cellulose synthase-like protein; Region: PLN02893 428406002796 Maltose O-acyltransferase (MAT)-like: This family is composed of maltose O-acetyltransferase, galactoside O-acetyltransferase (GAT), xenobiotic acyltransferase (XAT) and similar proteins. MAT and GAT catalyze the CoA-dependent acetylation of the...; Region: LbH_MAT_like; cd04647 428406002797 trimer interface [polypeptide binding]; other site 428406002798 active site 428406002799 substrate binding site [chemical binding]; other site 428406002800 CoA binding site [chemical binding]; other site 428406002801 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 428406002802 This family is most closely related to the GT1 family of glycosyltransferases. wbuB in E. coli is involved in the biosynthesis of the O26 O-antigen. It has been proposed to function as an N-acetyl-L-fucosamine (L-FucNAc) transferase; Region: GT1_wbuB_like; cd03794 428406002803 Acetyltransferase (isoleucine patch superfamily) [General function prediction only]; Region: WbbJ; COG0110 428406002804 Maltose O-acyltransferase (MAT)-like: This family is composed of maltose O-acetyltransferase, galactoside O-acetyltransferase (GAT), xenobiotic acyltransferase (XAT) and similar proteins. MAT and GAT catalyze the CoA-dependent acetylation of the...; Region: LbH_MAT_like; cd04647 428406002805 trimer interface [polypeptide binding]; other site 428406002806 active site 428406002807 substrate binding site [chemical binding]; other site 428406002808 CoA binding site [chemical binding]; other site 428406002809 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 428406002810 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary...; Region: AHBA_syn; cd00616 428406002811 inhibitor-cofactor binding pocket; inhibition site 428406002812 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406002813 catalytic residue [active] 428406002814 Bacterial sugar transferase; Region: Bac_transf; pfam02397 428406002815 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 428406002816 S-adenosylmethionine binding site [chemical binding]; other site 428406002817 Chain length determinant protein; Region: Wzz; cl15801 428406002818 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 428406002819 The phosphomannomutase/phosphoglucomutase (PMM/PGM) bifunctional enzyme catalyzes the reversible conversion of 1-phospho to 6-phospho-sugars (e.g. between mannose-1-phosphate and mannose-6-phosphate or glucose-1-phosphate and glucose-6-phosphate) via a...; Region: PMM_PGM; cd03089 428406002820 active site 428406002821 substrate binding site [chemical binding]; other site 428406002822 metal binding site [ion binding]; metal-binding site 428406002823 lipopolysaccharide heptosyltransferase I; Region: heptsyl_trn_I; TIGR02193 428406002824 Glycosyltransferase family 9 (heptosyltransferase); Region: Glyco_transf_9; pfam01075 428406002825 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 428406002826 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 428406002827 Heat shock protein [Posttranslational modification, protein turnover, chaperones]; Region: HslJ; COG3187 428406002828 outer membrane channel protein; Reviewed; Region: tolC; PRK09465 428406002829 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 428406002830 active site residue [active] 428406002831 Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: Pcm; COG2518 428406002832 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 428406002833 S-adenosylmethionine binding site [chemical binding]; other site 428406002834 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 428406002835 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 428406002836 Flagellin N-methylase; Region: FliB; cl00497 428406002837 Protein of unknown function (DUF1439); Region: DUF1439; cl06345 428406002838 undecaprenyl pyrophosphate phosphatase; Reviewed; Region: PRK00281 428406002839 Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis. Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing...; Region: OYE_YqiM_FMN; cd02932 428406002840 active site 428406002841 FMN binding site [chemical binding]; other site 428406002842 substrate binding site [chemical binding]; other site 428406002843 homotetramer interface [polypeptide binding]; other site 428406002844 catalytic residue [active] 428406002845 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 428406002846 S-adenosylmethionine binding site [chemical binding]; other site 428406002847 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406002848 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406002849 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 428406002850 dimerization interface [polypeptide binding]; other site 428406002851 substrate binding pocket [chemical binding]; other site 428406002852 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 428406002853 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 428406002854 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 428406002855 protein binding site [polypeptide binding]; other site 428406002856 Peptidase family M48; Region: Peptidase_M48; cl12018 428406002857 Phosphate-starvation-inducible E; Region: PsiE; pfam06146 428406002858 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 428406002859 TrkA-N domain; Region: TrkA_N; pfam02254 428406002860 TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains. Group I TRX is a small ancient protein that alter the redox...; Region: TRX_family; cd02947 428406002861 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 428406002862 catalytic residues [active] 428406002863 Uncharacterized conserved protein [Function unknown]; Region: HdeD; COG3247 428406002864 YfdX protein; Region: YfdX; pfam10938 428406002865 YfdX protein; Region: YfdX; pfam10938 428406002866 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 428406002867 Alpha-crystallin domain (ACD) of alpha-crystallin-type small(s) heat shock proteins (Hsps). sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is the Alpha-crystallin domain (ACD). sHsps are generally...; Region: ACD_sHsps-like; cd06464 428406002868 putative dimer interface [polypeptide binding]; other site 428406002869 FtsH Extracellular; Region: FtsH_ext; pfam06480 428406002870 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 428406002871 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406002872 Walker A motif; other site 428406002873 ATP binding site [chemical binding]; other site 428406002874 Walker B motif; other site 428406002875 arginine finger; other site 428406002876 Peptidase family M41; Region: Peptidase_M41; pfam01434 428406002877 cardiolipin synthetase; Reviewed; Region: cls; PRK01642 428406002878 Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial cardiolipin synthase; Region: PLDc_CLS_unchar2_1; cd09157 428406002879 putative active site [active] 428406002880 catalytic site [active] 428406002881 Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial cardiolipin synthase; Region: PLDc_CLS_unchar2_2; cd09163 428406002882 putative active site [active] 428406002883 catalytic site [active] 428406002884 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 428406002885 Transposase; Region: HTH_Tnp_1; pfam01527 428406002886 putative transposase OrfB; Reviewed; Region: PHA02517 428406002887 HTH-like domain; Region: HTH_21; pfam13276 428406002888 Integrase core domain; Region: rve; pfam00665 428406002889 Integrase core domain; Region: rve_3; pfam13683 428406002890 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 428406002891 Alpha-crystallin domain (ACD) of alpha-crystallin-type small(s) heat shock proteins (Hsps). sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is the Alpha-crystallin domain (ACD). sHsps are generally...; Region: ACD_sHsps-like; cd06464 428406002892 putative dimer interface [polypeptide binding]; other site 428406002893 Helix-turn-helix domain; Region: HTH_17; pfam12728 428406002894 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406002895 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406002896 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like; cd08414 428406002897 dimerization interface [polypeptide binding]; other site 428406002898 substrate binding pocket [chemical binding]; other site 428406002899 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; pfam05930 428406002900 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 428406002901 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 428406002902 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 428406002903 Magnesium ion binding site [ion binding]; other site 428406002904 integrating conjugative element, PFGI_1 class, ParB family protein; Region: ICE_PFGI_1_parB; TIGR03764 428406002905 ParB-like nuclease domain; Region: ParBc; pfam02195 428406002906 Protein of unknown function (DUF2857); Region: DUF2857; pfam11198 428406002907 Domain of unknown function (DUF1845); Region: DUF1845; pfam08900 428406002908 Protein of unknown function (DUF3158); Region: DUF3158; pfam11358 428406002909 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 428406002910 SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date...; Region: SSB_OBF; cd04496 428406002911 dimer interface [polypeptide binding]; other site 428406002912 ssDNA binding site [nucleotide binding]; other site 428406002913 tetramer (dimer of dimers) interface [polypeptide binding]; other site 428406002914 Domain of unknown function (DUF4158); Region: DUF4158; pfam13700 428406002915 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; pfam01526 428406002916 arsenical resistance protein ArsH; Region: resist_ArsH; TIGR02690 428406002917 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 428406002918 Arsenate Reductase (ArsC) family, ArsC subfamily; arsenic reductases similar to that encoded by arsC on the R733 plasmid of Escherichia coli. E. coli ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], the first step in the...; Region: ArsC_ArsC; cd03034 428406002919 ArsC family; Region: ArsC; pfam03960 428406002920 catalytic residues [active] 428406002921 Major Facilitator Superfamily; Region: MFS_1; pfam07690 428406002922 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406002923 putative substrate translocation pore; other site 428406002924 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 428406002925 Sodium Bile acid symporter family; Region: SBF; cl17470 428406002926 arsenical pump-driving ATPase; Region: arsen_driv_ArsA; TIGR04291 428406002927 ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces...; Region: ArsA; cd02035 428406002928 P loop; other site 428406002929 Nucleotide binding site [chemical binding]; other site 428406002930 DTAP/Switch II; other site 428406002931 Switch I; other site 428406002932 ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces...; Region: ArsA; cd02035 428406002933 DTAP/Switch II; other site 428406002934 Switch I; other site 428406002935 Arsenical resistance operon trans-acting repressor ArsD; Region: ArsD; pfam06953 428406002936 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 428406002937 Low molecular weight phosphatase family; Region: LMWPc; cd00115 428406002938 active site 428406002939 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_20; cd07254 428406002940 putative metal binding site [ion binding]; other site 428406002941 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 428406002942 putative DNA binding site [nucleotide binding]; other site 428406002943 putative Zn2+ binding site [ion binding]; other site 428406002944 Protein of unknown function (DUF3085); Region: DUF3085; pfam11284 428406002945 This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. A highly...; Region: PAPS_reductase; cd01713 428406002946 Active Sites [active] 428406002947 Protein of unknown function (DUF3577); Region: DUF3577; pfam12101 428406002948 Protein of unknown function (DUF3275); Region: DUF3275; pfam11679 428406002949 Domain of unknown function (DUF932); Region: DUF932; pfam06067 428406002950 Methyltransferase domain; Region: Methyltransf_26; pfam13659 428406002951 DEAD-like helicases superfamily; Region: DEXDc; smart00487 428406002952 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 428406002953 nucleotide binding region [chemical binding]; other site 428406002954 ATP-binding site [chemical binding]; other site 428406002955 conjugative transfer region protein, TIGR03748 family; Region: conj_PilL 428406002956 integrating conjugative element protein, PFL_4693 family; Region: conj_TIGR03759 428406002957 Protein of unknown function (DUF2859); Region: DUF2859; pfam11072 428406002958 conjugative coupling factor TraD, SXT/TOL subfamily; Region: SXT_TraD; TIGR03743 428406002959 conjugative coupling factor TraD, TOL family; Region: conj_TOL_TraD; TIGR03754 428406002960 integrating conjugative element membrane protein, PFL_4697 family; Region: conj_TIGR03747 428406002961 integrative conjugative element protein, RAQPRD family; Region: ICE_RAQPRD; TIGR01690 428406002962 Plasmid protein of unknown function (Plasmid_RAQPRD); Region: Plasmid_RAQPRD; pfam09686 428406002963 Protein of unknown function (DUF3262); Region: DUF3262; pfam11660 428406002964 integrating conjugative element membrane protein, PFL_4702 family; Region: conj_TIGR03745 428406002965 Protein of unknown function (DUF3487); Region: DUF3487; pfam11990 428406002966 integrating conjugative element protein, PFL_4703 family; Region: conj_TIGR03746 428406002967 Protein of unknown function (DUF3438); Region: DUF3438; pfam11920 428406002968 integrating conjugative element protein, PFL_4705 family; Region: conj_TIGR03752 428406002969 TATA element modulatory factor 1 TATA binding; Region: TMF_TATA_bd; pfam12325 428406002970 conjugative transfer region lipoprotein, TIGR03751 family; Region: conj_TIGR03751 428406002971 conjugative transfer ATPase, PFL_4706 family; Region: traC_PFL_4706; TIGR03744 428406002972 F pilus assembly Type-IV secretion system for plasmid transfer; Region: TraC_F_IV; pfam11130 428406002973 DsbA family; consists of DsbA and DsbA-like proteins, including DsbC, DsbG, glutathione (GSH) S-transferase kappa (GSTK), 2-hydroxychromene-2-carboxylate (HCCA) isomerase, an oxidoreductase (FrnE) presumed to be involved in frenolicin biosynthesis, a...; Region: DsbA_family; cd02972 428406002974 catalytic residues [active] 428406002975 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 428406002976 MPN+ (JAMM) motif; other site 428406002977 Zinc-binding site [ion binding]; other site 428406002978 Protein of unknown function (DUF1525); Region: DUF1525; pfam07511 428406002979 integrating conjugative element protein, PFL_4710 family; Region: conj_TIGR03756 428406002980 integrating conjugative element protein, PFL_4711 family; Region: conj_TIGR03755 428406002981 TraG-like protein, N-terminal region; Region: TraG_N; pfam07916 428406002982 Protein of unknown function (DUF3742); Region: DUF3742; pfam12553 428406002983 Toxin with endonuclease activity YhaV; Region: Toxin_YhaV; pfam11663 428406002984 Antidote-toxin recognition MazE; Region: Antitoxin-MazE; cl00877 428406002985 Regulators of stationary/sporulation gene expression [Transcription]; Region: AbrB; COG2002 428406002986 integrating conjugative element relaxase, PFL_4751 family; Region: ICE_TraI_Pfluor; TIGR03760 428406002987 Putative helicase; Region: TraI_2; pfam07514 428406002988 Protein of unknown function (DUF1528); Region: DUF1528; pfam07515 428406002989 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 428406002990 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 428406002991 non-specific DNA binding site [nucleotide binding]; other site 428406002992 salt bridge; other site 428406002993 sequence-specific DNA binding site [nucleotide binding]; other site 428406002994 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406002995 LysR substrate binding domain; Region: LysR_substrate; pfam03466 428406002996 dimerization interface [polypeptide binding]; other site 428406002997 integrase; Provisional; Region: PRK09692 428406002998 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall...; Region: INT_P4; cd00801 428406002999 active site 428406003000 Int/Topo IB signature motif; other site 428406003001 acetoacetyl-CoA synthetase; Provisional; Region: PRK03584 428406003002 Acetoacetyl-CoA synthetase (acetoacetate-CoA ligase, AACS); Region: AACS; cd05943 428406003003 acyl-activating enzyme (AAE) consensus motif; other site 428406003004 putative AMP binding site [chemical binding]; other site 428406003005 putative active site [active] 428406003006 putative CoA binding site [chemical binding]; other site 428406003007 succinic semialdehyde dehydrogenase; Region: PLN02278 428406003008 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 428406003009 tetramerization interface [polypeptide binding]; other site 428406003010 NAD(P) binding site [chemical binding]; other site 428406003011 catalytic residues [active] 428406003012 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 428406003013 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 428406003014 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 428406003015 N-acetyl-D-glucosamine binding site [chemical binding]; other site 428406003016 catalytic residue [active] 428406003017 aminotransferase; Validated; Region: PRK07337 428406003018 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 428406003019 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406003020 homodimer interface [polypeptide binding]; other site 428406003021 catalytic residue [active] 428406003022 transcription antitermination protein NusB; Reviewed; Region: nusB; PRK00202 428406003023 lumazine synthase (6,7-dimethyl-8-ribityllumazine synthase, LS), catalyzes the penultimate step in the biosynthesis of riboflavin (vitamin B2); type-I; Region: Lumazine_synthase-I; cd09209 428406003024 homopentamer interface [polypeptide binding]; other site 428406003025 active site 428406003026 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein; Provisional; Region: PRK14019 428406003027 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 428406003028 GTP cyclohydrolase II; Region: GTP_cyclohydro2; pfam00925 428406003029 dimerization interface [polypeptide binding]; other site 428406003030 active site 428406003031 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 428406003032 Lumazine binding domain; Region: Lum_binding; pfam00677 428406003033 Lumazine binding domain; Region: Lum_binding; pfam00677 428406003034 bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional; Region: ribD; PRK10786 428406003035 Riboflavin-specific deaminase. Riboflavin biosynthesis protein RibD (Diaminohydroxyphosphoribosylaminopyrimidine deaminase) catalyzes the deamination of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate, which is an intermediate step in the...; Region: Riboflavin_deaminase-reductase; cd01284 428406003036 catalytic motif [active] 428406003037 Zn binding site [ion binding]; other site 428406003038 RibD C-terminal domain; Region: RibD_C; cl17279 428406003039 Tfp pilus assembly protein FimT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimT; COG4970 428406003040 Type II transport protein GspH; Region: GspH; pfam12019 428406003041 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 428406003042 Acylphosphatase; Region: Acylphosphatase; cl00551 428406003043 Tfp pilus assembly protein PilX [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilX; COG4726 428406003044 Type IV pilus assembly protein PilX C-term; Region: PilX; pfam13681 428406003045 Tfp pilus assembly protein PilW [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilW; COG4966 428406003046 Type II transport protein GspH; Region: GspH; pfam12019 428406003047 type IV pilus modification protein PilV; Region: type_IV_pilV; TIGR02523 428406003048 Tfp pilus assembly protein PilW [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilW; COG4966 428406003049 Tfp pilus assembly protein PilX [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilX; COG4726 428406003050 Tfp pilus assembly protein, tip-associated adhesin PilY1 [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilY1; COG3419 428406003051 Neisseria PilC beta-propeller domain; Region: Neisseria_PilC; pfam05567 428406003052 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 428406003053 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 428406003054 Transposase, Mutator family; Region: Transposase_mut; pfam00872 428406003055 MULE transposase domain; Region: MULE; pfam10551 428406003056 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 428406003057 ATP cone domain; Region: ATP-cone; pfam03477 428406003058 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 428406003059 Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of hydroxymethyl...; Region: SHMT; cd00378 428406003060 dimer interface [polypeptide binding]; other site 428406003061 active site 428406003062 glycine-pyridoxal phosphate binding site [chemical binding]; other site 428406003063 folate binding site [chemical binding]; other site 428406003064 malonic semialdehyde reductase; Provisional; Region: PRK10538 428406003065 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 428406003066 NAD(P) binding site [chemical binding]; other site 428406003067 active site 428406003068 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 428406003069 active site 428406003070 TolQ protein; Region: tolQ; TIGR02796 428406003071 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 428406003072 TolR protein; Region: tolR; TIGR02801 428406003073 TolA protein; Region: tolA_full; TIGR02794 428406003074 TolA protein; Region: tolA_full; TIGR02794 428406003075 TonB C terminal; Region: TonB_2; pfam13103 428406003076 translocation protein TolB; Provisional; Region: tolB; PRK02889 428406003077 TolB amino-terminal domain; Region: TolB_N; pfam04052 428406003078 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 428406003079 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 428406003080 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 428406003081 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 428406003082 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 428406003083 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 428406003084 ligand binding site [chemical binding]; other site 428406003085 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 428406003086 ExsB is a transcription regulator related protein. It is a subfamily of a Adenosine nucleotide binding superfamily of proteins. This protein family is represented by a single member in nearly every completed large (> 1000 genes) prokaryotic genome. In...; Region: ExsB; cd01995 428406003087 Ligand Binding Site [chemical binding]; other site 428406003088 Predicted transporter component [General function prediction only]; Region: COG2391 428406003089 Helix-turn-helix domain of transposase family ISL3; Region: HTH_Tnp_ISL3; pfam13542 428406003090 Transposase; Region: DDE_Tnp_ISL3; pfam01610 428406003091 putative transposase OrfB; Reviewed; Region: PHA02517 428406003092 HTH-like domain; Region: HTH_21; pfam13276 428406003093 Integrase core domain; Region: rve; pfam00665 428406003094 Integrase core domain; Region: rve_3; pfam13683 428406003095 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 428406003096 active site 428406003097 metal binding site [ion binding]; metal-binding site 428406003098 Rhomboid family; Region: Rhomboid; cl11446 428406003099 Caspase domain; Region: Peptidase_C14; pfam00656 428406003100 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 428406003101 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 428406003102 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 428406003103 DNA binding residues [nucleotide binding] 428406003104 Xylose isomerase-like TIM barrel; Region: AP_endonuc_2; pfam01261 428406003105 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 428406003106 2-keto-3-deoxygluconate kinase (KdgK) phosphorylates 2-keto-3-deoxygluconate (KDG) to form 2-keto-3-deoxy-6-phosphogluconate (KDGP). KDG is the common intermediate product, that allows organisms to channel D-glucuronate and/or D-galacturinate into the...; Region: KdgK; cd01166 428406003107 substrate binding site [chemical binding]; other site 428406003108 ATP binding site [chemical binding]; other site 428406003109 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406003110 D-galactonate transporter; Region: 2A0114; TIGR00893 428406003111 putative substrate translocation pore; other site 428406003112 bifunctional glyoxylate/hydroxypyruvate reductase B; Provisional; Region: PRK15409 428406003113 D-glycerate dehydrogenase/hydroxypyruvate reductase (GDH); Region: GDH; cd05301 428406003114 dimerization interface [polypeptide binding]; other site 428406003115 ligand binding site [chemical binding]; other site 428406003116 NADP binding site [chemical binding]; other site 428406003117 catalytic site [active] 428406003118 Transcriptional regulators [Transcription]; Region: PurR; COG1609 428406003119 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 428406003120 DNA binding site [nucleotide binding] 428406003121 domain linker motif; other site 428406003122 Ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR; Region: PBP1_RegR_EndR_KdgR_like; cd06283 428406003123 putative ligand binding site [chemical binding]; other site 428406003124 putative dimerization interface [polypeptide binding]; other site 428406003125 Nucleoside 2-deoxyribosyltransferase [Nucleotide transport and metabolism]; Region: COG3613 428406003126 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 428406003127 active site 428406003128 Probable taurine catabolism dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: TauD; COG2175 428406003129 Clavaminic acid synthetase (CAS) -like; CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG oxygenases...; Region: CAS_like; cl00184 428406003130 active site 428406003131 iron coordination sites [ion binding]; other site 428406003132 substrate binding pocket [chemical binding]; other site 428406003133 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cd02883 428406003134 nudix motif; other site 428406003135 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG0390 428406003136 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: COG4619 428406003137 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 428406003138 Walker A/P-loop; other site 428406003139 ATP binding site [chemical binding]; other site 428406003140 Q-loop/lid; other site 428406003141 ABC transporter signature motif; other site 428406003142 Walker B; other site 428406003143 D-loop; other site 428406003144 H-loop/switch region; other site 428406003145 Protein of unknown function (DUF3318); Region: DUF3318; pfam11780 428406003146 Predicted membrane protein [Function unknown]; Region: COG5393 428406003147 Uncharacterized conserved protein [Function unknown]; Region: ElaB; COG4575 428406003148 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 428406003149 Peroxiredoxin (PRX) family, 1-cys PRX subfamily; composed of PRXs containing only one conserved cysteine, which serves as the peroxidatic cysteine. They are homodimeric thiol-specific antioxidant (TSA) proteins that confer a protective role in cells by...; Region: PRX_1cys; cd03016 428406003150 dimer interface [polypeptide binding]; other site 428406003151 decamer (pentamer of dimers) interface [polypeptide binding]; other site 428406003152 catalytic triad [active] 428406003153 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 428406003154 Glutaryl-CoA dehydrogenase; Region: GCD; cd01151 428406003155 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 428406003156 FAD binding site [chemical binding]; other site 428406003157 substrate binding pocket [chemical binding]; other site 428406003158 catalytic base [active] 428406003159 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 428406003160 Transcriptional regulator [Transcription]; Region: IclR; COG1414 428406003161 Bacterial transcriptional regulator; Region: IclR; pfam01614 428406003162 tryptophan 2,3-dioxygenase; Region: trp_2_3_diox; TIGR03036 428406003163 Kynureninase [Amino acid transport and metabolism]; Region: COG3844 428406003164 kynureninase; Region: kynureninase; TIGR01814 428406003165 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 428406003166 catalytic residue [active] 428406003167 arylformamidase; Region: trp_arylform; TIGR03035 428406003168 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 428406003169 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 428406003170 putative DNA binding site [nucleotide binding]; other site 428406003171 putative Zn2+ binding site [ion binding]; other site 428406003172 AsnC family; Region: AsnC_trans_reg; pfam01037 428406003173 Protein of unknown function (DUF3079); Region: DUF3079; pfam11278 428406003174 Flavin reductase like domain; Region: Flavin_Reduct; smart00903 428406003175 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 428406003176 putative DNA binding site [nucleotide binding]; other site 428406003177 putative Zn2+ binding site [ion binding]; other site 428406003178 Relaxase/Mobilisation nuclease domain; Region: Relaxase; pfam03432 428406003179 Bacterial mobilisation protein (MobC); Region: MobC; pfam05713 428406003180 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 428406003181 active site 428406003182 Int/Topo IB signature motif; other site 428406003183 DNA binding site [nucleotide binding] 428406003184 methionine sulfoxide reductase A; Provisional; Region: PRK14054 428406003185 Protein of unknown function DUF72; Region: DUF72; cl00777 428406003186 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 428406003187 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 428406003188 S-adenosylmethionine binding site [chemical binding]; other site 428406003189 pyridoxamine-phosphate oxidase; Region: pdxH; TIGR00558 428406003190 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 428406003191 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 428406003192 Membrane bound FAD containing D-sorbitol dehydrogenase; Region: FAD-SLDH; pfam12318 428406003193 Choline dehydrogenase and related flavoproteins [Amino acid transport and metabolism]; Region: BetA; COG2303 428406003194 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 428406003195 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 428406003196 Cytochrome c; Region: Cytochrom_C; pfam00034 428406003197 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 428406003198 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 428406003199 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 428406003200 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 428406003201 Family of activating enzymes (E1) of ubiquitin-like proteins related to the E.coli hypothetical protein ygdL. The common reaction mechanism catalyzed by E1-like enzymes begins with a nucleophilic attack of the C-terminal carboxylate of the ubiquitin-like...; Region: YgdL_like; cd00755 428406003202 putative ATP binding site [chemical binding]; other site 428406003203 putative substrate interface [chemical binding]; other site 428406003204 TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains. Group I TRX is a small ancient protein that alter the redox...; Region: TRX_family; cd02947 428406003205 catalytic residues [active] 428406003206 Hemerythrin; Region: Hemerythrin; cd12107 428406003207 Fe binding site [ion binding]; other site 428406003208 Predicted protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: COG3531 428406003209 DsbA family, FrnE-like subfamily; composed of uncharacterized proteins containing a CXXC motif with similarity to DsbA and FrnE. FrnE is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the...; Region: DsbA_FrnE_like; cd03025 428406003210 catalytic residues [active] 428406003211 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]; Region: COG3118 428406003212 TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains. Group I TRX is a small ancient protein that alter the redox...; Region: TRX_family; cd02947 428406003213 catalytic residues [active] 428406003214 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 428406003215 binding surface 428406003216 TPR motif; other site 428406003217 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK08314 428406003218 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 428406003219 Putative long-chain fatty acid CoA ligase; Region: LC_FACS_like; cd05935 428406003220 acyl-activating enzyme (AAE) consensus motif; other site 428406003221 putative AMP binding site [chemical binding]; other site 428406003222 putative active site [active] 428406003223 putative CoA binding site [chemical binding]; other site 428406003224 FOG: Ankyrin repeat [General function prediction only]; Region: Arp; COG0666 428406003225 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 428406003226 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 428406003227 Uncharacterized protein involved in cation transport [Inorganic ion transport and metabolism]; Region: ChaC; COG3703 428406003228 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cd06661 428406003229 putative active site pocket [active] 428406003230 dimerization interface [polypeptide binding]; other site 428406003231 putative catalytic residue [active] 428406003232 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 428406003233 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 428406003234 YaeQ protein; Region: YaeQ; pfam07152 428406003235 Predicted membrane protein (DUF2339); Region: DUF2339; pfam10101 428406003236 Protein of unknown function (DUF3999); Region: DUF3999; pfam13163 428406003237 Predicted membrane protein [Function unknown]; Region: COG3686 428406003238 S4 domain; Region: S4_2; cl17325 428406003239 Uncharacterized conserved protein [Function unknown]; Region: COG2353 428406003240 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 428406003241 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 428406003242 active site 428406003243 HIGH motif; other site 428406003244 nucleotide binding site [chemical binding]; other site 428406003245 catalytic core domain of glutaminyl-tRNA synthetase; Region: GlnRS_core; cd00807 428406003246 KMSKS motif; other site 428406003247 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 428406003248 lipase chaperone; Provisional; Region: PRK01294 428406003249 Proteobacterial lipase chaperone protein; Region: Lipase_chap; pfam03280 428406003250 Predicted acetyltransferases and hydrolases with the alpha/beta hydrolase fold [General function prediction only]; Region: LipA; COG1075 428406003251 PGAP1-like protein; Region: PGAP1; pfam07819 428406003252 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3333 428406003253 Tripartite tricarboxylate transporter TctB family; Region: TctB; pfam07331 428406003254 Predicted membrane protein [Function unknown]; Region: COG3556 428406003255 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 428406003256 CoA-transferase family III; Region: CoA_transf_3; pfam02515 428406003257 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 428406003258 Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain. AlaRS is a homodimer. It is responsible for the attachment of alanine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: AlaRS_core; cd00673 428406003259 motif 1; other site 428406003260 active site 428406003261 motif 2; other site 428406003262 motif 3; other site 428406003263 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 428406003264 DHHA1 domain; Region: DHHA1; pfam02272 428406003265 Purine nucleoside permease [Nucleotide transport and metabolism]; Region: NUP; COG5042 428406003266 Purine nucleoside permease [Nucleotide transport and metabolism]; Region: NUP; COG5042 428406003267 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 428406003268 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 428406003269 N-terminal plug; other site 428406003270 ligand-binding site [chemical binding]; other site 428406003271 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 428406003272 Band_7_stomatin_like: A subgroup of the band 7 domain of flotillin (reggie) like proteins similar to stomatin and podicin (two lipid raft-associated integral membrane proteins). Individual proteins of this band 7 domain family may cluster to form...; Region: Band_7_stomatin_like; cd03403 428406003273 Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Region: Clp_protease_NfeD_1; cd07020 428406003274 Membrane-bound serine protease (ClpP class) [Posttranslational modification, protein turnover, chaperones]; Region: NfeD; COG1030 428406003275 active site residues [active] 428406003276 dimer interface [polypeptide binding]; other site 428406003277 NfeD-like C-terminal, partner-binding; Region: NfeD; pfam01957 428406003278 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406003279 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406003280 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 428406003281 dimerization interface [polypeptide binding]; other site 428406003282 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406003283 putative substrate translocation pore; other site 428406003284 aldolase II superfamily protein; Provisional; Region: PRK07044 428406003285 intersubunit interface [polypeptide binding]; other site 428406003286 active site 428406003287 Zn2+ binding site [ion binding]; other site 428406003288 4-oxalocrotonate tautomerase; Provisional; Region: PRK00745 428406003289 active site 1 [active] 428406003290 dimer interface [polypeptide binding]; other site 428406003291 hexamer interface [polypeptide binding]; other site 428406003292 active site 2 [active] 428406003293 Threonine aldolase [Amino acid transport and metabolism]; Region: GLY1; COG2008 428406003294 Low-specificity threonine aldolase (TA). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). TA catalyzes the conversion of L-threonine or L-allo-threonine to glycine and acetaldehyde in a...; Region: TA_like; cd06502 428406003295 tetramer interface [polypeptide binding]; other site 428406003296 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406003297 catalytic residue [active] 428406003298 ADP-ribose pyrophosphatase [Nucleotide transport and metabolism]; Region: COG1051 428406003299 nudix motif; other site 428406003300 SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this...; Region: SirA_YedF_YeeD; cd00291 428406003301 CPxP motif; other site 428406003302 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 428406003303 Predicted extracellular nuclease [General function prediction only]; Region: COG2374 428406003304 YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate...; Region: YhcR_OBF_like; cd04486 428406003305 generic binding surface I; other site 428406003306 generic binding surface II; other site 428406003307 Mycoplasma pulmonis MnuA nuclease-like; Region: MnuA_DNase1-like; cd10283 428406003308 putative active site [active] 428406003309 putative catalytic site [active] 428406003310 putative Mg binding site IVb [ion binding]; other site 428406003311 putative phosphate binding site [ion binding]; other site 428406003312 putative DNA binding site [nucleotide binding]; other site 428406003313 putative Mg binding site IVa [ion binding]; other site 428406003314 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 428406003315 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 428406003316 substrate binding pocket [chemical binding]; other site 428406003317 membrane-bound complex binding site; other site 428406003318 hinge residues; other site 428406003319 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 428406003320 dimer interface [polypeptide binding]; other site 428406003321 phosphorylation site [posttranslational modification] 428406003322 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406003323 ATP binding site [chemical binding]; other site 428406003324 Mg2+ binding site [ion binding]; other site 428406003325 G-X-G motif; other site 428406003326 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406003327 active site 428406003328 phosphorylation site [posttranslational modification] 428406003329 intermolecular recognition site; other site 428406003330 dimerization interface [polypeptide binding]; other site 428406003331 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cd00088 428406003332 putative binding surface; other site 428406003333 active site 428406003334 P pilus assembly protein, pilin FimA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimA; COG3539 428406003335 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 428406003336 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 428406003337 Gram-negative pili assembly chaperone, C-terminal domain; Region: Pili_assembly_C; pfam02753 428406003338 P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimD; COG3188 428406003339 PapC N-terminal domain; Region: PapC_N; pfam13954 428406003340 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 428406003341 PapC C-terminal domain; Region: PapC_C; pfam13953 428406003342 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 428406003343 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 428406003344 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; pfam13005 428406003345 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 428406003346 IS66 C-terminal element; Region: DDE_Tnp_IS66_C; pfam13817 428406003347 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 428406003348 Transposase; Region: HTH_Tnp_1; cl17663 428406003349 P pilus assembly protein, pilin FimA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimA; COG3539 428406003350 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 428406003351 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 428406003352 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 428406003353 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 428406003354 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cl02931 428406003355 phosphoglycolate phosphatase; Provisional; Region: PRK13222 428406003356 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 428406003357 motif II; other site 428406003358 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 428406003359 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 428406003360 S-adenosylmethionine binding site [chemical binding]; other site 428406003361 Glycine zipper 2TM domain; Region: Rick_17kDa_Anti; cl10470 428406003362 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 428406003363 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 428406003364 ligand binding site [chemical binding]; other site 428406003365 DNA gyrase subunit A; Validated; Region: PRK05560 428406003366 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes...; Region: TOP4c; cd00187 428406003367 CAP-like domain; other site 428406003368 active site 428406003369 primary dimer interface [polypeptide binding]; other site 428406003370 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 428406003371 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 428406003372 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 428406003373 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 428406003374 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 428406003375 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 428406003376 Uncharacterized protein conserved in bacteria (DUF2059); Region: DUF2059; pfam09832 428406003377 Phosphoserine aminotransferase (PSAT) family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major group in this CD corresponds to phosphoserine aminotransferase (PSAT). PSAT is active as...; Region: PSAT_like; cd00611 428406003378 homodimer interface [polypeptide binding]; other site 428406003379 substrate-cofactor binding pocket; other site 428406003380 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406003381 catalytic residue [active] 428406003382 Chorismate mutase type II; Region: CM_2; cl00693 428406003383 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 428406003384 Prephenate dehydratase; Region: PDT; pfam00800 428406003385 C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme; Region: ACT_CM-PDT; cd04905 428406003386 putative L-Phe binding site [chemical binding]; other site 428406003387 histidinol-phosphate aminotransferase; Validated; Region: PRK02731 428406003388 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 428406003389 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406003390 homodimer interface [polypeptide binding]; other site 428406003391 catalytic residue [active] 428406003392 Prephenate dehydrogenase [Amino acid transport and metabolism]; Region: TyrA; COG0287 428406003393 prephenate dehydrogenase; Validated; Region: PRK08507 428406003394 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 428406003395 EPSP synthase domain. 3-phosphoshikimate 1-carboxyvinyltransferase (5-enolpyruvylshikimate-3-phosphate synthase) (EC 2.5.1.19) catalyses the reaction between shikimate-3-phosphate (S3P) and phosphoenolpyruvate (PEP) to form...; Region: EPSP_synthase; cd01556 428406003396 hinge; other site 428406003397 active site 428406003398 cytidylate kinase; Provisional; Region: cmk; PRK00023 428406003399 Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor; Region: CMPK; cd02020 428406003400 CMP-binding site; other site 428406003401 The sites determining sugar specificity; other site 428406003402 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 428406003403 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture...; Region: S1_RPS1_repeat_ec1_hs1; cd05687 428406003404 RNA binding site [nucleotide binding]; other site 428406003405 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture...; Region: S1_RPS1_repeat_ec2_hs2; cd04465 428406003406 RNA binding site [nucleotide binding]; other site 428406003407 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec3; cd05688 428406003408 RNA binding site [nucleotide binding]; other site 428406003409 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec4; cd05689 428406003410 RNA binding site [nucleotide binding]; other site 428406003411 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec5; cd05690 428406003412 RNA binding site [nucleotide binding]; other site 428406003413 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec6; cd05691 428406003414 RNA binding site [nucleotide binding]; other site 428406003415 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 428406003416 IHF dimer interface [polypeptide binding]; other site 428406003417 IHF - DNA interface [nucleotide binding]; other site 428406003418 Uncharacterized integral membrane protein [Function unknown]; Region: COG5416 428406003419 tetratricopeptide repeat protein; Provisional; Region: PRK11788 428406003420 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 428406003421 binding surface 428406003422 TPR motif; other site 428406003423 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 428406003424 binding surface 428406003425 TPR motif; other site 428406003426 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 428406003427 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 428406003428 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 428406003429 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 428406003430 RfaE encodes a bifunctional ADP-heptose synthase involved in the biosynthesis of the lipopolysaccharide (LPS) core precursor ADP-L-glycero-D-manno-heptose. LPS plays an important role in maintaining the structural integrity of the bacterial outer...; Region: RfaE_like; cd01172 428406003431 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 428406003432 putative ribose interaction site [chemical binding]; other site 428406003433 putative ADP binding site [chemical binding]; other site 428406003434 ADP-L-glycero-D-mannoheptose 6-epimerase (GME), extended (e) SDRs; Region: ADP_GME_SDR_e; cd05248 428406003435 ADP-L-glycero-D-manno-heptose-6-epimerase; Region: heptose_epim; TIGR02197 428406003436 NADP binding site [chemical binding]; other site 428406003437 homopentamer interface [polypeptide binding]; other site 428406003438 substrate binding site [chemical binding]; other site 428406003439 active site 428406003440 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 428406003441 cysteine synthase B; Region: cysM; TIGR01138 428406003442 CBS_like: This subgroup includes Cystathionine beta-synthase (CBS) and Cysteine synthase. CBS is a unique heme-containing enzyme that catalyzes a pyridoxal 5'-phosphate (PLP)-dependent condensation of serine and homocysteine to give cystathionine; Region: CBS_like; cd01561 428406003443 dimer interface [polypeptide binding]; other site 428406003444 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406003445 catalytic residue [active] 428406003446 Transglycosylase SLT domain; Region: SLT_2; pfam13406 428406003447 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 428406003448 N-acetyl-D-glucosamine binding site [chemical binding]; other site 428406003449 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 428406003450 Histone deacetylases and histone-like deacetylases, classII; Region: HDAC_classII_2; cd11599 428406003451 putative active site [active] 428406003452 Zn binding site [ion binding]; other site 428406003453 DL-methionine transporter ATP-binding subunit; Provisional; Region: metN; PRK11153 428406003454 ATP-binding cassette domain of methionine transporter; Region: ABC_MetN_methionine_transporter; cd03258 428406003455 Walker A/P-loop; other site 428406003456 ATP binding site [chemical binding]; other site 428406003457 Q-loop/lid; other site 428406003458 ABC transporter signature motif; other site 428406003459 Walker B; other site 428406003460 D-loop; other site 428406003461 H-loop/switch region; other site 428406003462 This domain is found at the C-terminus of ABC transporter proteins involved in D-methionine transport as well as a number of ferredoxin-like proteins; Region: NIL; smart00930 428406003463 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406003464 dimer interface [polypeptide binding]; other site 428406003465 conserved gate region; other site 428406003466 ABC-ATPase subunit interface; other site 428406003467 ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]; Region: NlpA; COG1464 428406003468 NLPA lipoprotein; Region: Lipoprotein_9; pfam03180 428406003469 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_beta; cd01714 428406003470 Ligand binding site [chemical binding]; other site 428406003471 Electron transfer flavoprotein domain; Region: ETF; pfam01012 428406003472 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 428406003473 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_alpha; cd01715 428406003474 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 428406003475 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 428406003476 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 428406003477 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 428406003478 active site 428406003479 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 428406003480 D-amino acid dehydrogenase small subunit; Validated; Region: PRK00711 428406003481 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 428406003482 leucine-responsive transcriptional regulator; Provisional; Region: PRK11169 428406003483 Winged helix-turn-helix DNA-binding; Region: HTH_24; pfam13412 428406003484 AsnC family; Region: AsnC_trans_reg; pfam01037 428406003485 Phosphodiesterase/alkaline phosphatase D [Inorganic ion transport and metabolism]; Region: PhoD; COG3540 428406003486 Bacillus subtilis PhoD and related proteins, metallophosphatase domain; Region: MPP_PhoD; cd07389 428406003487 putative active site [active] 428406003488 putative metal binding site [ion binding]; other site 428406003489 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 428406003490 DNA repair photolyase [DNA replication, recombination, and repair]; Region: SplB; COG1533 428406003491 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 428406003492 FeS/SAM binding site; other site 428406003493 Predicted membrane protein [Function unknown]; Region: XynA; COG2314 428406003494 Glucose / Sorbosone dehydrogenase; Region: GSDH; pfam07995 428406003495 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 428406003496 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 428406003497 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 428406003498 RimM N-terminal domain; Region: RimM; pfam01782 428406003499 PRC-barrel domain; Region: PRC; pfam05239 428406003500 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 428406003501 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 428406003502 Coenzyme A pyrophosphatase (CoAse), a member of the Nudix hydrolase superfamily, functions to catalyze the elimination of oxidized inactive CoA, which can inhibit CoA-utilizing enzymes. The need of CoAses mainly arises under conditions of oxidative...; Region: CoAse; cd03426 428406003503 putative active site [active] 428406003504 putative CoA binding site [chemical binding]; other site 428406003505 nudix motif; other site 428406003506 metal binding site [ion binding]; metal-binding site 428406003507 CobD/CbiB family protein; Provisional; Region: PRK07630 428406003508 Domain of unknown function (DUF2007); Region: DUF2007; pfam09413 428406003509 GTPase RsgA; Reviewed; Region: PRK00098 428406003510 S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of...; Region: S1_YloQ_GTPase; cd04466 428406003511 RNA binding site [nucleotide binding]; other site 428406003512 homodimer interface [polypeptide binding]; other site 428406003513 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 428406003514 GTPase/Zn-binding domain interface [polypeptide binding]; other site 428406003515 GTP/Mg2+ binding site [chemical binding]; other site 428406003516 G4 box; other site 428406003517 G5 box; other site 428406003518 G1 box; other site 428406003519 Switch I region; other site 428406003520 G2 box; other site 428406003521 G3 box; other site 428406003522 Switch II region; other site 428406003523 Peptidase family M48; Region: Peptidase_M48; cl12018 428406003524 Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]; Region: HtpX; COG0501 428406003525 DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Region: Orn; cd06135 428406003526 catalytic site [active] 428406003527 putative active site [active] 428406003528 putative substrate binding site [chemical binding]; other site 428406003529 dimer interface [polypeptide binding]; other site 428406003530 MogA_MoaB family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF) an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea; Region: MogA_MoaB; cd00886 428406003531 MPT binding site; other site 428406003532 trimer interface [polypeptide binding]; other site 428406003533 hypothetical protein; Provisional; Region: PRK05255 428406003534 peptidase PmbA; Provisional; Region: PRK11040 428406003535 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 428406003536 Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5; Region: DHFR; cd00209 428406003537 folate binding site [chemical binding]; other site 428406003538 NADP+ binding site [chemical binding]; other site 428406003539 thymidylate synthase; Reviewed; Region: thyA; PRK01827 428406003540 Thymidylate synthase and pyrimidine hydroxymethylase: Thymidylate synthase (TS) and deoxycytidylate hydroxymethylase (dCMP-HMase) are homologs that catalyze analogous alkylation of C5 of pyrimidine nucleotides. Both enzymes are involved in the...; Region: TS_Pyrimidine_HMase; cd00351 428406003541 dimerization interface [polypeptide binding]; other site 428406003542 active site 428406003543 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 428406003544 Threonine dehydratase: The first step in amino acid degradation is the removal of nitrogen. Although the nitrogen atoms of most amino acids are transferred to alpha-ketoglutarate before removal, the alpha-amino group of threonine can be directly...; Region: Thr-dehyd; cd01562 428406003545 tetramer interface [polypeptide binding]; other site 428406003546 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406003547 catalytic residue [active] 428406003548 integral membrane protein, YjbE family; Region: R_switched_YjbE; TIGR03717 428406003549 dimethylhistidine N-methyltransferase; Region: egtD_ergothio; TIGR03438 428406003550 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 428406003551 Uncharacterized conserved protein (DUF2260); Region: DUF2260; pfam10017 428406003552 ergothioneine biosynthesis protein EgtB; Region: egtB_TIGR03440 428406003553 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 428406003554 helicase 45; Provisional; Region: PTZ00424 428406003555 DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif; Region: DEADc; cd00268 428406003556 ATP binding site [chemical binding]; other site 428406003557 Mg++ binding site [ion binding]; other site 428406003558 motif III; other site 428406003559 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 428406003560 nucleotide binding region [chemical binding]; other site 428406003561 ATP-binding site [chemical binding]; other site 428406003562 glutamate and aspartate transporter subunit; Provisional; Region: PRK10797 428406003563 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 428406003564 substrate binding pocket [chemical binding]; other site 428406003565 membrane-bound complex binding site; other site 428406003566 hinge residues; other site 428406003567 ABC transporter ATPase component; Reviewed; Region: PRK11147 428406003568 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 428406003569 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 428406003570 ABC transporter; Region: ABC_tran_2; pfam12848 428406003571 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 428406003572 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 428406003573 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406003574 ATP binding site [chemical binding]; other site 428406003575 Mg2+ binding site [ion binding]; other site 428406003576 G-X-G motif; other site 428406003577 TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIA family of DNA topoisomerases similar to the B subunits of E. coli DNA gyrase and E. coli Topoisomerase IV which are; Region: TopoII_Trans_DNA_gyrase; cd00822 428406003578 anchoring element; other site 428406003579 dimer interface [polypeptide binding]; other site 428406003580 ATP binding site [chemical binding]; other site 428406003581 Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from...; Region: TOPRIM; cl00718 428406003582 active site 428406003583 metal binding site [ion binding]; metal-binding site 428406003584 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 428406003585 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 428406003586 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 428406003587 N-acetyl-D-glucosamine binding site [chemical binding]; other site 428406003588 catalytic residue [active] 428406003589 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 428406003590 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes...; Region: TOP4c; cd00187 428406003591 CAP-like domain; other site 428406003592 active site 428406003593 primary dimer interface [polypeptide binding]; other site 428406003594 Chromate transporter; Region: Chromate_transp; pfam02417 428406003595 Chromate transporter; Region: Chromate_transp; pfam02417 428406003596 putative proline-specific permease; Provisional; Region: proY; PRK10580 428406003597 citrate-proton symporter; Provisional; Region: PRK15075 428406003598 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406003599 putative substrate translocation pore; other site 428406003600 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 428406003601 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 428406003602 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 428406003603 Walker A/P-loop; other site 428406003604 ATP binding site [chemical binding]; other site 428406003605 Q-loop/lid; other site 428406003606 ABC transporter signature motif; other site 428406003607 Walker B; other site 428406003608 D-loop; other site 428406003609 H-loop/switch region; other site 428406003610 L-lactate permease; Region: Lactate_perm; cl00701 428406003611 L-lactate permease [Energy production and conversion]; Region: LldP; COG1620 428406003612 periplasmic multidrug efflux lipoprotein precursor; Reviewed; Region: PRK09578 428406003613 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 428406003614 HlyD family secretion protein; Region: HlyD_3; pfam13437 428406003615 multidrug efflux protein; Reviewed; Region: PRK09577 428406003616 Protein export membrane protein; Region: SecD_SecF; cl14618 428406003617 Esterase/lipase [General function prediction only]; Region: COG1647 428406003618 MASE1; Region: MASE1; cl17823 428406003619 PAS fold; Region: PAS_3; pfam08447 428406003620 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 428406003621 GST_N family, unknown subfamily 2; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of...; Region: GST_N_2; cd03047 428406003622 putative C-terminal domain interface [polypeptide binding]; other site 428406003623 putative GSH binding site (G-site) [chemical binding]; other site 428406003624 putative dimer interface [polypeptide binding]; other site 428406003625 C-terminal, alpha helical domain of an unknown subfamily 2 of Glutathione S-transferases; Region: GST_C_2; cd03180 428406003626 putative N-terminal domain interface [polypeptide binding]; other site 428406003627 putative dimer interface [polypeptide binding]; other site 428406003628 putative substrate binding pocket (H-site) [chemical binding]; other site 428406003629 Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]; Region: COG0436 428406003630 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 428406003631 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406003632 homodimer interface [polypeptide binding]; other site 428406003633 catalytic residue [active] 428406003634 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence...; Region: YjgF_YER057c_UK114_like_1; cd02199 428406003635 homotrimer interaction site [polypeptide binding]; other site 428406003636 putative active site [active] 428406003637 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 428406003638 EamA-like transporter family; Region: EamA; pfam00892 428406003639 Predicted metal-dependent hydrolases related to alanyl-tRNA synthetase HxxxH domain [General function prediction only]; Region: COG2872 428406003640 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 428406003641 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 428406003642 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 428406003643 DNA-binding site [nucleotide binding]; DNA binding site 428406003644 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 428406003645 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406003646 homodimer interface [polypeptide binding]; other site 428406003647 catalytic residue [active] 428406003648 heat shock protein 90; Provisional; Region: PRK05218 428406003649 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406003650 ATP binding site [chemical binding]; other site 428406003651 Mg2+ binding site [ion binding]; other site 428406003652 G-X-G motif; other site 428406003653 MUG-like Uracil-DNA glycosylase enzyme family; Region: UDG_MUG_like; cd10032 428406003654 putative active site [active] 428406003655 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 428406003656 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3812 428406003657 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]; Region: COG4700 428406003658 Phospholipase_D-nuclease N-terminal; Region: PLDc_N; pfam13396 428406003659 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 428406003660 S-adenosylmethionine binding site [chemical binding]; other site 428406003661 SnoaL-like domain; Region: SnoaL_2; pfam12680 428406003662 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3825 428406003663 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 428406003664 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 428406003665 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406003666 Walker A motif; other site 428406003667 ATP binding site [chemical binding]; other site 428406003668 Walker B motif; other site 428406003669 arginine finger; other site 428406003670 Cytochrome c; Region: Cytochrom_C; cl11414 428406003671 Cytochrome c; Region: Cytochrom_C; cl11414 428406003672 Domain of unknown function (DUF1841); Region: DUF1841; pfam08897 428406003673 EamA-like transporter family; Region: EamA; pfam00892 428406003674 EamA-like transporter family; Region: EamA; pfam00892 428406003675 Carboxypeptidase C (cathepsin A) [Amino acid transport and metabolism]; Region: COG2939 428406003676 Serine carboxypeptidase; Region: Peptidase_S10; cl08270 428406003677 Nitroreductase-like family 5. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and...; Region: Nitroreductase_5; cd02148 428406003678 putative FMN binding site [chemical binding]; other site 428406003679 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 428406003680 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 428406003681 minor groove reading motif; other site 428406003682 helix-hairpin-helix signature motif; other site 428406003683 substrate binding pocket [chemical binding]; other site 428406003684 active site 428406003685 ferredoxin; Provisional; Region: PRK06991 428406003686 Putative Fe-S cluster; Region: FeS; pfam04060 428406003687 4Fe-4S binding domain; Region: Fer4; pfam00037 428406003688 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 428406003689 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 428406003690 Poly-beta-hydroxyalkanoate depolymerase [Lipid metabolism]; Region: DepA; COG4553 428406003691 PHB de-polymerase C-terminus; Region: PHB_depo_C; pfam06850 428406003692 aromatic amino acid aminotransferase; Provisional; Region: PRK09257 428406003693 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 428406003694 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406003695 homodimer interface [polypeptide binding]; other site 428406003696 catalytic residue [active] 428406003697 excinuclease ABC subunit B; Provisional; Region: PRK05298 428406003698 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 428406003699 ATP binding site [chemical binding]; other site 428406003700 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 428406003701 nucleotide binding region [chemical binding]; other site 428406003702 ATP-binding site [chemical binding]; other site 428406003703 Ultra-violet resistance protein B; Region: UvrB; pfam12344 428406003704 UvrB/uvrC motif; Region: UVR; pfam02151 428406003705 Site-specific recombinase; Region: SpecificRecomb; cl15411 428406003706 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 428406003707 Ribokinase catalyses the phosphorylation of ribose to ribose-5-phosphate using ATP. This reaction is the first step in the ribose metabolism. It traps ribose within the cell after uptake and also prepares the sugar for use in the synthesis of nucleotides...; Region: ribokinase; cd01174 428406003708 substrate binding site [chemical binding]; other site 428406003709 dimer interface [polypeptide binding]; other site 428406003710 ATP binding site [chemical binding]; other site 428406003711 Transcriptional regulators [Transcription]; Region: PurR; COG1609 428406003712 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 428406003713 DNA binding site [nucleotide binding] 428406003714 domain linker motif; other site 428406003715 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 428406003716 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 428406003717 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 428406003718 TM-ABC transporter signature motif; other site 428406003719 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 428406003720 First domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_I; cd03216 428406003721 Walker A/P-loop; other site 428406003722 ATP binding site [chemical binding]; other site 428406003723 Q-loop/lid; other site 428406003724 ABC transporter signature motif; other site 428406003725 Walker B; other site 428406003726 D-loop; other site 428406003727 H-loop/switch region; other site 428406003728 Second domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_II; cd03215 428406003729 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: RbsB; COG1879 428406003730 Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily; Region: PBP1_ABC_sugar_binding_like; cd01536 428406003731 ligand binding site [chemical binding]; other site 428406003732 Predicted transcriptional regulator [Transcription]; Region: COG1959 428406003733 iron-sulfur cluster assembly transcription factor IscR; Region: IscR; TIGR02010 428406003734 cysteine desulfurase; Provisional; Region: PRK14012 428406003735 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 428406003736 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 428406003737 catalytic residue [active] 428406003738 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 428406003739 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 428406003740 trimerization site [polypeptide binding]; other site 428406003741 active site 428406003742 Fe-S cluster assembly scaffold protein [Posttranslational modification, protein turnover, chaperones]; Region: sufA; COG0316 428406003743 Protein of unknown function (DUF3565); Region: DUF3565; pfam12088 428406003744 co-chaperone HscB; Provisional; Region: hscB; PRK03578 428406003745 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s; Region: DnaJ; cd06257 428406003746 HSP70 interaction site [polypeptide binding]; other site 428406003747 HSCB C-terminal oligomerisation domain; Region: HSCB_C; pfam07743 428406003748 chaperone protein HscA; Provisional; Region: hscA; PRK05183 428406003749 Nucleotide-binding domain of HscA and similar proteins; Region: HscA_like_NBD; cd10236 428406003750 nucleotide binding site [chemical binding]; other site 428406003751 putative NEF/HSP70 interaction site [polypeptide binding]; other site 428406003752 SBD interface [polypeptide binding]; other site 428406003753 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 428406003754 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 428406003755 catalytic loop [active] 428406003756 iron binding site [ion binding]; other site 428406003757 FeS assembly protein IscX; Region: iscX_yfhJ; TIGR03412 428406003758 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 428406003759 LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop; Region: LysRS_N; cd04322 428406003760 dimer interface [polypeptide binding]; other site 428406003761 putative anticodon binding site; other site 428406003762 Lys_tRNA synthetase (LysRS) class II core domain. Class II LysRS is a dimer which attaches a lysine to the 3' OH group of ribose of the appropriate tRNA. Its assignment to class II aaRS is based upon its structure and the presence of three...; Region: LysRS_core; cd00775 428406003763 motif 1; other site 428406003764 active site 428406003765 motif 2; other site 428406003766 motif 3; other site 428406003767 short chain dehydrogenase; Provisional; Region: PRK07023 428406003768 sepiapterin reductase (SPR)-like, classical (c) SDRs; Region: SPR-like_SDR_c; cd05367 428406003769 NADP binding site [chemical binding]; other site 428406003770 homodimer interface [polypeptide binding]; other site 428406003771 active site 428406003772 peptide chain release factor 2; Validated; Region: prfB; PRK00578 428406003773 This domain is found in peptide chain release factors; Region: PCRF; smart00937 428406003774 RF-1 domain; Region: RF-1; pfam00472 428406003775 nicotinate phosphoribosyltransferase; Region: NAPRTase; TIGR01514 428406003776 Nicotinate phosphoribosyltransferase (NAPRTase), related to PncB. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting; Region: PncB_like; cd01401 428406003777 active site 428406003778 Uncharacterized conserved protein [Function unknown]; Region: COG1556 428406003779 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 428406003780 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl17221 428406003781 transmembrane helices; other site 428406003782 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 428406003783 D-glycerate dehydrogenase/hydroxypyruvate reductase (GDH); Region: GDH; cd05301 428406003784 dimerization interface [polypeptide binding]; other site 428406003785 ligand binding site [chemical binding]; other site 428406003786 NADP binding site [chemical binding]; other site 428406003787 catalytic site [active] 428406003788 Predicted nuclease of restriction endonuclease-like fold, RmuC family [General function prediction only]; Region: COG1322 428406003789 RmuC family; Region: RmuC; pfam02646 428406003790 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 428406003791 MoeA family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF), an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoeA; cd00887 428406003792 dimer interface [polypeptide binding]; other site 428406003793 putative functional site; other site 428406003794 putative MPT binding site; other site 428406003795 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 428406003796 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 428406003797 GTP binding site; other site 428406003798 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 428406003799 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 428406003800 FeS/SAM binding site; other site 428406003801 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 428406003802 Ribonucleases G and E [Translation, ribosomal structure and biogenesis]; Region: CafA; COG1530 428406003803 S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and...; Region: S1_RNase_E; cd04453 428406003804 homodimer interface [polypeptide binding]; other site 428406003805 oligonucleotide binding site [chemical binding]; other site 428406003806 23S rRNA pseudouridylate synthase C; Provisional; Region: PRK11025 428406003807 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cd00165 428406003808 RNA binding surface [nucleotide binding]; other site 428406003809 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 428406003810 active site 428406003811 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 428406003812 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 428406003813 motif II; other site 428406003814 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes; Region: Rieske; cd03467 428406003815 iron-sulfur cluster [ion binding]; other site 428406003816 [2Fe-2S] cluster binding site [ion binding]; other site 428406003817 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 428406003818 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 428406003819 tandem repeat interface [polypeptide binding]; other site 428406003820 oligomer interface [polypeptide binding]; other site 428406003821 active site residues [active] 428406003822 Uncharacterized subfamily of the tetrapyrrole methylase family similar to ribosomal RNA small subunit methyltransferase I (RsmI); Region: RsmI_like; cd11649 428406003823 putative SAM binding site [chemical binding]; other site 428406003824 homodimer interface [polypeptide binding]; other site 428406003825 Maf-like protein; Region: Maf; pfam02545 428406003826 Nucleotide binding protein Maf. Maf has been implicated in inhibition of septum formation in eukaryotes, bacteria and archaea, but homologs in B.subtilis and S.cerevisiae are nonessential for cell division. Maf has been predicted to be a nucleotide- or...; Region: Maf; cd00555 428406003827 active site 428406003828 dimer interface [polypeptide binding]; other site 428406003829 Uncharacterized ACR, COG1399; Region: DUF177; cl00616 428406003830 50S ribosomal protein L32; Validated; Region: rpmF; PRK01110 428406003831 putative phosphate acyltransferase; Provisional; Region: PRK05331 428406003832 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 428406003833 Ketoacyl-acyl carrier protein synthase III (KASIII) initiates the elongation in type II fatty acid synthase systems. It is found in bacteria and plants. Elongation of fatty acids in the type II systems occurs by Claisen condensation of malonyl-acyl...; Region: KAS_III; cd00830 428406003834 dimer interface [polypeptide binding]; other site 428406003835 active site 428406003836 CoA binding pocket [chemical binding]; other site 428406003837 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 428406003838 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 428406003839 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 428406003840 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 428406003841 NAD(P) binding site [chemical binding]; other site 428406003842 homotetramer interface [polypeptide binding]; other site 428406003843 homodimer interface [polypeptide binding]; other site 428406003844 active site 428406003845 acyl carrier protein; Provisional; Region: acpP; PRK00982 428406003846 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 428406003847 Beta-ketoacyl-acyl carrier protein (ACP) synthase (KAS), type I and II. KASs are responsible for the elongation steps in fatty acid biosynthesis. KASIII catalyses the initial condensation and KAS I and II catalyze further elongation steps by Claisen...; Region: KAS_I_II; cd00834 428406003848 dimer interface [polypeptide binding]; other site 428406003849 active site 428406003850 RNA polymerase sigma factor RpoE; Region: RpoE_Sigma70; TIGR02939 428406003851 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 428406003852 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 428406003853 DNA binding residues [nucleotide binding] 428406003854 Negative regulator of sigma E activity [Signal transduction mechanisms]; Region: RseA; COG3073 428406003855 Anti sigma-E protein RseA, N-terminal domain; Region: RseA_N; pfam03872 428406003856 Negative regulator of sigma E activity [Signal transduction mechanisms]; Region: RseB; COG3026 428406003857 anti-sigma E factor; Provisional; Region: rseB; PRK09455 428406003858 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 428406003859 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 428406003860 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 428406003861 protein binding site [polypeptide binding]; other site 428406003862 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 428406003863 protein binding site [polypeptide binding]; other site 428406003864 Glutaredoxin-like domain (DUF836); Region: DUF836; pfam05768 428406003865 GTP-binding protein LepA; Provisional; Region: PRK05433 428406003866 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 428406003867 G1 box; other site 428406003868 putative GEF interaction site [polypeptide binding]; other site 428406003869 GTP/Mg2+ binding site [chemical binding]; other site 428406003870 Switch I region; other site 428406003871 G2 box; other site 428406003872 G3 box; other site 428406003873 Switch II region; other site 428406003874 G4 box; other site 428406003875 G5 box; other site 428406003876 lepA_II: This subfamily represents the domain II of LepA, a GTP-binding protein localized in the cytoplasmic membrane. The N-terminal domain of LepA shares regions of homology to translation factors. In terms of interaction with the ribosome, EF-G, EF-Tu...; Region: lepA_II; cd03699 428406003877 lepA_C: This family represents the C-terminal region of LepA, a GTP-binding protein localized in the cytoplasmic membrane. LepA is ubiquitous in Bacteria and Eukaryota (e.g. Saccharomyces cerevisiae GUF1p), but is missing from Archaea. LepA exhibits...; Region: lepA_C; cd03709 428406003878 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 428406003879 signal peptidase I; Provisional; Region: PRK10861 428406003880 The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are...; Region: S26_SPase_I; cd06530 428406003881 Catalytic site [active] 428406003882 The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are...; Region: S26_SPase_I; cd06530 428406003883 ribonuclease III; Reviewed; Region: rnc; PRK00102 428406003884 RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in...; Region: RIBOc; cd00593 428406003885 dimerization interface [polypeptide binding]; other site 428406003886 active site 428406003887 metal binding site [ion binding]; metal-binding site 428406003888 Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III; Region: DSRM; cd00048 428406003889 dsRNA binding site [nucleotide binding]; other site 428406003890 GTPase Era; Reviewed; Region: era; PRK00089 428406003891 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 428406003892 G1 box; other site 428406003893 GTP/Mg2+ binding site [chemical binding]; other site 428406003894 Switch I region; other site 428406003895 G2 box; other site 428406003896 Switch II region; other site 428406003897 G3 box; other site 428406003898 G4 box; other site 428406003899 G5 box; other site 428406003900 KH domain; Region: KH_2; pfam07650 428406003901 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 428406003902 Recombination protein O N terminal; Region: RecO_N; pfam11967 428406003903 Recombination protein O C terminal; Region: RecO_C; pfam02565 428406003904 Pyridoxine 5'-phosphate (PNP) synthase domain; pyridoxal 5'-phosphate is the active form of vitamin B6 that acts as an essential, ubiquitous coenzyme in amino acid metabolism. In bacteria, formation of pyridoxine 5'-phosphate is a step in...; Region: PNPsynthase; cd00003 428406003905 active site 428406003906 hydrophilic channel; other site 428406003907 dimerization interface [polypeptide binding]; other site 428406003908 catalytic residues [active] 428406003909 active site lid [active] 428406003910 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 428406003911 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 428406003912 beta-hexosaminidase; Provisional; Region: PRK05337 428406003913 elongation factor P; Validated; Region: PRK00529 428406003914 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 428406003915 S1_EF-P_repeat_1: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with...; Region: S1_EF-P_repeat_1; cd04470 428406003916 RNA binding site [nucleotide binding]; other site 428406003917 S1_EF-P_repeat_2: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with...; Region: S1_EF-P_repeat_2; cd05794 428406003918 RNA binding site [nucleotide binding]; other site 428406003919 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4394 428406003920 Uncharacterized protein conserved in bacteria (DUF2331); Region: DUF2331; pfam10093 428406003921 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 428406003922 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 428406003923 GIY-YIG motif/motif A; other site 428406003924 active site 428406003925 catalytic site [active] 428406003926 putative DNA binding site [nucleotide binding]; other site 428406003927 metal binding site [ion binding]; metal-binding site 428406003928 UvrB/uvrC motif; Region: UVR; pfam02151 428406003929 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 428406003930 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 428406003931 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 428406003932 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406003933 active site 428406003934 phosphorylation site [posttranslational modification] 428406003935 intermolecular recognition site; other site 428406003936 dimerization interface [polypeptide binding]; other site 428406003937 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 428406003938 DNA binding site [nucleotide binding] 428406003939 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4254 428406003940 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 428406003941 FecR protein; Region: FecR; pfam04773 428406003942 Predicted transmembrane sensor domain [Signal transduction mechanisms]; Region: COG4252 428406003943 CHASE2 domain; Region: CHASE2; pfam05226 428406003944 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 428406003945 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 428406003946 dimer interface [polypeptide binding]; other site 428406003947 phosphorylation site [posttranslational modification] 428406003948 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406003949 ATP binding site [chemical binding]; other site 428406003950 G-X-G motif; other site 428406003951 Per1-like; Region: Per1; cl02172 428406003952 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 428406003953 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 428406003954 DNA binding site [nucleotide binding] 428406003955 Transglycosylase associated protein; Region: Transgly_assoc; cl00978 428406003956 Transcriptional regulators [Transcription]; Region: FadR; COG2186 428406003957 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 428406003958 DNA-binding site [nucleotide binding]; DNA binding site 428406003959 FCD domain; Region: FCD; pfam07729 428406003960 glucarate dehydratase; Region: glucar-dehydr; TIGR03247 428406003961 D-Glucarate dehydratase (GlucD) catalyzes the dehydration of both D-glucarate and L-idarate to form 5-keto-4-deoxy-D-glucarate (5-KDG) , the initial reaction of the catabolic pathway for (D)-glucarate. GlucD belongs to the enolase superfamily of enzymes; Region: D-glucarate_dehydratase; cd03323 428406003962 active site 428406003963 tetramer interface [polypeptide binding]; other site 428406003964 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406003965 D-galactonate transporter; Region: 2A0114; TIGR00893 428406003966 putative substrate translocation pore; other site 428406003967 Alpha-glucosidases, family 31 of glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: COG1501 428406003968 Galactose mutarotase-like; Region: Gal_mutarotas_2; pfam13802 428406003969 Glycosyl hydrolase family 31 (GH31) domain of a bacterial protein family represented by Escherichia coli protein Aec37. The gene encoding Aec37 (aec-37) is located within a genomic island (AGI-3) isolated from the extraintestinal avian pathogenic...; Region: GH31_glycosidase_Aec37; cd06599 428406003970 putative active site [active] 428406003971 putative catalytic site [active] 428406003972 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 428406003973 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 428406003974 trimer interface [polypeptide binding]; other site 428406003975 eyelet of channel; other site 428406003976 aldose 1-epimerase, similar to Escherichia coli YphB; Region: Aldose_epim_Ec_YphB; cd09021 428406003977 active site 428406003978 catalytic residues [active] 428406003979 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 428406003980 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 428406003981 active site 428406003982 DNA binding site [nucleotide binding] 428406003983 Int/Topo IB signature motif; other site 428406003984 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 428406003985 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 428406003986 non-specific DNA binding site [nucleotide binding]; other site 428406003987 salt bridge; other site 428406003988 sequence-specific DNA binding site [nucleotide binding]; other site 428406003989 Tubulin/FtsZ: Family includes tubulin alpha-, beta-, gamma-, delta-, and epsilon-tubulins as well as FtsZ, all of which are involved in polymer formation. Tubulin is the major component of microtubules, but also exists as a heterodimer and as a curved...; Region: Tubulin_FtsZ; cl10017 428406003990 Protein of unknown function (DUF4064); Region: DUF4064; pfam13273 428406003991 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 428406003992 HTH-like domain; Region: HTH_21; pfam13276 428406003993 Integrase core domain; Region: rve; pfam00665 428406003994 Integrase core domain; Region: rve_3; pfam13683 428406003995 Bacterial protein of unknown function (DUF924); Region: DUF924; cl01561 428406003996 ALDH subfamily: Coniferyl aldehyde dehydrogenase, ALDH families 3, 13, and 14, and other related proteins; Region: ALDH_F3-13-14_CALDH-like; cd07087 428406003997 NAD-dependent aldehyde dehydrogenases [Energy production and conversion]; Region: PutA; COG1012 428406003998 NAD(P) binding site [chemical binding]; other site 428406003999 catalytic residues [active] 428406004000 short chain dehydrogenase; Provisional; Region: PRK12744 428406004001 tetrahydroxynaphthalene/trihydroxynaphthalene reductase-like, classical (c) SDRs; Region: THN_reductase-like_SDR_c; cd05362 428406004002 NADP binding site [chemical binding]; other site 428406004003 homodimer interface [polypeptide binding]; other site 428406004004 active site 428406004005 substrate binding site [chemical binding]; other site 428406004006 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406004007 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406004008 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_3; cd08472 428406004009 putative effector binding pocket; other site 428406004010 putative dimerization interface [polypeptide binding]; other site 428406004011 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 428406004012 Transposase; Region: DEDD_Tnp_IS110; pfam01548 428406004013 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 428406004014 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 428406004015 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406004016 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 428406004017 dimerization interface [polypeptide binding]; other site 428406004018 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 428406004019 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 428406004020 Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins; Region: PBP1_STKc_like; cd06326 428406004021 putative ligand binding site [chemical binding]; other site 428406004022 transposase/IS protein; Provisional; Region: PRK09183 428406004023 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406004024 Walker A motif; other site 428406004025 ATP binding site [chemical binding]; other site 428406004026 Walker B motif; other site 428406004027 arginine finger; other site 428406004028 Winged helix-turn-helix DNA-binding; Region: HTH_24; pfam13412 428406004029 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG4584 428406004030 Integrase core domain; Region: rve; pfam00665 428406004031 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 428406004032 Part of AAA domain; Region: AAA_19; pfam13245 428406004033 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 428406004034 Family description; Region: UvrD_C_2; pfam13538 428406004035 Helix-turn-helix domain; Region: HTH_17; pfam12728 428406004036 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 428406004037 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406004038 C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold; Region: PBP2_CysL_like; cd08420 428406004039 putative dimerization interface [polypeptide binding]; other site 428406004040 Predicted membrane protein [Function unknown]; Region: COG2855 428406004041 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4312 428406004042 Ferredoxin [Energy production and conversion]; Region: COG1146 428406004043 4Fe-4S binding domain; Region: Fer4; cl02805 428406004044 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 428406004045 ssDNA exonuclease RecJ; Provisional; Region: PRK11070 428406004046 DHH family; Region: DHH; pfam01368 428406004047 DHHA1 domain; Region: DHHA1; pfam02272 428406004048 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4255 428406004049 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 428406004050 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 428406004051 FtsX-like permease family; Region: FtsX; pfam02687 428406004052 lipoprotein releasing system, ATP-binding protein; Region: LolD_lipo_ex; TIGR02211 428406004053 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 428406004054 Walker A/P-loop; other site 428406004055 ATP binding site [chemical binding]; other site 428406004056 Q-loop/lid; other site 428406004057 ABC transporter signature motif; other site 428406004058 Walker B; other site 428406004059 D-loop; other site 428406004060 H-loop/switch region; other site 428406004061 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 428406004062 active site 428406004063 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 428406004064 DNA internalization-related competence protein ComEC/Rec2; Region: ComEC_Rec2; TIGR00361 428406004065 Competence protein; Region: Competence; pfam03772 428406004066 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 428406004067 Uncharacterized conserved protein [Function unknown]; Region: COG2308 428406004068 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2307 428406004069 A predicted alpha-helical domain with a conserved ER motif; Region: Alpha-E; pfam04168 428406004070 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 428406004071 Bacterial transglutaminase-like N-terminal region; Region: Bact_transglu_N; pfam08379 428406004072 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 428406004073 Predicted proteasome-type protease [Posttranslational modification, protein turnover, chaperones]; Region: COG3484 428406004074 Bacterial proteasome, beta subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that...; Region: proteasome_beta_bacterial; cd03765 428406004075 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 428406004076 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 428406004077 CTP synthetase; Validated; Region: pyrG; PRK05380 428406004078 CTP synthetase (CTPs) is a two-domain protein, which consists of an N-terminal synthetase domain and C-terminal glutaminase domain. The enzymes hydrolyze the amide bond of glutamine to ammonia and glutamate at the glutaminase domains and transfer nascent...; Region: CTGs; cd03113 428406004079 Catalytic site [active] 428406004080 active site 428406004081 UTP binding site [chemical binding]; other site 428406004082 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 428406004083 active site 428406004084 putative oxyanion hole; other site 428406004085 catalytic triad [active] 428406004086 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 428406004087 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 428406004088 Uncharacterized conserved protein [Function unknown]; Region: COG5470 428406004089 enolase; Provisional; Region: eno; PRK00077 428406004090 Enolase: Enolases are homodimeric enzymes that catalyse the reversible dehydration of 2-phospho-D-glycerate to phosphoenolpyruvate as part of the glycolytic and gluconeogenesis pathways. The reaction is facilitated by the presence of metal ions; Region: enolase; cd03313 428406004091 dimer interface [polypeptide binding]; other site 428406004092 metal binding site [ion binding]; metal-binding site 428406004093 substrate binding pocket [chemical binding]; other site 428406004094 cell division protein FtsB; Reviewed; Region: ftsB; PRK00888 428406004095 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 428406004096 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 428406004097 Heat shock protein 33 (Hsp33): Cytosolic protein that acts as a molecular chaperone under oxidative conditions. In normal (reducing) cytosolic conditions, four conserved Cys residues are coordinated by a Zn ion. Under oxidative stress (such as heat...; Region: Hsp33; cd00498 428406004098 dimerization interface [polypeptide binding]; other site 428406004099 domain crossover interface; other site 428406004100 redox-dependent activation switch; other site 428406004101 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 428406004102 Gamma carbonic anhydrase-like: This family is composed of gamma carbonic anhydrase (CA), Ferripyochelin Binding Protein (FBP), E. coli paaY protein, and similar proteins. CAs are zinc-containing enzymes that catalyze the reversible hydration of carbon...; Region: LbH_gamma_CA_like; cd04645 428406004103 trimer interface [polypeptide binding]; other site 428406004104 putative metal binding site [ion binding]; other site 428406004105 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 428406004106 dinuclear metal binding motif [ion binding]; other site 428406004107 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 428406004108 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 428406004109 Predicted thiol-disulfide oxidoreductase [General function prediction only]; Region: COG3011 428406004110 Domain of unknown function (DUF4166); Region: DUF4166; pfam13761 428406004111 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 428406004112 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 428406004113 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 428406004114 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 428406004115 active site 428406004116 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 428406004117 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 428406004118 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the...; Region: S2P-M50_like_1; cd06158 428406004119 Peptidase family M50; Region: Peptidase_M50; pfam02163 428406004120 active site 428406004121 putative substrate binding region [chemical binding]; other site 428406004122 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 428406004123 active site 428406004124 HIGH motif; other site 428406004125 dimer interface [polypeptide binding]; other site 428406004126 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 428406004127 active site 428406004128 KMSKS motif; other site 428406004129 Methyltransferase domain; Region: Methyltransf_23; pfam13489 428406004130 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 428406004131 S-adenosylmethionine binding site [chemical binding]; other site 428406004132 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 428406004133 dihydrodipicolinate synthase; Region: dapA; TIGR00674 428406004134 dimer interface [polypeptide binding]; other site 428406004135 active site 428406004136 catalytic residue [active] 428406004137 Uncharacterized lipoprotein [Cell envelope biogenesis, outer membrane]; Region: NlpB; COG3317 428406004138 NlpB/DapX lipoprotein; Region: Lipoprotein_18; pfam06804 428406004139 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 428406004140 Uncharacterized conserved protein [Function unknown]; Region: COG2850 428406004141 Cupin-like domain; Region: Cupin_8; pfam13621 428406004142 FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]; Region: SlpA; COG1047 428406004143 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 428406004144 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 428406004145 MutS domain I; Region: MutS_I; pfam01624 428406004146 MutS domain II; Region: MutS_II; pfam05188 428406004147 MutS domain III; Region: MutS_III; pfam05192 428406004148 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 428406004149 Walker A/P-loop; other site 428406004150 ATP binding site [chemical binding]; other site 428406004151 Q-loop/lid; other site 428406004152 ABC transporter signature motif; other site 428406004153 Walker B; other site 428406004154 D-loop; other site 428406004155 H-loop/switch region; other site 428406004156 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406004157 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406004158 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 428406004159 dimerization interface [polypeptide binding]; other site 428406004160 Cache domain; Region: Cache_2; pfam08269 428406004161 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 428406004162 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 428406004163 dimer interface [polypeptide binding]; other site 428406004164 putative CheW interface [polypeptide binding]; other site 428406004165 ligand binding domain of Tar- and Tsr-related chemoreceptors; Region: Tar_Tsr_LBD; cl00144 428406004166 dimer interface [polypeptide binding]; other site 428406004167 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 428406004168 dimerization interface [polypeptide binding]; other site 428406004169 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 428406004170 dimer interface [polypeptide binding]; other site 428406004171 putative CheW interface [polypeptide binding]; other site 428406004172 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2258 428406004173 MOSC domain; Region: MOSC; pfam03473 428406004174 3-alpha domain; Region: 3-alpha; pfam03475 428406004175 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 428406004176 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 428406004177 catalytic triad [active] 428406004178 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 428406004179 IMPase, inositol monophosphatase and related domains. A family of Mg++ dependent phosphatases, inhibited by lithium, many of which may act on inositol monophosphate substrate. They dephosphorylate inositol phosphate to generate inositol, which may be...; Region: IMPase; cd01639 428406004180 active site 428406004181 dimerization interface [polypeptide binding]; other site 428406004182 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 428406004183 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 428406004184 Serine acetyltransferase [Amino acid transport and metabolism]; Region: CysE; COG1045 428406004185 Serine acetyltransferase (SAT): SAT catalyzes the CoA-dependent acetylation of the side chain hydroxyl group of L-serine to form O-acetylserine, as the first step of a two-step biosynthetic pathway in bacteria and plants leading to the formation of...; Region: LbH_SAT; cd03354 428406004186 trimer interface [polypeptide binding]; other site 428406004187 active site 428406004188 substrate binding site [chemical binding]; other site 428406004189 CoA binding site [chemical binding]; other site 428406004190 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 428406004191 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 428406004192 putative active site [active] 428406004193 putative metal binding site [ion binding]; other site 428406004194 cyclophilin_EcCYP_like: cyclophilin-type A-like peptidylprolyl cis- trans isomerase (PPIase) domain similar to the cytosolic E. coli cyclophilin A and Streptomyces antibioticus SanCyp18. Compared to the archetypal cyclophilin Human cyclophilin A, these...; Region: cyclophilin_EcCYP_like; cd01920 428406004195 substrate binding site [chemical binding]; other site 428406004196 cyclophilin_EcCYP_like: cyclophilin-type A-like peptidylprolyl cis- trans isomerase (PPIase) domain similar to the cytosolic E. coli cyclophilin A and Streptomyces antibioticus SanCyp18. Compared to the archetypal cyclophilin Human cyclophilin A, these...; Region: cyclophilin_EcCYP_like; cd01920 428406004197 substrate binding site [chemical binding]; other site 428406004198 TPR repeat; Region: TPR_11; pfam13414 428406004199 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 428406004200 binding surface 428406004201 TPR motif; other site 428406004202 TPR repeat; Region: TPR_11; pfam13414 428406004203 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 428406004204 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 428406004205 active site 428406004206 HIGH motif; other site 428406004207 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 428406004208 KMSKS motif; other site 428406004209 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 428406004210 tRNA binding surface [nucleotide binding]; other site 428406004211 anticodon binding site; other site 428406004212 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 428406004213 endonuclease III; Region: ENDO3c; smart00478 428406004214 minor groove reading motif; other site 428406004215 helix-hairpin-helix signature motif; other site 428406004216 substrate binding pocket [chemical binding]; other site 428406004217 active site 428406004218 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated; Region: PRK05724 428406004219 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 428406004220 N-terminal domain of predicted ATPase of the PP-loop faimly implicated in cell cycle control [Cell division and chromosome partitioning]. This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases...; Region: PP-ATPase; cd01992 428406004221 tRNA(Ile)-lysidine synthetase; Provisional; Region: tilS; PRK10660 428406004222 Ligand Binding Site [chemical binding]; other site 428406004223 TilS substrate binding domain; Region: TilS; pfam09179 428406004224 TilS substrate C-terminal domain; Region: TilS_C; pfam11734 428406004225 aspartate kinase; Reviewed; Region: PRK06635 428406004226 AAK_AKii-LysC-BS: Amino Acid Kinase Superfamily (AAK), AKii; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis 168, and the lysine plus threonine-sensitive...; Region: AAK_AKii-LysC-BS; cd04261 428406004227 putative nucleotide binding site [chemical binding]; other site 428406004228 putative catalytic residues [active] 428406004229 putative Mg ion binding site [ion binding]; other site 428406004230 putative aspartate binding site [chemical binding]; other site 428406004231 ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related proteins; Region: ACT_AKii-LysC-BS-like_1; cd04913 428406004232 putative allosteric regulatory site; other site 428406004233 ACT domains of the lysine-sensitive, aspartokinase (AK) isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related domains; Region: ACT_AKii-LysC-BS-like_2; cd04936 428406004234 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK06997 428406004235 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 428406004236 NAD binding site [chemical binding]; other site 428406004237 homotetramer interface [polypeptide binding]; other site 428406004238 homodimer interface [polypeptide binding]; other site 428406004239 substrate binding site [chemical binding]; other site 428406004240 active site 428406004241 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 428406004242 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_14; cd08497 428406004243 The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like; cl01709 428406004244 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4174 428406004245 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406004246 dimer interface [polypeptide binding]; other site 428406004247 conserved gate region; other site 428406004248 putative PBP binding loops; other site 428406004249 ABC-ATPase subunit interface; other site 428406004250 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4239 428406004251 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406004252 dimer interface [polypeptide binding]; other site 428406004253 conserved gate region; other site 428406004254 putative PBP binding loops; other site 428406004255 ABC-ATPase subunit interface; other site 428406004256 ABC-type uncharacterized transport system, duplicated ATPase component [General function prediction only]; Region: COG4172 428406004257 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 428406004258 Walker A/P-loop; other site 428406004259 ATP binding site [chemical binding]; other site 428406004260 Q-loop/lid; other site 428406004261 ABC transporter signature motif; other site 428406004262 Walker B; other site 428406004263 D-loop; other site 428406004264 H-loop/switch region; other site 428406004265 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 428406004266 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 428406004267 Walker A/P-loop; other site 428406004268 ATP binding site [chemical binding]; other site 428406004269 Q-loop/lid; other site 428406004270 ABC transporter signature motif; other site 428406004271 Walker B; other site 428406004272 D-loop; other site 428406004273 H-loop/switch region; other site 428406004274 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 428406004275 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 428406004276 NlpC/P60 family; Region: NLPC_P60; pfam00877 428406004277 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 428406004278 Patatin-like phospholipase domain containing protein 6, protein 7, and fungal NTE1; Region: Pat_PNPLA6_PNPLA7_NTE1_like; cd07205 428406004279 nucleophile elbow; other site 428406004280 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 428406004281 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 428406004282 active site 428406004283 HIGH motif; other site 428406004284 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 428406004285 active site 428406004286 KMSKS motif; other site 428406004287 multidrug efflux protein; Reviewed; Region: PRK01766 428406004288 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Vibrio cholerae NorM; Region: MATE_NorM_like; cd13131 428406004289 cation binding site [ion binding]; other site 428406004290 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 428406004291 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl17364 428406004292 50S ribosomal protein L31 type B; Reviewed; Region: rpmE2; PRK01678 428406004293 Phosphoenolpyruvate:glucose-phosphotransferase regulator; Region: MtfA; pfam06167 428406004294 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 428406004295 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406004296 active site 428406004297 phosphorylation site [posttranslational modification] 428406004298 intermolecular recognition site; other site 428406004299 dimerization interface [polypeptide binding]; other site 428406004300 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 428406004301 DNA binding residues [nucleotide binding] 428406004302 dimerization interface [polypeptide binding]; other site 428406004303 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 428406004304 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406004305 Walker A motif; other site 428406004306 ATP binding site [chemical binding]; other site 428406004307 Walker B motif; other site 428406004308 arginine finger; other site 428406004309 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 428406004310 transcription termination factor Rho; Provisional; Region: rho; PRK09376 428406004311 Rho termination factor, N-terminal domain; Region: Rho_N; smart00959 428406004312 Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA...; Region: Rho_CSD; cd04459 428406004313 RNA binding site [nucleotide binding]; other site 428406004314 Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase. It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the...; Region: rho_factor; cd01128 428406004315 multimer interface [polypeptide binding]; other site 428406004316 Walker A motif; other site 428406004317 ATP binding site [chemical binding]; other site 428406004318 Walker B motif; other site 428406004319 TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains. Group I TRX is a small ancient protein that alter the redox...; Region: TRX_family; cd02947 428406004320 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 428406004321 catalytic residues [active] 428406004322 Inactivated superfamily I helicase [DNA replication, recombination, and repair]; Region: COG3893 428406004323 RecB family exonuclease [DNA replication, recombination, and repair]; Region: COG2887 428406004324 double-strand break repair helicase AddA, alphaproteobacterial type; Region: addA_alphas; TIGR02784 428406004325 Family description; Region: UvrD_C_2; pfam13538 428406004326 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 428406004327 DNA polymerase III, subunit gamma and tau; Region: dnaX_nterm; TIGR02397 428406004328 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406004329 Walker A motif; other site 428406004330 ATP binding site [chemical binding]; other site 428406004331 Walker B motif; other site 428406004332 DNA polymerase III subunit delta'; Validated; Region: PRK08485 428406004333 arginine finger; other site 428406004334 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 428406004335 hypothetical protein; Validated; Region: PRK00153 428406004336 Uncharacterized enzyme involved in biosynthesis of extracellular polysaccharides [General function prediction only]; Region: COG2329 428406004337 recombination protein RecR; Reviewed; Region: recR; PRK00076 428406004338 RecR protein; Region: RecR; pfam02132 428406004339 TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in Escherichia coli RecR. RecR participates in the RecFOR pathway of homologous recombinational repair in prokaryotes. This pathway provides a...; Region: TOPRIM_recR; cd01025 428406004340 putative active site [active] 428406004341 putative metal-binding site [ion binding]; other site 428406004342 tetramer interface [polypeptide binding]; other site 428406004343 Carbohydrate-selective porin, OprB family; Region: OprB; pfam04966 428406004344 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406004345 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406004346 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_1; cd08421 428406004347 putative dimerization interface [polypeptide binding]; other site 428406004348 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 428406004349 CoA-transferase family III; Region: CoA_transf_3; pfam02515 428406004350 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 428406004351 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 428406004352 membrane-bound complex binding site; other site 428406004353 hinge residues; other site 428406004354 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 428406004355 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 428406004356 Walker A/P-loop; other site 428406004357 ATP binding site [chemical binding]; other site 428406004358 Q-loop/lid; other site 428406004359 ABC transporter signature motif; other site 428406004360 Walker B; other site 428406004361 D-loop; other site 428406004362 H-loop/switch region; other site 428406004363 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 428406004364 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406004365 dimer interface [polypeptide binding]; other site 428406004366 conserved gate region; other site 428406004367 putative PBP binding loops; other site 428406004368 ABC-ATPase subunit interface; other site 428406004369 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 428406004370 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 428406004371 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 428406004372 Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a...; Region: OYE_like_FMN; cd02933 428406004373 FMN binding site [chemical binding]; other site 428406004374 active site 428406004375 substrate binding site [chemical binding]; other site 428406004376 catalytic residue [active] 428406004377 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 428406004378 Quinone oxidoreductase (QOR); Region: QOR1; cd08241 428406004379 NAD(P) binding site [chemical binding]; other site 428406004380 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 428406004381 Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: Pcm; COG2518 428406004382 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 428406004383 S-adenosylmethionine binding site [chemical binding]; other site 428406004384 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 428406004385 Peptidase family M23; Region: Peptidase_M23; pfam01551 428406004386 RNA polymerase sigma factor RpoS; Region: rpoS_proteo; TIGR02394 428406004387 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 428406004388 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 428406004389 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 428406004390 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 428406004391 DNA binding residues [nucleotide binding] 428406004392 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 428406004393 putative catalytic site [active] 428406004394 putative metal binding site [ion binding]; other site 428406004395 putative phosphate binding site [ion binding]; other site 428406004396 putative catalytic site [active] 428406004397 putative phosphate binding site [ion binding]; other site 428406004398 putative metal binding site [ion binding]; other site 428406004399 23S rRNA m(5)U1939 methyltransferase; Reviewed; Region: rumA; PRK13168 428406004400 TRAM domain; Region: TRAM; cl01282 428406004401 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 428406004402 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 428406004403 S-adenosylmethionine binding site [chemical binding]; other site 428406004404 YccA-like proteins; Region: YccA_like; cd10433 428406004405 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 428406004406 Nucleoside diphosphate kinase Group I (NDPk_I)-like: NDP kinase domains are present in a large family of structurally and functionally conserved proteins from bacteria to humans that generally catalyze the transfer of gamma-phosphates of a nucleoside...; Region: NDPk_I; cd04413 428406004407 active site 428406004408 multimer interface [polypeptide binding]; other site 428406004409 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK11194 428406004410 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 428406004411 FeS/SAM binding site; other site 428406004412 Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilF; COG3063 428406004413 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 428406004414 binding surface 428406004415 TPR motif; other site 428406004416 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 428406004417 binding surface 428406004418 TPR motif; other site 428406004419 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]; Region: COG1426 428406004420 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 428406004421 non-specific DNA binding site [nucleotide binding]; other site 428406004422 salt bridge; other site 428406004423 sequence-specific DNA binding site [nucleotide binding]; other site 428406004424 Domain of unknown function (DUF4115); Region: DUF4115; pfam13464 428406004425 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 428406004426 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 428406004427 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 428406004428 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 428406004429 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for...; Region: HisRS-like_core; cd00773 428406004430 dimer interface [polypeptide binding]; other site 428406004431 motif 1; other site 428406004432 active site 428406004433 motif 2; other site 428406004434 motif 3; other site 428406004435 HisRS Histidyl-anticodon binding domain. HisRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is...; Region: HisRS_anticodon; cd00859 428406004436 anticodon binding site; other site 428406004437 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 428406004438 Uncharacterized protein conserved in bacteria (DUF2133); Region: DUF2133; pfam09976 428406004439 outer membrane assembly lipoprotein YfgL; Region: assembly_YfgL; TIGR03300 428406004440 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 428406004441 Trp docking motif [polypeptide binding]; other site 428406004442 active site 428406004443 GTP-binding protein Der; Reviewed; Region: PRK00093 428406004444 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 428406004445 G1 box; other site 428406004446 GTP/Mg2+ binding site [chemical binding]; other site 428406004447 Switch I region; other site 428406004448 G2 box; other site 428406004449 Switch II region; other site 428406004450 G3 box; other site 428406004451 G4 box; other site 428406004452 G5 box; other site 428406004453 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 428406004454 G1 box; other site 428406004455 GTP/Mg2+ binding site [chemical binding]; other site 428406004456 Switch I region; other site 428406004457 G2 box; other site 428406004458 G3 box; other site 428406004459 Switch II region; other site 428406004460 G4 box; other site 428406004461 G5 box; other site 428406004462 bacterial Hfq-like; Region: Hfq; cd01716 428406004463 hexamer interface [polypeptide binding]; other site 428406004464 Sm1 motif; other site 428406004465 RNA binding site [nucleotide binding]; other site 428406004466 Sm2 motif; other site 428406004467 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 428406004468 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 428406004469 HflX GTPase family; Region: HflX; cd01878 428406004470 G1 box; other site 428406004471 GTP/Mg2+ binding site [chemical binding]; other site 428406004472 Switch I region; other site 428406004473 G2 box; other site 428406004474 G3 box; other site 428406004475 Switch II region; other site 428406004476 G4 box; other site 428406004477 G5 box; other site 428406004478 Bacterial membrane protein N terminal; Region: HflK_N; pfam12221 428406004479 HflK protein; Region: hflK; TIGR01933 428406004480 Band_7_HflK: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfK (High frequency of lysogenization K). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflK; cd03404 428406004481 Band_7_HflC: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfC (High frequency of lysogenization C). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflC; cd03405 428406004482 HflC protein; Region: hflC; TIGR01932 428406004483 Uncharacterized protein conserved in bacteria (DUF2065); Region: DUF2065; pfam09838 428406004484 ATP phosphoribosyltransferase regulatory subunit; Provisional; Region: PRK12421 428406004485 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for...; Region: HisRS-like_core; cd00773 428406004486 dimer interface [polypeptide binding]; other site 428406004487 motif 1; other site 428406004488 active site 428406004489 motif 2; other site 428406004490 motif 3; other site 428406004491 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 428406004492 Adenylosuccinate synthetase (AdSS) catalyzes the first step in the de novo biosynthesis of AMP. IMP and L-aspartate are conjugated in a two-step reaction accompanied by the hydrolysis of GTP to GDP in the presence of Mg2+. In the first step, the...; Region: AdSS; cd03108 428406004493 GDP-binding site [chemical binding]; other site 428406004494 ACT binding site; other site 428406004495 IMP binding site; other site 428406004496 Predicted phosphoribosyltransferases [General function prediction only]; Region: COG2236 428406004497 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 428406004498 active site 428406004499 ribonuclease R; Region: RNase_R; TIGR02063 428406004500 Ribonuclease B OB domain; Region: OB_RNB; pfam08206 428406004501 RNB domain; Region: RNB; pfam00773 428406004502 S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase...; Region: S1_RNase_R; cd04471 428406004503 RNA binding site [nucleotide binding]; other site 428406004504 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional; Region: PRK11181 428406004505 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 428406004506 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 428406004507 NAD-dependent deacetylase; Provisional; Region: PRK00481 428406004508 SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which...; Region: SIRT5_Af1_CobB; cd01412 428406004509 NAD+ binding site [chemical binding]; other site 428406004510 substrate binding site [chemical binding]; other site 428406004511 Zn binding site [ion binding]; other site 428406004512 transaldolase-like protein; Provisional; Region: PTZ00411 428406004513 Transaldolases including both TalA and TalB; Region: Transaldolase_TalAB; cd00957 428406004514 active site 428406004515 dimer interface [polypeptide binding]; other site 428406004516 catalytic residue [active] 428406004517 RPI_A: Ribose 5-phosphate isomerase type A (RPI_A) subfamily; RPI catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate, the first step of the non-oxidative branch of the pentose phosphate pathway. This reaction leads to the...; Region: RPI_A; cd01398 428406004518 tetramer (dimer of dimers) interface [polypeptide binding]; other site 428406004519 active site 428406004520 dimer interface [polypeptide binding]; other site 428406004521 oxidative damage protection protein; Provisional; Region: PRK05408 428406004522 N-acetylglutamate synthase; Validated; Region: PRK05279 428406004523 AAK_NAGS-ABP: N-acetylglutamate (NAG) kinase-like domain of the NAG Synthase (NAGS) of the arginine-biosynthesis pathway (ABP) found in gamma- and beta-proteobacteria and higher plant chloroplasts. Domain architecture of these NAGS consisted of an...; Region: AAK_NAGS-ABP; cd04237 428406004524 putative feedback inhibition sensing region; other site 428406004525 putative nucleotide binding site [chemical binding]; other site 428406004526 putative substrate binding site [chemical binding]; other site 428406004527 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 428406004528 Coenzyme A binding pocket [chemical binding]; other site 428406004529 ATP-dependent helicase HrpA; Region: DEAH_box_HrpA; TIGR01967 428406004530 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 428406004531 ATP binding site [chemical binding]; other site 428406004532 putative Mg++ binding site [ion binding]; other site 428406004533 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 428406004534 nucleotide binding region [chemical binding]; other site 428406004535 ATP-binding site [chemical binding]; other site 428406004536 Helicase associated domain (HA2); Region: HA2; pfam04408 428406004537 Oligonucleotide/oligosaccharide-binding (OB)-fold; Region: OB_NTP_bind; pfam07717 428406004538 Domain of unknown function (DUF3418); Region: DUF3418; pfam11898 428406004539 Uncharacterized conserved protein [Function unknown]; Region: COG3391 428406004540 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 428406004541 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 428406004542 Catalytic NodB homology domain of rhizobial NodB-like proteins; Region: CE4_NodB_like_6s_7s; cd10917 428406004543 NodB motif; other site 428406004544 active site 428406004545 catalytic site [active] 428406004546 metal binding site [ion binding]; metal-binding site 428406004547 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 428406004548 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; pfam04116 428406004549 Etoposide-induced protein 2.4 (EI24); Region: EI24; pfam07264 428406004550 Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]; Region: CinA; COG1058 428406004551 Competence-damaged protein. CinA is the first gene in the competence- inducible (cin) operon and is thought to be specifically required at some stage in the process of transformation. This domain is closely related to a domain, found in a variety of...; Region: cinA; cd00885 428406004552 putative MPT binding site; other site 428406004553 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 428406004554 active site residue [active] 428406004555 glutamine synthetase; Provisional; Region: glnA; PRK09469 428406004556 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 428406004557 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 428406004558 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 428406004559 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 428406004560 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 428406004561 putative active site [active] 428406004562 heme pocket [chemical binding]; other site 428406004563 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 428406004564 dimer interface [polypeptide binding]; other site 428406004565 phosphorylation site [posttranslational modification] 428406004566 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406004567 ATP binding site [chemical binding]; other site 428406004568 Mg2+ binding site [ion binding]; other site 428406004569 G-X-G motif; other site 428406004570 nitrogen regulation protein NR(I); Region: ntrC; TIGR01818 428406004571 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406004572 active site 428406004573 phosphorylation site [posttranslational modification] 428406004574 intermolecular recognition site; other site 428406004575 dimerization interface [polypeptide binding]; other site 428406004576 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406004577 Walker A motif; other site 428406004578 ATP binding site [chemical binding]; other site 428406004579 Walker B motif; other site 428406004580 arginine finger; other site 428406004581 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 428406004582 HAD-superfamily hydrolase, subfamily IIB; Region: HAD-SF-IIB; TIGR01484 428406004583 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 428406004584 active site 428406004585 motif I; other site 428406004586 motif II; other site 428406004587 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 428406004588 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 428406004589 ABC-type polysaccharide transport system, permease component [Carbohydrate transport and metabolism]; Region: LplB; COG4209 428406004590 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406004591 dimer interface [polypeptide binding]; other site 428406004592 conserved gate region; other site 428406004593 putative PBP binding loops; other site 428406004594 ABC-ATPase subunit interface; other site 428406004595 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 428406004596 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406004597 dimer interface [polypeptide binding]; other site 428406004598 conserved gate region; other site 428406004599 putative PBP binding loops; other site 428406004600 ABC-ATPase subunit interface; other site 428406004601 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 428406004602 The N-terminal ATPase domain of the maltose transporter, MalK; Region: ABC_MalK_N; cd03301 428406004603 Walker A/P-loop; other site 428406004604 ATP binding site [chemical binding]; other site 428406004605 Q-loop/lid; other site 428406004606 ABC transporter signature motif; other site 428406004607 Walker B; other site 428406004608 D-loop; other site 428406004609 H-loop/switch region; other site 428406004610 TOBE domain; Region: TOBE_2; pfam08402 428406004611 cytoplasmic glycerophosphodiester phosphodiesterase; Provisional; Region: ugpQ; PRK09454 428406004612 Glycerophosphodiester phosphodiesterase domain in Escherichia coli cytosolic glycerophosphodiester phosphodiesterase UgpQ and similar proteins; Region: GDPD_EcUgpQ_like; cd08562 428406004613 putative active site [active] 428406004614 catalytic site [active] 428406004615 putative metal binding site [ion binding]; other site 428406004616 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 428406004617 Thiamine pyrophosphate (TPP) family, E1 of OGDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the 2-oxoglutarate dehydrogenase multienzyme complex (OGDC). OGDC catalyzes the oxidative decarboxylation of...; Region: TPP_E1_OGDC_like; cd02016 428406004618 TPP-binding site [chemical binding]; other site 428406004619 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 428406004620 dimer interface [polypeptide binding]; other site 428406004621 PYR/PP interface [polypeptide binding]; other site 428406004622 TPP binding site [chemical binding]; other site 428406004623 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 428406004624 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 428406004625 E3 interaction surface; other site 428406004626 lipoyl attachment site [posttranslational modification]; other site 428406004627 e3 binding domain; Region: E3_binding; pfam02817 428406004628 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 428406004629 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 428406004630 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 428406004631 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 428406004632 Predicted ATPase [General function prediction only]; Region: COG1485 428406004633 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 428406004634 Walker B; other site 428406004635 D-loop; other site 428406004636 H-loop/switch region; other site 428406004637 Phosphosulfolactate phosphohydrolase and related enzymes [Coenzyme metabolism / General function prediction only]; Region: COG2045 428406004638 2-phosphosulpholactate phosphatase; Region: 2-ph_phosp; cl00895 428406004639 Putative metal-binding domain of cation transport ATPase; Region: ATPase-cat_bd; pfam12156 428406004640 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 428406004641 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 428406004642 metal-binding site [ion binding] 428406004643 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 428406004644 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 428406004645 motif II; other site 428406004646 Uncharacterized protein, possibly involved in nitrogen fixation [Inorganic ion transport and metabolism]; Region: FixS; COG3197 428406004647 Cytochrome cbb3 oxidase subunit I. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction...; Region: cbb3_Oxidase_I; cd01661 428406004648 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 428406004649 Low-spin heme binding site [chemical binding]; other site 428406004650 Putative water exit pathway; other site 428406004651 Binuclear center (active site) [active] 428406004652 Putative proton exit pathway; other site 428406004653 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 428406004654 cbb3-type cytochrome c oxidase subunit II; Provisional; Region: PRK14487 428406004655 Cytochrome cbb oxidase CcoQ. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction of O2...; Region: cbb3_Oxidase_CcoQ; cl00282 428406004656 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 428406004657 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 428406004658 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 428406004659 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 428406004660 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 428406004661 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 428406004662 FixH; Region: FixH; pfam05751 428406004663 fumarate/nitrate reduction transcriptional regulator; Provisional; Region: PRK11161 428406004664 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 428406004665 ligand binding site [chemical binding]; other site 428406004666 flexible hinge region; other site 428406004667 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 428406004668 putative switch regulator; other site 428406004669 non-specific DNA interactions [nucleotide binding]; other site 428406004670 DNA binding site [nucleotide binding] 428406004671 sequence specific DNA binding site [nucleotide binding]; other site 428406004672 putative cAMP binding site [chemical binding]; other site 428406004673 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 428406004674 Chromosome segregation and condensation protein B [DNA replication, recombination and repair]; Region: scpB; COG1386 428406004675 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 428406004676 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cd00165 428406004677 RNA binding surface [nucleotide binding]; other site 428406004678 Pseudouridine synthase, Escherichia coli RluB like; Region: PseudoU_synth_RluB; cd02556 428406004679 probable active site [active] 428406004680 ribosome maturation protein RimP; Reviewed; Region: PRK00092 428406004681 Sm and related proteins; Region: Sm_like; cl00259 428406004682 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 428406004683 putative oligomer interface [polypeptide binding]; other site 428406004684 putative RNA binding site [nucleotide binding]; other site 428406004685 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 428406004686 NusA N-terminal domain; Region: NusA_N; pfam08529 428406004687 S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three...; Region: S1_NusA; cd04455 428406004688 RNA binding site [nucleotide binding]; other site 428406004689 homodimer interface [polypeptide binding]; other site 428406004690 NusA-like KH domain; Region: KH_5; pfam13184 428406004691 NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of...; Region: NusA_KH; cd02134 428406004692 G-X-X-G motif; other site 428406004693 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 428406004694 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 428406004695 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 428406004696 translation initiation factor IF-2; Region: IF-2; TIGR00487 428406004697 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 428406004698 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 428406004699 G1 box; other site 428406004700 putative GEF interaction site [polypeptide binding]; other site 428406004701 GTP/Mg2+ binding site [chemical binding]; other site 428406004702 Switch I region; other site 428406004703 G2 box; other site 428406004704 G3 box; other site 428406004705 Switch II region; other site 428406004706 G4 box; other site 428406004707 G5 box; other site 428406004708 This family represents the domain II of bacterial Initiation Factor 2 (IF2) and its eukaryotic mitochondrial homologue mtIF2. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell; Region: IF2_mtIF2_II; cd03702 428406004709 Translation-initiation factor 2; Region: IF-2; pfam11987 428406004710 mtIF2_IVc: this family represents the C2 subdomain of domain IV of mitochondrial translation initiation factor 2 (mtIF2) which adopts a beta-barrel fold displaying a high degree of structural similarity with domain II of the translation elongation factor...; Region: mtIF2_IVc; cd03692 428406004711 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 428406004712 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK01851 428406004713 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 428406004714 RNA binding site [nucleotide binding]; other site 428406004715 active site 428406004716 Pseudouridine synthase II TruB, C-terminal; Region: TruB-C_2; pfam09157 428406004717 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 428406004718 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406004719 putative substrate translocation pore; other site 428406004720 multidrug efflux system protein EmrA; Provisional; Region: PRK15136 428406004721 HlyD family secretion protein; Region: HlyD_3; pfam13437 428406004722 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 428406004723 MarR family; Region: MarR_2; cl17246 428406004724 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 428406004725 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 428406004726 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 428406004727 G1 box; other site 428406004728 putative GEF interaction site [polypeptide binding]; other site 428406004729 GTP/Mg2+ binding site [chemical binding]; other site 428406004730 Switch I region; other site 428406004731 G2 box; other site 428406004732 G3 box; other site 428406004733 Switch II region; other site 428406004734 G4 box; other site 428406004735 G5 box; other site 428406004736 BipA_TypA_II: domain II of BipA (also called TypA) having homology to domain II of the elongation factors (EFs) EF-G and EF-Tu. BipA is a highly conserved protein with global regulatory properties in Escherichia coli. BipA is phosphorylated on a...; Region: BipA_TypA_II; cd03691 428406004737 BipA_TypA_C: a C-terminal portion of BipA or TypA having homology to the C terminal domains of the elongation factors EF-G and EF-2. A member of the ribosome binding GTPase superfamily, BipA is widely distributed in bacteria and plants. BipA is a highly...; Region: BipA_TypA_C; cd03710 428406004738 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 428406004739 active site residue [active] 428406004740 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 428406004741 active site residue [active] 428406004742 Member of the Rhodanese Homology Domain superfamily, repeat 3. This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 3rd repeat which does not contain the putative...; Region: 4RHOD_Repeat_3; cd01534 428406004743 active site residue [active] 428406004744 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 428406004745 active site residue [active] 428406004746 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406004747 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406004748 The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of closely related homologs, contains the type 2 periplasmic binding fold; Region: PBP2_LrhA_like; cd08439 428406004749 putative dimerization interface [polypeptide binding]; other site 428406004750 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 428406004751 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; pfam04116 428406004752 3-hydroxyisobutyryl-CoA hydrolase; Provisional; Region: PRK05617 428406004753 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 428406004754 substrate binding site [chemical binding]; other site 428406004755 oxyanion hole (OAH) forming residues; other site 428406004756 trimer interface [polypeptide binding]; other site 428406004757 2-enoyl-CoA Hydratase C-terminal region; Region: ECH_C; pfam13766 428406004758 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 428406004759 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 428406004760 PGAP1-like protein; Region: PGAP1; pfam07819 428406004761 Ketosteroid isomerase homolog [Function unknown]; Region: COG4319 428406004762 SnoaL-like domain; Region: SnoaL_3; pfam13474 428406004763 transcriptional regulator; Provisional; Region: PRK10632 428406004764 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 428406004765 putative effector binding pocket; other site 428406004766 dimerization interface [polypeptide binding]; other site 428406004767 Uncharacterized ACR, COG2135; Region: DUF159; pfam02586 428406004768 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 428406004769 PAS domain; Region: PAS_9; pfam13426 428406004770 putative active site [active] 428406004771 heme pocket [chemical binding]; other site 428406004772 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 428406004773 PAS domain; Region: PAS_9; pfam13426 428406004774 putative active site [active] 428406004775 heme pocket [chemical binding]; other site 428406004776 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 428406004777 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 428406004778 metal binding site [ion binding]; metal-binding site 428406004779 active site 428406004780 I-site; other site 428406004781 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 428406004782 tRNA-dihydrouridine synthase A; Provisional; Region: PRK11815 428406004783 Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also...; Region: DUS_like_FMN; cd02801 428406004784 FMN binding site [chemical binding]; other site 428406004785 active site 428406004786 catalytic residues [active] 428406004787 substrate binding site [chemical binding]; other site 428406004788 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4994 428406004789 hypothetical protein; Provisional; Region: PRK06156 428406004790 M20 Peptidase Xaa-His dipeptidase (PepV) degrades hydrophobic dipeptides; Region: M20_PepV; cd03888 428406004791 active site 428406004792 metal binding site [ion binding]; metal-binding site 428406004793 Cupin domain; Region: Cupin_2; cl17218 428406004794 LexA repressor; Validated; Region: PRK00215 428406004795 LexA DNA binding domain; Region: LexA_DNA_bind; pfam01726 428406004796 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC...; Region: S24_LexA-like; cd06529 428406004797 Catalytic site [active] 428406004798 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 428406004799 Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently...; Region: FNR1; cd06195 428406004800 FAD binding pocket [chemical binding]; other site 428406004801 FAD binding motif [chemical binding]; other site 428406004802 phosphate binding motif [ion binding]; other site 428406004803 beta-alpha-beta structure motif; other site 428406004804 NAD binding pocket [chemical binding]; other site 428406004805 Type II (periplasmic) bacterial L-asparaginase; Region: L-asparaginase_II; cd08964 428406004806 active site 428406004807 homodimer interface [polypeptide binding]; other site 428406004808 homotetramer interface [polypeptide binding]; other site 428406004809 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 428406004810 Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold; Region: RPA_2b-aaRSs_OBF_like; cl09930 428406004811 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 428406004812 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 428406004813 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 428406004814 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 428406004815 replicative DNA helicase; Provisional; Region: PRK07004 428406004816 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 428406004817 DnaB helicase C terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a...; Region: DnaB_C; cd00984 428406004818 Walker A motif; other site 428406004819 ATP binding site [chemical binding]; other site 428406004820 Walker B motif; other site 428406004821 DNA binding loops [nucleotide binding] 428406004822 Phosphate transport regulator (distant homolog of PhoU) [Inorganic ion transport and metabolism]; Region: COG1392 428406004823 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 428406004824 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 428406004825 NlpC/P60 family; Region: NLPC_P60; pfam00877 428406004826 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]; Region: COG1875 428406004827 PIN domain of bacterial Smg6-like homologs with PhoH-like ATPase domains; Region: PIN_PhoHL-ATPase; cd09883 428406004828 putative active site [active] 428406004829 PhoH-like protein; Region: PhoH; pfam02562 428406004830 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 428406004831 Peroxiredoxin (PRX) family, Bacterioferritin comigratory protein (BCP) subfamily; composed of thioredoxin-dependent thiol peroxidases, widely expressed in pathogenic bacteria, that protect cells against toxicity from reactive oxygen species by reducing...; Region: PRX_BCP; cd03017 428406004832 catalytic triad [active] 428406004833 Catalytic domain of Escherichia coli 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD and other bacterial homologs; Region: CE4_ArnD; cd10939 428406004834 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD; Provisional; Region: PRK15394 428406004835 putative active site [active] 428406004836 putative catalytic site [active] 428406004837 putative Zn binding site [ion binding]; other site 428406004838 NAD-dependent epimerase/dehydratase family protein; Provisional; Region: PRK11908 428406004839 Arna decarboxylase_like, extended (e) SDRs; Region: Arna_like_SDR_e; cd05257 428406004840 NAD binding site [chemical binding]; other site 428406004841 substrate binding site [chemical binding]; other site 428406004842 active site 428406004843 putative formyltransferase; Provisional; Region: PRK06988 428406004844 Formyltransferase, catalytic core domain; Region: FMT_core; cl00395 428406004845 active site 428406004846 substrate binding site [chemical binding]; other site 428406004847 cosubstrate binding site; other site 428406004848 catalytic site [active] 428406004849 C-terminal subdomain of the formyltransferase domain on ArnA, which modifies lipid A with 4-amino-4-deoxy-l-arabinose; Region: Arna_FMT_C; cd08702 428406004850 active site 428406004851 hexamer interface [polypeptide binding]; other site 428406004852 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 428406004853 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 428406004854 Ligand binding site; other site 428406004855 Putative Catalytic site; other site 428406004856 DXD motif; other site 428406004857 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 428406004858 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary...; Region: AHBA_syn; cd00616 428406004859 inhibitor-cofactor binding pocket; inhibition site 428406004860 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406004861 catalytic residue [active] 428406004862 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol flippase subunit ArnF; Provisional; Region: PRK02971 428406004863 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 428406004864 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl17364 428406004865 Xcc1710_like family, specific to proteobacteria. Xcc1710 is a hypothetical protein from Xanthomonas campestris pv. campestris str. ATCC 33913, similar to Mth938, a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome; Region: Xcc1710_like; cd05560 428406004866 aminotransferase AlaT; Validated; Region: PRK09265 428406004867 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 428406004868 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406004869 homodimer interface [polypeptide binding]; other site 428406004870 catalytic residue [active] 428406004871 homoserine dehydrogenase; Provisional; Region: PRK06349 428406004872 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 428406004873 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 428406004874 ACT_HSDH_Hom CD includes the C-terminal ACT domain of the NAD(P)H-dependent, homoserine dehydrogenase (HSDH) and related domains; Region: ACT_HSDH-Hom; cd04881 428406004875 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 428406004876 Threonine synthase catalyzes the final step of threonine biosynthesis. The conversion of O-phosphohomoserine into threonine and inorganic phosphate is pyridoxal 5'-phosphate dependent. The Thr-synth_1 CD includes members from higher plants; Region: Thr-synth_2; cd01560 428406004877 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406004878 catalytic residue [active] 428406004879 Uracil-DNA glycosylases (UDG) and related enzymes; Region: UDG_like; cl00483 428406004880 ligand binding site [chemical binding]; other site 428406004881 active site 428406004882 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 428406004883 MoeA family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF), an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoeA; cd00887 428406004884 dimer interface [polypeptide binding]; other site 428406004885 putative functional site; other site 428406004886 putative MPT binding site; other site 428406004887 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 428406004888 MoaE interaction surface [polypeptide binding]; other site 428406004889 MoeB interaction surface [polypeptide binding]; other site 428406004890 thiocarboxylated glycine; other site 428406004891 MoaE family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor for a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoaE; cd00756 428406004892 MoaE homodimer interface [polypeptide binding]; other site 428406004893 MoaD interaction [polypeptide binding]; other site 428406004894 active site residues [active] 428406004895 chromosome condensation membrane protein; Provisional; Region: PRK14196 428406004896 3HB-oligomer hydrolase (3HBOH); Region: 3HBOH; pfam10605 428406004897 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 428406004898 Clp amino terminal domain; Region: Clp_N; pfam02861 428406004899 Clp amino terminal domain; Region: Clp_N; pfam02861 428406004900 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406004901 Walker A motif; other site 428406004902 ATP binding site [chemical binding]; other site 428406004903 Walker B motif; other site 428406004904 arginine finger; other site 428406004905 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406004906 Walker A motif; other site 428406004907 ATP binding site [chemical binding]; other site 428406004908 Walker B motif; other site 428406004909 arginine finger; other site 428406004910 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 428406004911 Transposase, Mutator family; Region: Transposase_mut; pfam00872 428406004912 MULE transposase domain; Region: MULE; pfam10551 428406004913 60S ribosomal protein L19-like protein; Provisional; Region: PTZ00436 428406004914 ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: Sbp; COG1613 428406004915 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 428406004916 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 428406004917 FMN reductase, SsuE family; Region: FMN_reduc_SsuE; TIGR03567 428406004918 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 428406004919 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 428406004920 substrate binding pocket [chemical binding]; other site 428406004921 membrane-bound complex binding site; other site 428406004922 hinge residues; other site 428406004923 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 428406004924 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 428406004925 substrate binding pocket [chemical binding]; other site 428406004926 membrane-bound complex binding site; other site 428406004927 hinge residues; other site 428406004928 alkanesulfonate monooxygenase; Provisional; Region: PRK00719 428406004929 Alkanesulfonate monoxygenase is the monoxygenase of a two-component system that catalyzes the conversion of alkanesulfonates to the corresponding aldehyde and sulfite. Alkanesulfonate monoxygenase (SsuD) has an absolute requirement for reduced flavin...; Region: Alkanesulfonate_monoxygenase; cd01094 428406004930 active site 428406004931 dimer interface [polypeptide binding]; other site 428406004932 non-prolyl cis peptide bond; other site 428406004933 insertion regions; other site 428406004934 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 428406004935 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406004936 putative PBP binding loops; other site 428406004937 ABC-ATPase subunit interface; other site 428406004938 aliphatic sulfonates transport ATP-binding subunit; Provisional; Region: ssuB; PRK11247 428406004939 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 428406004940 Walker A/P-loop; other site 428406004941 ATP binding site [chemical binding]; other site 428406004942 Q-loop/lid; other site 428406004943 ABC transporter signature motif; other site 428406004944 Walker B; other site 428406004945 D-loop; other site 428406004946 H-loop/switch region; other site 428406004947 Molybdopterin-binding protein [Coenzyme metabolism]; Region: MopI; COG3585 428406004948 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 428406004949 Serine hydrolase; Region: Ser_hydrolase; pfam06821 428406004950 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 428406004951 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406004952 dimer interface [polypeptide binding]; other site 428406004953 conserved gate region; other site 428406004954 putative PBP binding loops; other site 428406004955 ABC-ATPase subunit interface; other site 428406004956 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406004957 dimer interface [polypeptide binding]; other site 428406004958 conserved gate region; other site 428406004959 putative PBP binding loops; other site 428406004960 ABC-ATPase subunit interface; other site 428406004961 ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: CysA; COG1118 428406004962 ATP-binding cassette domain of the sulfate transporter; Region: ABC_CysA_sulfate_importer; cd03296 428406004963 Walker A/P-loop; other site 428406004964 ATP binding site [chemical binding]; other site 428406004965 Q-loop/lid; other site 428406004966 ABC transporter signature motif; other site 428406004967 Walker B; other site 428406004968 D-loop; other site 428406004969 H-loop/switch region; other site 428406004970 TOBE-like domain; Region: TOBE_3; pfam12857 428406004971 transcriptional regulator CysB-like protein; Reviewed; Region: PRK12683 428406004972 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406004973 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 428406004974 substrate binding site [chemical binding]; other site 428406004975 dimerization interface [polypeptide binding]; other site 428406004976 2TM domain; Region: 2TM; pfam13239 428406004977 Predicted signal transduction protein with a C-terminal ATPase domain [Signal transduction mechanisms]; Region: COG2972 428406004978 Histidine kinase; Region: His_kinase; pfam06580 428406004979 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406004980 ATP binding site [chemical binding]; other site 428406004981 Mg2+ binding site [ion binding]; other site 428406004982 G-X-G motif; other site 428406004983 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cl17736 428406004984 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 428406004985 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406004986 active site 428406004987 phosphorylation site [posttranslational modification] 428406004988 intermolecular recognition site; other site 428406004989 dimerization interface [polypeptide binding]; other site 428406004990 LytTr DNA-binding domain; Region: LytTR; smart00850 428406004991 thiamine pyrophosphate protein; Validated; Region: PRK08199 428406004992 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 428406004993 PYR/PP interface [polypeptide binding]; other site 428406004994 dimer interface [polypeptide binding]; other site 428406004995 TPP binding site [chemical binding]; other site 428406004996 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 428406004997 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cd00568 428406004998 TPP-binding site [chemical binding]; other site 428406004999 ribonuclease activity regulator protein RraA; Provisional; Region: PRK09372 428406005000 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cd06661 428406005001 putative active site pocket [active] 428406005002 dimerization interface [polypeptide binding]; other site 428406005003 putative catalytic residue [active] 428406005004 isocitrate lyase; Provisional; Region: PRK15063 428406005005 Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate...; Region: ICL_PEPM; cd00377 428406005006 tetramer interface [polypeptide binding]; other site 428406005007 active site 428406005008 Mg2+/Mn2+ binding site [ion binding]; other site 428406005009 Transcriptional regulators [Transcription]; Region: GntR; COG1802 428406005010 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 428406005011 DNA-binding site [nucleotide binding]; DNA binding site 428406005012 FCD domain; Region: FCD; pfam07729 428406005013 Hydantoin racemase [Amino acid transport and metabolism]; Region: COG4126 428406005014 uncharacterized nucleobase-cation-symport-1 (NCS1) transporter subfamily; solute-binding domain; Region: SLC-NCS1sbd_u1; cd11555 428406005015 Permease for cytosine/purines, uracil, thiamine, allantoin; Region: Transp_cyt_pur; pfam02133 428406005016 Na binding site [ion binding]; other site 428406005017 putative substrate binding site [chemical binding]; other site 428406005018 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 428406005019 Ligand Binding Site [chemical binding]; other site 428406005020 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406005021 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 428406005022 putative effector binding pocket; other site 428406005023 dimerization interface [polypeptide binding]; other site 428406005024 2-haloalkanoic acid dehalogenase, type II; Region: HAD_type_II; TIGR01428 428406005025 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 428406005026 motif II; other site 428406005027 malate synthase A; Region: malate_syn_A; TIGR01344 428406005028 Malate synthase A (MSA), present in some bacteria, plants and fungi. Prokaryotic MSAs tend to be monomeric, whereas eukaryotic enzymes are homomultimers. In general, malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to...; Region: malate_synt_A; cd00727 428406005029 active site 428406005030 DUF1857, an uncharacterized ligand-binding domain of the SRPBCC domain superfamily; Region: SRPBCC_DUF1857; cd08863 428406005031 putative hydrophobic ligand binding site [chemical binding]; other site 428406005032 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 428406005033 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406005034 putative substrate translocation pore; other site 428406005035 Acyl CoA binding protein (ACBP) binds thiol esters of long fatty acids and coenzyme A in a one-to-one binding mode with high specificity and affinity. Acyl-CoAs are important intermediates in fatty lipid synthesis and fatty acid degradation and play a...; Region: ACBP; cl00221 428406005036 acyl-CoA binding pocket [chemical binding]; other site 428406005037 CoA binding site [chemical binding]; other site 428406005038 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 428406005039 Glycoprotease family; Region: Peptidase_M22; pfam00814 428406005040 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 428406005041 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 428406005042 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 428406005043 Fe-S cluster binding site [ion binding]; other site 428406005044 active site 428406005045 lysophospholipid transporter LplT; Provisional; Region: PRK11195 428406005046 alanine racemase; Reviewed; Region: alr; PRK00053 428406005047 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 428406005048 active site 428406005049 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 428406005050 substrate binding site [chemical binding]; other site 428406005051 catalytic residues [active] 428406005052 dimer interface [polypeptide binding]; other site 428406005053 DNA repair protein RadA; Provisional; Region: PRK11823 428406005054 Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of...; Region: Sms; cd01121 428406005055 Walker A motif/ATP binding site; other site 428406005056 ATP binding site [chemical binding]; other site 428406005057 Walker B motif; other site 428406005058 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 428406005059 disulfide bond formation protein B; Provisional; Region: PRK02110 428406005060 Uncharacterized conserved protein [Function unknown]; Region: COG1683 428406005061 formyl-CoA transferase; Region: oxalate_frc; TIGR03253 428406005062 CoA-transferase family III; Region: CoA_transf_3; pfam02515 428406005063 putative ABC transporter ATP-binding protein; Provisional; Region: PRK10636 428406005064 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 428406005065 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 428406005066 ABC transporter; Region: ABC_tran_2; pfam12848 428406005067 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 428406005068 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 428406005069 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 428406005070 RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate...; Region: SIS_RpiR; cd05013 428406005071 putative active site [active] 428406005072 L-Asparaginase type 2. L-Asparaginase hydrolyzes L-asparagine to L-aspartate and ammonia. The proenzyme undergoes an autoproteolytic cleavage into alpha and beta subunits to expose a threonine residue which becomes the N-terminal residue of the beta...; Region: Asparaginase_2; cd04701 428406005073 catalytic nucleophile [active] 428406005074 glutathione transporter ATP-binding protein; Provisional; Region: PRK10261 428406005075 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 428406005076 Walker A/P-loop; other site 428406005077 ATP binding site [chemical binding]; other site 428406005078 Q-loop/lid; other site 428406005079 ABC transporter signature motif; other site 428406005080 Walker B; other site 428406005081 D-loop; other site 428406005082 H-loop/switch region; other site 428406005083 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; pfam08352 428406005084 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 428406005085 Walker A/P-loop; other site 428406005086 ATP binding site [chemical binding]; other site 428406005087 Q-loop/lid; other site 428406005088 ABC transporter signature motif; other site 428406005089 Walker B; other site 428406005090 D-loop; other site 428406005091 H-loop/switch region; other site 428406005092 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 428406005093 glutathione ABC transporter substrate-binding protein GsiB; Provisional; Region: PRK15413 428406005094 The substrate-binding component of an uncharacterized ABC-type peptide import system Ylib contains the type 2 periplasmic binding fold; Region: PBP2_Ylib_like; cd08499 428406005095 glutathione ABC transporter permease GsiC; Provisional; Region: PRK15081 428406005096 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406005097 dimer interface [polypeptide binding]; other site 428406005098 conserved gate region; other site 428406005099 putative PBP binding loops; other site 428406005100 ABC-ATPase subunit interface; other site 428406005101 glutathione ABC transporter permease GsiD; Provisional; Region: PRK15082 428406005102 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 428406005103 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406005104 dimer interface [polypeptide binding]; other site 428406005105 conserved gate region; other site 428406005106 putative PBP binding loops; other site 428406005107 ABC-ATPase subunit interface; other site 428406005108 L-Aminopeptidase D-amidase/D-esterase (DmpA) family; DmpA catalyzes the release of N-terminal D and L amino acids from peptide susbtrates. DmpA is synthesized as a single polypeptide precursor, which is autocatalytically cleaved to the active...; Region: DmpA; cd02253 428406005109 homodimer interface [polypeptide binding]; other site 428406005110 homotetramer interface [polypeptide binding]; other site 428406005111 active site pocket [active] 428406005112 cleavage site 428406005113 Peptidase M55, D-aminopeptidase dipeptide-binding protein family; Region: DAP_dppA_1; cd08663 428406005114 SxDxEG motif; other site 428406005115 active site 428406005116 metal binding site [ion binding]; metal-binding site 428406005117 homopentamer interface [polypeptide binding]; other site 428406005118 Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis]; Region: HemK; COG2890 428406005119 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 428406005120 S-adenosylmethionine binding site [chemical binding]; other site 428406005121 Adenylyl cyclase (AC) class IV-like, a subgroup of the CYTH-like superfamily; Region: CYTH-like_AC_IV-like; cd07890 428406005122 putative active site [active] 428406005123 putative metal binding residues [ion binding]; other site 428406005124 signature motif; other site 428406005125 putative triphosphate binding site [ion binding]; other site 428406005126 dimer interface [polypeptide binding]; other site 428406005127 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 428406005128 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 428406005129 metal binding site [ion binding]; metal-binding site 428406005130 dimer interface [polypeptide binding]; other site 428406005131 Arsenate Reductase (ArsC) family, Yffb subfamily; Yffb is an uncharacterized bacterial protein encoded by the yffb gene, related to the thioredoxin-fold arsenic reductases, ArsC. The structure of Yffb and the conservation of the catalytic cysteine...; Region: ArsC_Yffb; cd03035 428406005132 ArsC family; Region: ArsC; pfam03960 428406005133 putative catalytic residues [active] 428406005134 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 428406005135 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate (THDP) N-succinyltransferase (also called THP succinyltransferase): THDP N-succinyltransferase catalyzes the conversion of tetrahydrodipicolinate and succinyl-CoA to N-succinyltetrahydrodipicolinate and CoA; Region: LbH_THP_succinylT; cd03350 428406005136 trimer interface [polypeptide binding]; other site 428406005137 active site 428406005138 substrate binding site [chemical binding]; other site 428406005139 CoA binding site [chemical binding]; other site 428406005140 succinyldiaminopimelate transaminase; Provisional; Region: PRK09147 428406005141 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 428406005142 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406005143 homodimer interface [polypeptide binding]; other site 428406005144 catalytic residue [active] 428406005145 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 428406005146 EamA-like transporter family; Region: EamA; cl17759 428406005147 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 428406005148 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 428406005149 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 428406005150 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 428406005151 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 428406005152 Walker A/P-loop; other site 428406005153 ATP binding site [chemical binding]; other site 428406005154 Q-loop/lid; other site 428406005155 SMC proteins Flexible Hinge Domain; Region: SMC_hinge; smart00968 428406005156 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 428406005157 ABC transporter signature motif; other site 428406005158 Walker B; other site 428406005159 D-loop; other site 428406005160 H-loop/switch region; other site 428406005161 ZipA, C-terminal domain (FtsZ-binding); Region: ZipA_C; smart00771 428406005162 Ligase N family; Region: LIGANc; smart00532 428406005163 NAD+ dependent DNA ligase adenylation domain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor, but using the same basic reaction...; Region: LIGANc; cd00114 428406005164 nucleotide binding pocket [chemical binding]; other site 428406005165 K-X-D-G motif; other site 428406005166 catalytic site [active] 428406005167 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 428406005168 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 428406005169 Helix-hairpin-helix motif; Region: HHH_2; pfam12826 428406005170 Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo...; Region: BRCT; cd00027 428406005171 Dimer interface [polypeptide binding]; other site 428406005172 BRCT sequence motif; other site 428406005173 Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of the N-terminal formyl group in a growing polypeptide chain following translation initiation during protein synthesis in prokaryotes. These enzymes utilize Fe(II)...; Region: Pep_deformylase; cd00487 428406005174 active site 428406005175 catalytic residues [active] 428406005176 metal binding site [ion binding]; metal-binding site 428406005177 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 428406005178 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cd00165 428406005179 RNA binding surface [nucleotide binding]; other site 428406005180 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 428406005181 active site 428406005182 PII uridylyl-transferase; Provisional; Region: PRK03059 428406005183 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 428406005184 metal binding triad; other site 428406005185 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 428406005186 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 428406005187 Zn2+ binding site [ion binding]; other site 428406005188 Mg2+ binding site [ion binding]; other site 428406005189 ACT domain family, ACT_UUR-like_1, includes the first of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains; Region: ACT_UUR-like_1; cd04900 428406005190 C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains; Region: ACT_ACR-UUR-like_2; cd04899 428406005191 Methionine Aminopeptidase 1. E.C. 3.4.11.18. Also known as methionyl aminopeptidase and Peptidase M. Catalyzes release of N-terminal amino acids, preferentially methionine, from peptides and arylamides; Region: MetAP1; cd01086 428406005192 active site 428406005193 Ribosomal protein S2 (RPS2), involved in formation of the translation initiation complex, where it might contact the messenger RNA and several components of the ribosome. It has been shown that in Escherichia coli RPS2 is essential for the binding of...; Region: RPS2; cd01425 428406005194 rRNA interaction site [nucleotide binding]; other site 428406005195 S8 interaction site; other site 428406005196 putative laminin-1 binding site; other site 428406005197 elongation factor Ts; Provisional; Region: tsf; PRK09377 428406005198 UBA/TS-N domain; Region: UBA; pfam00627 428406005199 Elongation factor TS; Region: EF_TS; pfam00889 428406005200 Elongation factor TS; Region: EF_TS; pfam00889 428406005201 UMP kinase (UMPK)-Ec, the microbial/chloroplast uridine monophosphate kinase (uridylate kinase) enzyme that catalyzes UMP phosphorylation and plays a key role in pyrimidine nucleotide biosynthesis; regulation of this process is via feed-back control and...; Region: AAK_UMPK-PyrH-Ec; cd04254 428406005202 putative nucleotide binding site [chemical binding]; other site 428406005203 uridine monophosphate binding site [chemical binding]; other site 428406005204 homohexameric interface [polypeptide binding]; other site 428406005205 ribosome recycling factor; Reviewed; Region: frr; PRK00083 428406005206 Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are "recycled" and ready for another...; Region: RRF; cd00520 428406005207 hinge region; other site 428406005208 Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl...; Region: CIS_IPPS; cl00230 428406005209 Undecaprenyl pyrophosphate synthase [Lipid metabolism]; Region: UppS; COG0020 428406005210 catalytic residue [active] 428406005211 putative FPP diphosphate binding site; other site 428406005212 putative FPP binding hydrophobic cleft; other site 428406005213 dimer interface [polypeptide binding]; other site 428406005214 putative IPP diphosphate binding site; other site 428406005215 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 428406005216 CDP-diglyceride synthase; Provisional; Region: cdsA; PRK11624 428406005217 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 428406005218 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 428406005219 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 428406005220 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 428406005221 RseP-like Site-2 proteases (S2P), zinc metalloproteases (MEROPS family M50A), cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. In Escherichia coli, the S2P homolog...; Region: S2P-M50_PDZ_RseP-like; cd06163 428406005222 zinc metallopeptidase RseP; Provisional; Region: PRK10779 428406005223 active site 428406005224 PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated; Region: PDZ; cl00117 428406005225 putative substrate binding region [chemical binding]; other site 428406005226 PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated; Region: PDZ; cl00117 428406005227 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic...; Region: S2P-M50; cl10020 428406005228 putative substrate binding region [chemical binding]; other site 428406005229 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 428406005230 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 428406005231 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 428406005232 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 428406005233 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 428406005234 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 428406005235 Surface antigen; Region: Bac_surface_Ag; pfam01103 428406005236 periplasmic chaperone; Provisional; Region: PRK10780 428406005237 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 428406005238 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 428406005239 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 428406005240 UDP-3-O-acyl-glucosamine N-acyltransferase (LpxD): The enzyme catalyzes the transfer of 3-hydroxymyristic acid or 3-hydroxy-arachidic acid, depending on the organism, from the acyl carrier protein (ACP) to UDP-3-O-acyl-glucosamine to produce UDP-2; Region: LbH_LpxD; cd03352 428406005241 trimer interface [polypeptide binding]; other site 428406005242 active site 428406005243 UDP-GlcNAc binding site [chemical binding]; other site 428406005244 lipid binding site [chemical binding]; lipid-binding site 428406005245 FabZ is a 17kD beta-hydroxyacyl-acyl carrier protein (ACP) dehydratase that primarily catalyzes the dehydration of beta-hydroxyacyl-ACP to trans-2-acyl-ACP, the third step in the elongation phase of the bacterial/ plastid, type II, fatty-acid...; Region: FabZ; cd01288 428406005246 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 428406005247 UDP-N-acetylglucosamine O-acyltransferase (UDP-GlcNAc acyltransferase): Proteins in this family catalyze the transfer of (R)-3-hydroxymyristic acid from its acyl carrier protein thioester to UDP-GlcNAc. It is the first enzyme in the lipid A biosynthetic...; Region: LbH_UDP-GlcNAc_AT; cd03351 428406005248 active site 428406005249 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 428406005250 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 428406005251 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 428406005252 RNA/DNA hybrid binding site [nucleotide binding]; other site 428406005253 active site 428406005254 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 428406005255 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 428406005256 A family including aminopeptidase P, aminopeptidase M, and prolidase. Also known as metallopeptidase family M24. This family of enzymes is able to cleave amido-, imido- and amidino-containing bonds. Members exibit relatively narrow substrate specificity...; Region: APP_MetAP; cd01066 428406005257 active site 428406005258 short chain dehydrogenase; Validated; Region: PRK05855 428406005259 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 428406005260 classical (c) SDRs; Region: SDR_c; cd05233 428406005261 NAD(P) binding site [chemical binding]; other site 428406005262 active site 428406005263 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG3687 428406005264 Predicted metal-dependent hydrolase; Region: Metal_hydrol; pfam10118 428406005265 PEP synthetase regulatory protein; Provisional; Region: PRK05339 428406005266 phosphoenolpyruvate synthase; Validated; Region: PRK06464 428406005267 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 428406005268 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 428406005269 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 428406005270 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 428406005271 Band_7_stomatin_like: A subgroup of the band 7 domain of flotillin (reggie) like proteins similar to stomatin and podicin (two lipid raft-associated integral membrane proteins). Individual proteins of this band 7 domain family may cluster to form...; Region: Band_7_stomatin_like; cd03403 428406005272 Small protein B (SmpB) is a component of the trans-translation system in prokaryotes for releasing stalled ribosome from damaged messenger RNAs; Region: SmpB; cd09294 428406005273 SmpB-tmRNA interface; other site 428406005274 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 428406005275 putative coenzyme Q binding site [chemical binding]; other site 428406005276 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2914 428406005277 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 428406005278 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 428406005279 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl17186 428406005280 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein. IMPDH is an essential enzyme that catalyzes the first step unique to GTP synthesis, playing a...; Region: CBS_pair_IMPDH; cd04601 428406005281 IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of...; Region: IMPDH; cd00381 428406005282 active site 428406005283 GMP synthase; Reviewed; Region: guaA; PRK00074 428406005284 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 428406005285 AMP/PPi binding site [chemical binding]; other site 428406005286 candidate oxyanion hole; other site 428406005287 catalytic triad [active] 428406005288 potential glutamine specificity residues [chemical binding]; other site 428406005289 The C-terminal domain of GMP synthetase. It contains two subdomains; the ATP pyrophosphatase domain which closes to the N-termial and the dimerization domain at C-terminal end. The ATP-PPase is a twisted, five-stranded parallel beta-sheet sandwiched...; Region: GMP_synthase_C; cd01997 428406005290 ATP Binding subdomain [chemical binding]; other site 428406005291 Ligand Binding sites [chemical binding]; other site 428406005292 Dimerization subdomain; other site 428406005293 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 428406005294 DNA-binding site [nucleotide binding]; DNA binding site 428406005295 RNA-binding motif; other site 428406005296 Glutamine cyclotransferase [Posttranslational modification, protein turnover, chaperones]; Region: COG3823 428406005297 Bacterial protein of unknown function (DUF899); Region: DUF899; pfam05988 428406005298 Predicted metal-binding integral membrane protein (DUF2182); Region: DUF2182; pfam09948 428406005299 Predicted Na+/dicarboxylate symporter [General function prediction only]; Region: COG1823 428406005300 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 428406005301 pca operon transcription factor PcaQ; Region: TF_pcaQ; TIGR02424 428406005302 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406005303 The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold; Region: PBP2_GbpR; cd08435 428406005304 putative dimerization interface [polypeptide binding]; other site 428406005305 Protocatechuate 3,4-dioxygenase (3,4-PCD) , beta subunit. 3,4-PCD catalyzes the oxidative ring cleavage of 3,4-dihydroxybenzoate to produce beta-carboxy-cis,cis-muconate. 3,4-PCDs are large aggregates of 12 protomers, each composed of an alpha- and...; Region: 3,4-PCD_beta; cd03464 428406005306 heterodimer interface [polypeptide binding]; other site 428406005307 multimer interface [polypeptide binding]; other site 428406005308 protocatechuate 3,4-dioxygenase, beta subunit; Region: protocat_beta; TIGR02422 428406005309 active site 428406005310 Protocatechuate 3,4-dioxygenase beta subunit [Secondary metabolites biosynthesis, transport, and catabolism]; Region: PcaH; COG3485 428406005311 Protocatechuate 3,4-dioxygenase (3,4-PCD) , alpha subunit. 3,4-PCD catalyzes the oxidative ring cleavage of 3,4-dihydroxybenzoate to produce beta-carboxy-cis,cis-muconate. 3,4-PCDs are large aggregates of 12 protomers, each composed of an alpha- and...; Region: 3,4-PCD_alpha; cd03463 428406005312 heterodimer interface [polypeptide binding]; other site 428406005313 active site 428406005314 2'-5' RNA ligase [Translation, ribosomal structure and biogenesis]; Region: LigT; COG1514 428406005315 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 428406005316 Predicted protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: COG3531 428406005317 DsbA family, FrnE-like subfamily; composed of uncharacterized proteins containing a CXXC motif with similarity to DsbA and FrnE. FrnE is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the...; Region: DsbA_FrnE_like; cd03025 428406005318 catalytic residues [active] 428406005319 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 428406005320 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406005321 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406005322 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 428406005323 putative effector binding pocket; other site 428406005324 dimerization interface [polypeptide binding]; other site 428406005325 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406005326 Major Facilitator Superfamily; Region: MFS_1; pfam07690 428406005327 putative substrate translocation pore; other site 428406005328 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 428406005329 Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate...; Region: ICL_PEPM; cd00377 428406005330 tetramer interface [polypeptide binding]; other site 428406005331 active site 428406005332 Mg2+/Mn2+ binding site [ion binding]; other site 428406005333 2-hydroxychromene-2-carboxylate isomerase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: NahD; COG3917 428406005334 DsbA family, 2-hydroxychromene-2-carboxylate (HCCA) isomerase subfamily; HCCA isomerase is a glutathione (GSH) dependent enzyme involved in the naphthalene catabolic pathway. It converts HCCA, a hemiketal formed spontaneously after ring cleavage of 1; Region: DsbA_HCCA_Iso; cd03022 428406005335 putative catalytic residue [active] 428406005336 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 428406005337 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406005338 The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 428406005339 dimerization interface [polypeptide binding]; other site 428406005340 substrate binding pocket [chemical binding]; other site 428406005341 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406005342 putative substrate translocation pore; other site 428406005343 Major Facilitator Superfamily; Region: MFS_1; pfam07690 428406005344 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 428406005345 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 428406005346 6-pyruvoyl tetrahydropterin synthase; Region: PTPS; pfam01242 428406005347 active site 428406005348 Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn dependent and catalyze the deamination of nucleosides. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a...; Region: nucleoside_deaminase; cd01285 428406005349 nucleoside/Zn binding site; other site 428406005350 dimer interface [polypeptide binding]; other site 428406005351 catalytic motif [active] 428406005352 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 428406005353 dimer interface [polypeptide binding]; other site 428406005354 catalytic triad [active] 428406005355 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 428406005356 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 428406005357 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 428406005358 ABC transporter; Region: ABC_tran_2; pfam12848 428406005359 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 428406005360 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 428406005361 succinate CoA transferase; Region: YgfH_subfam; TIGR03458 428406005362 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 428406005363 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406005364 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406005365 The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold; Region: PBP2_CidR; cd08438 428406005366 putative dimerization interface [polypeptide binding]; other site 428406005367 Rhodococcus ruber 6-oxolauric acid dehydrogenase-like; Region: ALDH_CddD_SSP0762; cd07138 428406005368 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 428406005369 NAD binding site [chemical binding]; other site 428406005370 catalytic residues [active] 428406005371 Predicted Fe-S protein [General function prediction only]; Region: COG3313 428406005372 Glucoamylase and related glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: SGA1; COG3387 428406005373 Glycosyl hydrolases family 15; Region: Glyco_hydro_15; pfam00723 428406005374 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4320 428406005375 Uncharacterized protein conserved in bacteria (DUF2252); Region: DUF2252; pfam10009 428406005376 phospho-2-dehydro-3-deoxyheptonate aldolase; Provisional; Region: PRK12755 428406005377 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 428406005378 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 428406005379 ligand binding domain of Tar- and Tsr-related chemoreceptors; Region: Tar_Tsr_LBD; cd00181 428406005380 dimer interface [polypeptide binding]; other site 428406005381 ligand binding site [chemical binding]; other site 428406005382 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 428406005383 dimerization interface [polypeptide binding]; other site 428406005384 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 428406005385 dimer interface [polypeptide binding]; other site 428406005386 putative CheW interface [polypeptide binding]; other site 428406005387 magnesium transport protein MgtC; Provisional; Region: PRK15385 428406005388 MgtC family; Region: MgtC; pfam02308 428406005389 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 428406005390 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 428406005391 NAD(P) binding site [chemical binding]; other site 428406005392 active site 428406005393 Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family [Posttranslational modification, protein turnover, chaperones]; Region: XdhC; COG1975 428406005394 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 428406005395 XdhC Rossmann domain; Region: XdhC_C; pfam13478 428406005396 Carbon monoxide dehydrogenase subunit G (CoxG); Region: CoxG; cd05018 428406005397 putative hydrophobic ligand binding site [chemical binding]; other site 428406005398 Protein containing von Willebrand factor type A (vWA) domain [General function prediction only]; Region: CoxE; COG3552 428406005399 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cd00198 428406005400 metal ion-dependent adhesion site (MIDAS); other site 428406005401 MoxR-like ATPases [General function prediction only]; Region: COG0714 428406005402 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406005403 Walker A motif; other site 428406005404 ATP binding site [chemical binding]; other site 428406005405 Walker B motif; other site 428406005406 arginine finger; other site 428406005407 Aerobic-type carbon monoxide dehydrogenase, middle subunit CoxM/CutM homologs [Energy production and conversion]; Region: CoxM; COG1319 428406005408 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; smart01092 428406005409 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 428406005410 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 428406005411 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 428406005412 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 428406005413 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 428406005414 Uncharacterized protein conserved in bacteria [Function unknown]; Region: CreA; COG3045 428406005415 CreA protein; Region: CreA; pfam05981 428406005416 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406005417 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406005418 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 428406005419 putative effector binding pocket; other site 428406005420 dimerization interface [polypeptide binding]; other site 428406005421 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406005422 putative substrate translocation pore; other site 428406005423 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406005424 Membrane carboxypeptidase (penicillin-binding protein) [Cell envelope biogenesis, outer membrane]; Region: MrcB; COG0744 428406005425 Transglycosylase; Region: Transgly; pfam00912 428406005426 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 428406005427 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406005428 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406005429 The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in benzoate catabolism; contains the type 2 periplasmic binding fold; Region: PBP2_BenM_CatM_CatR; cd08445 428406005430 dimerizarion interface [polypeptide binding]; other site 428406005431 CrgA pocket; other site 428406005432 substrate binding pocket [chemical binding]; other site 428406005433 muconate and chloromuconate cycloisomerases; Region: mucon_cyclo; TIGR02534 428406005434 Muconate Lactonizing Enzyme (MLE), an homooctameric enzyme, catalyses the conversion of cis,cis-muconate (CCM) to muconolactone (ML) in the catechol branch of the beta-ketoadipate pathway. This pathway is used in soil microbes to breakdown lignin-derived...; Region: MLE; cd03318 428406005435 octamer interface [polypeptide binding]; other site 428406005436 active site 428406005437 muconolactone delta-isomerase; Region: muco_delta; TIGR03221 428406005438 catechol 1,2-dioxygenase, proteobacterial; Region: catechol_proteo; TIGR02439 428406005439 Catechol 1,2 dioxygenase (1,2-CTD) catalyzes an intradiol cleavage reaction of catechol to form cis,cis-muconate. 1,2-CTDs is homodimers with one catalytic non-heme ferric ion per monomer. They belong to the aromatic dioxygenase family, a family of...; Region: 1,2-CTD; cd03460 428406005440 dimer interface [polypeptide binding]; other site 428406005441 active site 428406005442 benzoate 1,2-dioxygenase, large subunit; Region: benzo_1_2_benA; TIGR03229 428406005443 Rieske non-heme iron oxygenase (RO) family, 2-Halobenzoate 1,2-dioxygenase (HBDO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to...; Region: Rieske_RO_Alpha_HBDO; cd03542 428406005444 C-terminal catalytic domain of the oxygenase alpha subunit of Pseudomonas resinovorans strain CA10 anthranilate 1,2-dioxygenase and related aromatic ring hydroxylating dioxygenases; Region: RHO_alpha_C_AntDO-like; cd08879 428406005445 putative alpha subunit interface [polypeptide binding]; other site 428406005446 putative active site [active] 428406005447 putative substrate binding site [chemical binding]; other site 428406005448 Fe binding site [ion binding]; other site 428406005449 Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the...; Region: ring_hydroxylating_dioxygenases_beta; cd00667 428406005450 inter-subunit interface; other site 428406005451 anthranilate dioxygenase reductase; Provisional; Region: antC; PRK11872 428406005452 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 428406005453 catalytic loop [active] 428406005454 iron binding site [ion binding]; other site 428406005455 Benzoate dioxygenase reductase (BenDO) FAD/NAD binding domain. Oxygenases oxidize hydrocarbons using dioxygen as the oxidant. As a Class I bacterial dioxygenases, benzoate dioxygenase like proteins combine an [2Fe-2S] cluster containing N-terminal...; Region: BenDO_FAD_NAD; cd06209 428406005456 FAD binding pocket [chemical binding]; other site 428406005457 FAD binding motif [chemical binding]; other site 428406005458 phosphate binding motif [ion binding]; other site 428406005459 beta-alpha-beta structure motif; other site 428406005460 NAD binding pocket [chemical binding]; other site 428406005461 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase; Provisional; Region: benD; PRK12823 428406005462 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase (DHB DH)-like, classical (c) SDR; Region: DHB_DH-like_SDR_c; cd08937 428406005463 putative NAD(P) binding site [chemical binding]; other site 428406005464 active site 428406005465 benzoate transport; Region: 2A0115; TIGR00895 428406005466 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406005467 putative substrate translocation pore; other site 428406005468 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406005469 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK06943 428406005470 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 428406005471 inhibitor-cofactor binding pocket; inhibition site 428406005472 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406005473 catalytic residue [active] 428406005474 8-amino-7-oxononanoate synthase; Reviewed; Region: PRK05958 428406005475 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 428406005476 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 428406005477 catalytic residue [active] 428406005478 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 428406005479 AAA domain; Region: AAA_26; pfam13500 428406005480 Protein of unknown function (DUF1653); Region: DUF1653; cl01949 428406005481 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 428406005482 active site 428406005483 catalytic residues [active] 428406005484 metal binding site [ion binding]; metal-binding site 428406005485 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406005486 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406005487 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_1; cd08421 428406005488 putative dimerization interface [polypeptide binding]; other site 428406005489 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 428406005490 CoA-transferase family III; Region: CoA_transf_3; pfam02515 428406005491 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 428406005492 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 428406005493 substrate binding site [chemical binding]; other site 428406005494 ligand binding site [chemical binding]; other site 428406005495 isopropylmalate isomerase small subunit; Provisional; Region: leuD; PRK01641 428406005496 Aconatase-like swivel domain of 3-isopropylmalate dehydratase and related uncharacterized proteins. 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate...; Region: IPMI_Swivel; cd01577 428406005497 substrate binding site [chemical binding]; other site 428406005498 benzoate transport; Region: 2A0115; TIGR00895 428406005499 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406005500 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406005501 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406005502 putative substrate translocation pore; other site 428406005503 Cupin; Region: Cupin_6; pfam12852 428406005504 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 428406005505 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 428406005506 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 428406005507 putative DNA-binding transcriptional regulator; Provisional; Region: PRK09791 428406005508 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406005509 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 428406005510 dimerization interface [polypeptide binding]; other site 428406005511 citrate-proton symporter; Provisional; Region: PRK15075 428406005512 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406005513 putative substrate translocation pore; other site 428406005514 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 428406005515 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like1; cd05666 428406005516 metal binding site [ion binding]; metal-binding site 428406005517 putative dimer interface [polypeptide binding]; other site 428406005518 amidase; Provisional; Region: PRK07486 428406005519 Amidase; Region: Amidase; pfam01425 428406005520 The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 428406005521 dimerization interface [polypeptide binding]; other site 428406005522 substrate binding pocket [chemical binding]; other site 428406005523 Predicted phosphohydrolases [General function prediction only]; Region: Icc; COG1409 428406005524 Enterobacter aerogenes GpdQ and related proteins, metallophosphatase domain; Region: MPP_GpdQ; cd07402 428406005525 active site 428406005526 metal binding site [ion binding]; metal-binding site 428406005527 hexamer interface [polypeptide binding]; other site 428406005528 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 428406005529 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 428406005530 Walker A/P-loop; other site 428406005531 ATP binding site [chemical binding]; other site 428406005532 Q-loop/lid; other site 428406005533 ABC transporter signature motif; other site 428406005534 Walker B; other site 428406005535 D-loop; other site 428406005536 H-loop/switch region; other site 428406005537 TOBE domain; Region: TOBE_2; pfam08402 428406005538 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 428406005539 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406005540 dimer interface [polypeptide binding]; other site 428406005541 conserved gate region; other site 428406005542 putative PBP binding loops; other site 428406005543 ABC-ATPase subunit interface; other site 428406005544 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 428406005545 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406005546 dimer interface [polypeptide binding]; other site 428406005547 conserved gate region; other site 428406005548 putative PBP binding loops; other site 428406005549 ABC-ATPase subunit interface; other site 428406005550 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 428406005551 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 428406005552 Transcriptional regulators [Transcription]; Region: PurR; COG1609 428406005553 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 428406005554 DNA binding site [nucleotide binding] 428406005555 domain linker motif; other site 428406005556 Ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_GntR_like_2; cd06282 428406005557 putative dimerization interface [polypeptide binding]; other site 428406005558 putative ligand binding site [chemical binding]; other site 428406005559 ergothioneine biosynthesis protein EgtB; Region: egtB_TIGR03440 428406005560 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 428406005561 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 428406005562 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 428406005563 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 428406005564 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 428406005565 active site 428406005566 PilZ domain; Region: PilZ; cl01260 428406005567 DNA polymerase III subunit delta'; Validated; Region: PRK06964 428406005568 DNA polymerase III subunit delta'; Validated; Region: PRK08485 428406005569 thymidylate kinase; Validated; Region: tmk; PRK00698 428406005570 Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor. TMPK represents the rate-limiting step...; Region: TMPK; cd01672 428406005571 TMP-binding site; other site 428406005572 ATP-binding site [chemical binding]; other site 428406005573 YceG-like family; Region: YceG; pfam02618 428406005574 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 428406005575 dimerization interface [polypeptide binding]; other site 428406005576 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 428406005577 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 428406005578 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 428406005579 Uncharacterized conserved protein [Function unknown]; Region: COG3332 428406005580 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 428406005581 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; pfam04116 428406005582 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406005583 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406005584 LysR substrate binding domain; Region: LysR_substrate; pfam03466 428406005585 dimerization interface [polypeptide binding]; other site 428406005586 Acetyltransferase (GNAT) domain; Region: Acetyltransf_5; pfam13444 428406005587 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 428406005588 Coenzyme A binding pocket [chemical binding]; other site 428406005589 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 428406005590 active site 428406005591 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cd00312 428406005592 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 428406005593 substrate binding pocket [chemical binding]; other site 428406005594 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 428406005595 Iron-containing alcohol dehydrogenases-like, involved in the linear alkylbenzenesulfonate (LAS) degradation pathway; Region: Fe-ADH7; cd08192 428406005596 putative active site [active] 428406005597 metal binding site [ion binding]; metal-binding site 428406005598 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 428406005599 hypothetical protein; Provisional; Region: PRK06194 428406005600 classical (c) SDRs; Region: SDR_c; cd05233 428406005601 NAD(P) binding site [chemical binding]; other site 428406005602 active site 428406005603 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 428406005604 Glutathione S-transferase (GST) family, N-terminal domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic...; Region: GST_N_family; cd00570 428406005605 C-terminal domain interface [polypeptide binding]; other site 428406005606 GSH binding site (G-site) [chemical binding]; other site 428406005607 dimer interface [polypeptide binding]; other site 428406005608 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 428406005609 dimer interface [polypeptide binding]; other site 428406005610 N-terminal domain interface [polypeptide binding]; other site 428406005611 substrate binding pocket (H-site) [chemical binding]; other site 428406005612 hypothetical protein; Provisional; Region: PRK06208 428406005613 intersubunit interface [polypeptide binding]; other site 428406005614 active site 428406005615 Zn2+ binding site [ion binding]; other site 428406005616 Putative NADP-dependent oxidoreductases [General function prediction only]; Region: COG2130 428406005617 Prostaglandin dehydrogenases; Region: PGDH; cd05288 428406005618 NAD(P) binding site [chemical binding]; other site 428406005619 substrate binding site [chemical binding]; other site 428406005620 dimer interface [polypeptide binding]; other site 428406005621 Beta-lactamase; Region: Beta-lactamase; pfam00144 428406005622 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 428406005623 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 428406005624 CoenzymeA binding site [chemical binding]; other site 428406005625 subunit interaction site [polypeptide binding]; other site 428406005626 PHB binding site; other site 428406005627 gluconate 5-dehydrogenase; Provisional; Region: PRK08213 428406005628 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 428406005629 NAD(P) binding site [chemical binding]; other site 428406005630 active site 428406005631 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 428406005632 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 428406005633 Putative acyl-CoA dehydrogenases similar to fadE5; Region: ACAD_fadE5; cd01153 428406005634 FAD binding site [chemical binding]; other site 428406005635 substrate binding site [chemical binding]; other site 428406005636 catalytic residues [active] 428406005637 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 428406005638 acetyl-CoA acetyltransferase; Provisional; Region: PRK07108 428406005639 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 428406005640 dimer interface [polypeptide binding]; other site 428406005641 active site 428406005642 Nicotinamidase/pyrazinamidase (PZase). Nicotinamidase, a ubiquitous enzyme in prokaryotes, converts nicotinamide to nicotinic acid (niacin) and ammonia, which in turn can be recycled to make nicotinamide adenine dinucleotide (NAD). The same enzyme is...; Region: nicotinamidase; cd01011 428406005643 Isochorismatase family; Region: Isochorismatase; pfam00857 428406005644 catalytic triad [active] 428406005645 metal binding site [ion binding]; metal-binding site 428406005646 conserved cis-peptide bond; other site 428406005647 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 428406005648 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 428406005649 substrate binding site [chemical binding]; other site 428406005650 oxyanion hole (OAH) forming residues; other site 428406005651 trimer interface [polypeptide binding]; other site 428406005652 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 428406005653 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 428406005654 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 428406005655 lysine transporter; Provisional; Region: PRK10836 428406005656 lysine transporter; Provisional; Region: PRK10836 428406005657 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 428406005658 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 428406005659 Walker A/P-loop; other site 428406005660 ATP binding site [chemical binding]; other site 428406005661 Q-loop/lid; other site 428406005662 ABC transporter signature motif; other site 428406005663 Walker B; other site 428406005664 D-loop; other site 428406005665 H-loop/switch region; other site 428406005666 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 428406005667 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 428406005668 Walker A/P-loop; other site 428406005669 ATP binding site [chemical binding]; other site 428406005670 Q-loop/lid; other site 428406005671 ABC transporter signature motif; other site 428406005672 Walker B; other site 428406005673 D-loop; other site 428406005674 H-loop/switch region; other site 428406005675 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 428406005676 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 428406005677 TM-ABC transporter signature motif; other site 428406005678 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 428406005679 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 428406005680 TM-ABC transporter signature motif; other site 428406005681 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 428406005682 Periplasmic solute-binding domain of active transport proteins; Region: PBP1_SBP_like_3; cd06329 428406005683 putative ligand binding site [chemical binding]; other site 428406005684 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07008 428406005685 Fatty acyl-CoA synthetases similar to LC-FACS from Thermus thermophiles; Region: ttLC_FACS_AlkK_like; cd12119 428406005686 dimer interface [polypeptide binding]; other site 428406005687 acyl-activating enzyme (AAE) consensus motif; other site 428406005688 putative active site [active] 428406005689 AMP binding site [chemical binding]; other site 428406005690 putative CoA binding site [chemical binding]; other site 428406005691 Uncharacterized conserved protein [Function unknown]; Region: COG0397 428406005692 hypothetical protein; Validated; Region: PRK00029 428406005693 methionine sulfoxide reductase B; Provisional; Region: PRK00222 428406005694 SelR domain; Region: SelR; pfam01641 428406005695 intracellular septation protein A; Reviewed; Region: PRK00259 428406005696 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 428406005697 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 428406005698 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 428406005699 Type I periplasmic ligand-binding domain of uncharacterized ABC-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_uncharacterized_transporter; cd06325 428406005700 zinc binding site [ion binding]; other site 428406005701 putative ligand binding site [chemical binding]; other site 428406005702 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 428406005703 Transmembrane subunit (TM) of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which are involved in the uptake of branched-chain amino acids (AAs), as well as TMs of transporters involved in the uptake of...; Region: TM_PBP1_branched-chain-AA_like; cd06574 428406005704 TM-ABC transporter signature motif; other site 428406005705 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: PhnK; COG1101 428406005706 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 428406005707 Walker A/P-loop; other site 428406005708 ATP binding site [chemical binding]; other site 428406005709 Q-loop/lid; other site 428406005710 ABC transporter signature motif; other site 428406005711 Walker B; other site 428406005712 D-loop; other site 428406005713 H-loop/switch region; other site 428406005714 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 428406005715 Phage late control gene D protein (GPD); Region: Phage_GPD; pfam05954 428406005716 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 428406005717 Putative type VI secretion system Rhs element Vgr; Region: T6SS_Vgr; pfam13296 428406005718 Uncharacterized protein conserved in bacteria (DUF2345); Region: DUF2345; pfam10106 428406005719 Predicted membrane protein [Function unknown]; Region: COG4682 428406005720 yiaA/B two helix domain; Region: YiaAB; pfam05360 428406005721 yiaA/B two helix domain; Region: YiaAB; pfam05360 428406005722 Domain of unknown function (DUF4123); Region: DUF4123; pfam13503 428406005723 Protein of unknown function (DUF3304); Region: DUF3304; pfam11745 428406005724 Protein of unknown function (DUF3304); Region: DUF3304; pfam11745 428406005725 Protein of unknown function (DUF3304); Region: DUF3304; pfam11745 428406005726 Protein of unknown function (DUF3304); Region: DUF3304; pfam11745 428406005727 Uncharacterized conserved protein (DUF2235); Region: DUF2235; pfam09994 428406005728 PAAR motif; Region: PAAR_motif; pfam05488 428406005729 Uncharacterized protein conserved in bacteria (DUF2077); Region: DUF2077; pfam09850 428406005730 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 428406005731 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 428406005732 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 428406005733 dimer interface [polypeptide binding]; other site 428406005734 phosphorylation site [posttranslational modification] 428406005735 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406005736 ATP binding site [chemical binding]; other site 428406005737 Mg2+ binding site [ion binding]; other site 428406005738 G-X-G motif; other site 428406005739 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 428406005740 ATP-binding cassette domain of the polyamine transporter; Region: ABC_PotA_N; cd03300 428406005741 Walker A/P-loop; other site 428406005742 ATP binding site [chemical binding]; other site 428406005743 Q-loop/lid; other site 428406005744 ABC transporter signature motif; other site 428406005745 Walker B; other site 428406005746 D-loop; other site 428406005747 H-loop/switch region; other site 428406005748 TOBE domain; Region: TOBE_2; pfam08402 428406005749 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 428406005750 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 428406005751 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406005752 dimer interface [polypeptide binding]; other site 428406005753 conserved gate region; other site 428406005754 putative PBP binding loops; other site 428406005755 ABC-ATPase subunit interface; other site 428406005756 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 428406005757 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406005758 dimer interface [polypeptide binding]; other site 428406005759 conserved gate region; other site 428406005760 putative PBP binding loops; other site 428406005761 ABC-ATPase subunit interface; other site 428406005762 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 428406005763 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 428406005764 NAD(P) binding site [chemical binding]; other site 428406005765 active site 428406005766 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406005767 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406005768 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_3; cd08472 428406005769 putative effector binding pocket; other site 428406005770 putative dimerization interface [polypeptide binding]; other site 428406005771 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 428406005772 Beta-lactamase; Region: Beta-lactamase; pfam00144 428406005773 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 428406005774 PurL subunit of the formylglycinamide ribonucleotide amidotransferase (FGAR-AT), first repeat. FGAR-AT catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to formylglycinamidine ribonucleotide (FGAM), ADP; Region: PurL_repeat1; cd02203 428406005775 dimerization interface [polypeptide binding]; other site 428406005776 ATP binding site [chemical binding]; other site 428406005777 PurL subunit of the formylglycinamide ribonucleotide amidotransferase (FGAR-AT), second repeat. FGAR-AT catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to formylglycinamidine ribonucleotide (FGAM), ADP; Region: PurL_repeat2; cd02204 428406005778 dimerization interface [polypeptide binding]; other site 428406005779 ATP binding site [chemical binding]; other site 428406005780 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 428406005781 putative active site [active] 428406005782 catalytic triad [active] 428406005783 Predicted transcription regulator, contains HTH domain (MarR family) [Transcription]; Region: COG5631 428406005784 Uncharacterized conserved protein [Function unknown]; Region: COG0062 428406005785 putative carbohydrate kinase; Provisional; Region: PRK10565 428406005786 B.subtilis YXKO protein of unknown function and related proteins. Based on the conservation of the ATP binding site, the substrate binding site and the Mg2+binding site and structural homology this group is a member of the ribokinase-like superfamily; Region: YXKO-related; cd01171 428406005787 putative substrate binding site [chemical binding]; other site 428406005788 putative ATP binding site [chemical binding]; other site 428406005789 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 428406005790 Phosphoglucose isomerase (PGI) contains two SIS (Sugar ISomerase) domains. This classification is based on the alignment of the first SIS domain. PGI is a multifunctional enzyme which as an intracellular dimer catalyzes the reversible isomerization of...; Region: SIS_PGI_1; cd05015 428406005791 active site 428406005792 dimer interface [polypeptide binding]; other site 428406005793 Phosphoglucose isomerase (PGI) contains two SIS (Sugar ISomerase) domains. This classification is based on the alignment of the second SIS domain. PGI is a multifunctional enzyme which as an intracellular dimer catalyzes the reversible isomerization of...; Region: SIS_PGI_2; cd05016 428406005794 dimer interface [polypeptide binding]; other site 428406005795 active site 428406005796 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG4181 428406005797 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 428406005798 Walker A/P-loop; other site 428406005799 ATP binding site [chemical binding]; other site 428406005800 Q-loop/lid; other site 428406005801 ABC transporter signature motif; other site 428406005802 Walker B; other site 428406005803 D-loop; other site 428406005804 H-loop/switch region; other site 428406005805 Lysophospholipase L1-like subgroup of SGNH-hydrolases. The best characterized member in this family is TesA, an E. coli periplasmic protein with thioesterase, esterase, arylesterase, protease and lysophospholipase activity; Region: Lysophospholipase_L1_like; cd01822 428406005806 active site 428406005807 catalytic triad [active] 428406005808 oxyanion hole [active] 428406005809 switch loop; other site 428406005810 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 428406005811 The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are...; Region: S26_SPase_I; cd06530 428406005812 Catalytic site [active] 428406005813 The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are...; Region: S26_SPase_I; cd06530 428406005814 SurA N-terminal domain; Region: SurA_N_3; cl07813 428406005815 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 428406005816 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 428406005817 IHF dimer interface [polypeptide binding]; other site 428406005818 IHF - DNA interface [nucleotide binding]; other site 428406005819 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 428406005820 Found in ATP-dependent protease La (LON); Region: LON; smart00464 428406005821 Found in ATP-dependent protease La (LON); Region: LON; smart00464 428406005822 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406005823 Walker A motif; other site 428406005824 ATP binding site [chemical binding]; other site 428406005825 Walker B motif; other site 428406005826 arginine finger; other site 428406005827 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 428406005828 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 428406005829 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 428406005830 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406005831 Walker A motif; other site 428406005832 ATP binding site [chemical binding]; other site 428406005833 Walker B motif; other site 428406005834 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 428406005835 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 428406005836 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 428406005837 oligomer interface [polypeptide binding]; other site 428406005838 active site residues [active] 428406005839 trigger factor; Provisional; Region: tig; PRK01490 428406005840 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 428406005841 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 428406005842 bifunctional tRNA (mnm(5)s(2)U34)-methyltransferase/FAD-dependent cmnm(5)s(2)U34 oxidoreductase; Reviewed; Region: mnmC; PRK01747 428406005843 Uncharacterized conserved protein [Function unknown]; Region: COG4121 428406005844 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406005845 metabolite-proton symporter; Region: 2A0106; TIGR00883 428406005846 putative substrate translocation pore; other site 428406005847 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 428406005848 CoA-transferase family III; Region: CoA_transf_3; pfam02515 428406005849 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 428406005850 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 428406005851 active site 428406005852 DNA-binding transcriptional regulator HcaR; Provisional; Region: PRK09906 428406005853 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406005854 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 428406005855 dimerization interface [polypeptide binding]; other site 428406005856 Heme/copper-type cytochrome/quinol oxidase, subunit 4 [Energy production and conversion]; Region: CyoD; COG3125 428406005857 Ubiquinol oxidase subunit III subfamily. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously...; Region: Ubiquinol_oxidase_III; cd02863 428406005858 Subunit I/III interface [polypeptide binding]; other site 428406005859 Subunit III/IV interface [polypeptide binding]; other site 428406005860 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 428406005861 Ubiquinol oxidase subunit I. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously pumps protons...; Region: Ubiquinol_Oxidase_I; cd01662 428406005862 D-pathway; other site 428406005863 Putative ubiquinol binding site [chemical binding]; other site 428406005864 Low-spin heme (heme b) binding site [chemical binding]; other site 428406005865 Putative water exit pathway; other site 428406005866 Binuclear center (heme o3/CuB) [ion binding]; other site 428406005867 K-pathway; other site 428406005868 Putative proton exit pathway; other site 428406005869 cytochrome o ubiquinol oxidase subunit II; Region: CyoA; TIGR01433 428406005870 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 428406005871 COX Aromatic Rich Motif; Region: COX_ARM; pfam06481 428406005872 metabolite-proton symporter; Region: 2A0106; TIGR00883 428406005873 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406005874 putative substrate translocation pore; other site 428406005875 CsbD-like; Region: CsbD; pfam05532 428406005876 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 428406005877 benzoate transport; Region: 2A0115; TIGR00895 428406005878 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406005879 putative substrate translocation pore; other site 428406005880 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406005881 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406005882 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_1; cd08421 428406005883 putative dimerization interface [polypeptide binding]; other site 428406005884 ApbE family; Region: ApbE; pfam02424 428406005885 FMN-binding domain; Region: FMN_bind; pfam04205 428406005886 Phosphate-selective porin O and P; Region: Porin_O_P; pfam07396 428406005887 Di-haem cytochrome c peroxidase; Region: CCP_MauG; pfam03150 428406005888 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 428406005889 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 428406005890 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 428406005891 HlyD family secretion protein; Region: HlyD_3; pfam13437 428406005892 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 428406005893 active site lid residues [active] 428406005894 substrate binding pocket [chemical binding]; other site 428406005895 catalytic residues [active] 428406005896 substrate-Mg2+ binding site; other site 428406005897 aspartate-rich region 1; other site 428406005898 aspartate-rich region 2; other site 428406005899 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4102 428406005900 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5267 428406005901 osmolarity response regulator; Provisional; Region: ompR; PRK09468 428406005902 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406005903 active site 428406005904 phosphorylation site [posttranslational modification] 428406005905 intermolecular recognition site; other site 428406005906 dimerization interface [polypeptide binding]; other site 428406005907 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 428406005908 DNA binding site [nucleotide binding] 428406005909 osmolarity sensor protein; Provisional; Region: envZ; PRK09467 428406005910 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 428406005911 dimerization interface [polypeptide binding]; other site 428406005912 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406005913 ATP binding site [chemical binding]; other site 428406005914 Mg2+ binding site [ion binding]; other site 428406005915 G-X-G motif; other site 428406005916 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 428406005917 Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic hydroperoxides; Region: PRX_Typ2cys; cd03015 428406005918 dimer interface [polypeptide binding]; other site 428406005919 decamer (pentamer of dimers) interface [polypeptide binding]; other site 428406005920 catalytic triad [active] 428406005921 peroxidatic and resolving cysteines [active] 428406005922 alkylhydroperoxidase, AhpD family; Region: ahpD; TIGR00777 428406005923 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 428406005924 MECDP_synthase (2-C-methyl-D-erythritol-2,4-cyclodiphosphate synthase), encoded by the ispF gene, catalyzes the formation of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MEC) in the non-mevalonate deoxyxylulose (DOXP) pathway for isoprenoid biosynthesis; Region: MECDP_synthase; cd00554 428406005925 homotrimer interaction site [polypeptide binding]; other site 428406005926 zinc binding site [ion binding]; other site 428406005927 CDP-binding sites; other site 428406005928 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 428406005929 substrate binding site; other site 428406005930 dimer interface; other site 428406005931 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 428406005932 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 428406005933 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 428406005934 ATP binding site [chemical binding]; other site 428406005935 putative Mg++ binding site [ion binding]; other site 428406005936 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 428406005937 nucleotide binding region [chemical binding]; other site 428406005938 ATP-binding site [chemical binding]; other site 428406005939 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 428406005940 acetylornithine deacetylase; Provisional; Region: PRK07522 428406005941 M20 Peptidase acetylornithine deacetylase; Region: M20_ArgE; cd03894 428406005942 metal binding site [ion binding]; metal-binding site 428406005943 putative dimer interface [polypeptide binding]; other site 428406005944 Domain of unknown function (DUF4072); Region: DUF4072; pfam13284 428406005945 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 428406005946 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 428406005947 motif II; other site 428406005948 Protein of unknown function (DUF1016); Region: DUF1016; pfam06250 428406005949 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 428406005950 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 428406005951 cystathionine beta-lyase; Provisional; Region: PRK07050 428406005952 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 428406005953 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 428406005954 catalytic residue [active] 428406005955 beta-ketothiolase; Provisional; Region: PRK09051 428406005956 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 428406005957 dimer interface [polypeptide binding]; other site 428406005958 active site 428406005959 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 428406005960 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 428406005961 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 428406005962 FeS/SAM binding site; other site 428406005963 tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; Region: COG0042 428406005964 Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also...; Region: DUS_like_FMN; cd02801 428406005965 FMN binding site [chemical binding]; other site 428406005966 active site 428406005967 catalytic residues [active] 428406005968 substrate binding site [chemical binding]; other site 428406005969 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5394 428406005970 PHB/PHA accumulation regulator DNA-binding domain; Region: PHB_acc_N; pfam07879 428406005971 PHB accumulation regulatory domain; Region: PHB_acc; pfam05233 428406005972 acetyacetyl-CoA reductase; Provisional; Region: PRK12938 428406005973 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 428406005974 NAD(P) binding site [chemical binding]; other site 428406005975 homotetramer interface [polypeptide binding]; other site 428406005976 homodimer interface [polypeptide binding]; other site 428406005977 active site 428406005978 putative acyltransferase; Provisional; Region: PRK05790 428406005979 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 428406005980 dimer interface [polypeptide binding]; other site 428406005981 active site 428406005982 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 428406005983 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 428406005984 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 428406005985 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 428406005986 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 428406005987 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cd00165 428406005988 RNA binding surface [nucleotide binding]; other site 428406005989 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 428406005990 active site 428406005991 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 428406005992 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 428406005993 DEAD/DEAH box helicase; Region: DEAD; pfam00270 428406005994 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 428406005995 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 428406005996 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 428406005997 Likely ribonuclease with RNase H fold; Region: YqgFc; smart00732 428406005998 S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression; Region: S1_Tex; cd05685 428406005999 RNA binding site [nucleotide binding]; other site 428406006000 K+ transporter [Inorganic ion transport and metabolism]; Region: Kup; COG3158 428406006001 potassium uptake protein; Region: kup; TIGR00794 428406006002 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK05286 428406006003 Dihydroorotate dehydrogenase (DHOD) class 2. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires...; Region: DHOD_2_like; cd04738 428406006004 quinone interaction residues [chemical binding]; other site 428406006005 active site 428406006006 catalytic residues [active] 428406006007 FMN binding site [chemical binding]; other site 428406006008 substrate binding site [chemical binding]; other site 428406006009 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_Hydrolase_4; cd04511 428406006010 nudix motif; other site 428406006011 leucyl/phenylalanyl-tRNA--protein transferase; Reviewed; Region: aat; PRK00301 428406006012 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 428406006013 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 428406006014 Arginine-tRNA-protein transferase, C terminus; Region: ATE_C; pfam04377 428406006015 Predicted membrane protein [Function unknown]; Region: XynA; COG2314 428406006016 Uncharacterized conserved protein containing a ferredoxin-like domain [Energy production and conversion]; Region: COG1139 428406006017 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 428406006018 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 428406006019 Domain of unknown function (DUF3390); Region: DUF3390; pfam11870 428406006020 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 428406006021 Cysteine-rich domain; Region: CCG; pfam02754 428406006022 Cysteine-rich domain; Region: CCG; pfam02754 428406006023 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 428406006024 Transcriptional regulator [Transcription]; Region: IclR; COG1414 428406006025 Bacterial transcriptional regulator; Region: IclR; pfam01614 428406006026 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 428406006027 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 428406006028 Nitroreductase family. Members of this family utilize FMN as a cofactor and catalyze reduction of a variety of nitroaromatic compounds, including nitrofurans, nitrobenzens, nitrophenol, nitrobenzoate and quinones by using either NADH or NADPH as a source...; Region: Nitroreductase; cd02136 428406006029 putative FMN binding site [chemical binding]; other site 428406006030 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 428406006031 active site 428406006032 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 428406006033 EamA-like transporter family; Region: EamA; pfam00892 428406006034 EamA-like transporter family; Region: EamA; pfam00892 428406006035 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 428406006036 Histone deacetylase class IV also known as histone deacetylase 11; Region: HDAC_classIV; cd09993 428406006037 putative active site [active] 428406006038 Zn binding site [ion binding]; other site 428406006039 Phasin protein; Region: Phasin_2; pfam09361 428406006040 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 428406006041 E3 interaction surface; other site 428406006042 lipoyl attachment site [posttranslational modification]; other site 428406006043 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 428406006044 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 428406006045 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 428406006046 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 428406006047 proteasome_protease_HslV. This group contains the eukaryotic proteosome alpha and beta subunits and the prokaryotic protease hslV subunit. Proteasomes are large multimeric self-compartmentalizing proteases, involved in the clearance of misfolded proteins; Region: proteasome_protease_HslV; cd01906 428406006048 active site 428406006049 dihydrolipoamide acetyltransferase; Reviewed; Region: PRK11855 428406006050 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 428406006051 E3 interaction surface; other site 428406006052 lipoyl attachment site [posttranslational modification]; other site 428406006053 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 428406006054 E3 interaction surface; other site 428406006055 lipoyl attachment site [posttranslational modification]; other site 428406006056 e3 binding domain; Region: E3_binding; pfam02817 428406006057 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 428406006058 pyruvate dehydrogenase subunit E1; Reviewed; Region: aceE; PRK09405 428406006059 Thiamine pyrophosphate (TPP) family, E1 of E. coli PDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the Escherichia coli pyruvate dehydrogenase multienzyme complex (PDC). PDC catalyzes the oxidative...; Region: TPP_E1_EcPDC_like; cd02017 428406006060 dimer interface [polypeptide binding]; other site 428406006061 TPP-binding site [chemical binding]; other site 428406006062 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 428406006063 PAS domain S-box; Region: sensory_box; TIGR00229 428406006064 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 428406006065 putative active site [active] 428406006066 heme pocket [chemical binding]; other site 428406006067 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 428406006068 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 428406006069 dimer interface [polypeptide binding]; other site 428406006070 phosphorylation site [posttranslational modification] 428406006071 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406006072 ATP binding site [chemical binding]; other site 428406006073 Mg2+ binding site [ion binding]; other site 428406006074 G-X-G motif; other site 428406006075 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 428406006076 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406006077 active site 428406006078 phosphorylation site [posttranslational modification] 428406006079 intermolecular recognition site; other site 428406006080 dimerization interface [polypeptide binding]; other site 428406006081 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 428406006082 DNA binding residues [nucleotide binding] 428406006083 dimerization interface [polypeptide binding]; other site 428406006084 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14189 428406006085 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 428406006086 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 428406006087 homodimer interface [polypeptide binding]; other site 428406006088 NADP binding site [chemical binding]; other site 428406006089 substrate binding site [chemical binding]; other site 428406006090 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 428406006091 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 428406006092 active site 428406006093 Zn binding site [ion binding]; other site 428406006094 Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: ExoIII-like_AP-endo; cd09086 428406006095 putative catalytic site [active] 428406006096 putative phosphate binding site [ion binding]; other site 428406006097 active site 428406006098 metal binding site A [ion binding]; metal-binding site 428406006099 DNA binding site [nucleotide binding] 428406006100 putative AP binding site [nucleotide binding]; other site 428406006101 putative metal binding site B [ion binding]; other site 428406006102 homoprotocatechuate degradation operon regulator, HpaR; Region: HpaR; TIGR02337 428406006103 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 428406006104 HpcH/HpaI aldolase/citrate lyase family; Region: HpcH_HpaI; cl17231 428406006105 2-oxo-hepta-3-ene-1,7-dioic acid hydratase; Region: HpaH; TIGR02312 428406006106 5-carboxymethyl-2-hydroxymuconate isomerase (CHMI) is a trimeric enzyme catalyzing the isomerization of the unsaturated ketone 5-(carboxymethyl)-2-hydroxymuconate to 5-(carboxymethyl)-2-oxo-3-hexene-1,6-dionate. This is one step in the...; Region: CHMI; cd00580 428406006107 putative substrate binding pocket [chemical binding]; other site 428406006108 trimer interface [polypeptide binding]; other site 428406006109 The Class III extradiol dioxygenase, homoprotocatechuate 2,3-dioxygenase, catalyzes the key ring cleavage step in the metabolism of homoprotocatechuate; Region: HPCD; cd07370 428406006110 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 428406006111 putative active site [active] 428406006112 putative metal binding site [ion binding]; other site 428406006113 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase; Region: HpaE; TIGR02299 428406006114 Human aldehyde dehydrogenase family 8 member A1-like; Region: ALDH_F8_HMSADH; cd07093 428406006115 NAD binding site [chemical binding]; other site 428406006116 catalytic residues [active] 428406006117 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase, C-terminal subunit; Region: HpaG-C-term; TIGR02303 428406006118 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 428406006119 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase, C-terminal subunit; Region: HpaG-C-term; TIGR02303 428406006120 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 428406006121 Protein of unknown function (DUF1488); Region: DUF1488; pfam07369 428406006122 amino acid transporter; Region: 2A0306; TIGR00909 428406006123 C-terminus of AA_permease; Region: AA_permease_C; pfam13906 428406006124 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 428406006125 active site 428406006126 DNA polymerase IV; Validated; Region: PRK02406 428406006127 DNA binding site [nucleotide binding] 428406006128 aldose 1-epimerase superfamily; Region: Aldose_epim; cl14648 428406006129 active site 428406006130 catalytic residues [active] 428406006131 Uncharacterized homolog of gamma-carboxymuconolactone decarboxylase subunit [Function unknown]; Region: COG0599 428406006132 Cupin; Region: Cupin_6; pfam12852 428406006133 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 428406006134 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 428406006135 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 428406006136 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Region: HTH_MlrA-like_sg2; cd04765 428406006137 DNA binding residues [nucleotide binding] 428406006138 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 428406006139 IHF dimer interface [polypeptide binding]; other site 428406006140 IHF - DNA interface [nucleotide binding]; other site 428406006141 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 428406006142 tRNA-binding-domain-containing prokaryotic phenylalanly tRNA synthetase (PheRS) beta chain. PheRS aminoacylate phenylalanine transfer RNAs (tRNAphe). PheRSs belong structurally to class II aminoacyl tRNA synthetases (aaRSs) but, as they aminoacylate...; Region: tRNA_bind_bactPheRS; cd02796 428406006143 putative tRNA-binding site [nucleotide binding]; other site 428406006144 B3/4 domain; Region: B3_4; pfam03483 428406006145 tRNA synthetase B5 domain; Region: B5; smart00874 428406006146 Phenylalanyl-tRNA synthetase (PheRS) beta chain core domain. PheRS belongs to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure. While class II aaRSs generally aminoacylate the 3'-OH ribose of the appropriate tRNA, PheRS is an...; Region: PheRS_beta_core; cd00769 428406006147 dimer interface [polypeptide binding]; other site 428406006148 motif 1; other site 428406006149 motif 3; other site 428406006150 motif 2; other site 428406006151 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; smart00896 428406006152 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 428406006153 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 428406006154 Phenylalanyl-tRNA synthetase (PheRS) alpha chain catalytic core domain. PheRS belongs to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs. This domain is primarily responsible...; Region: PheRS_alpha_core; cd00496 428406006155 dimer interface [polypeptide binding]; other site 428406006156 motif 1; other site 428406006157 active site 428406006158 motif 2; other site 428406006159 motif 3; other site 428406006160 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 428406006161 23S rRNA binding site [nucleotide binding]; other site 428406006162 L21 binding site [polypeptide binding]; other site 428406006163 L13 binding site [polypeptide binding]; other site 428406006164 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 428406006165 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 428406006166 TGS _ThrRS_N: ThrRS (threonyl-tRNA Synthetase) is a class II tRNA synthetase that couples threonine to its cognate tRNA. In addition to its catalytic and anticodon-binding domains, ThrRS has an N-terminal TGS domain, named after the ThrRS, GTPase, and...; Region: TGS_ThrRS_N; cd01667 428406006167 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 428406006168 Threonyl-tRNA synthetase (ThrRS) class II core catalytic domain. ThrRS is a homodimer. It is responsible for the attachment of threonine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: ThrRS_core; cd00771 428406006169 active site 428406006170 dimer interface [polypeptide binding]; other site 428406006171 motif 1; other site 428406006172 motif 2; other site 428406006173 motif 3; other site 428406006174 ThrRS Threonyl-anticodon binding domain. ThrRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is...; Region: ThrRS_anticodon; cd00860 428406006175 anticodon binding site; other site 428406006176 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 428406006177 HD domain; Region: HD_4; pfam13328 428406006178 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 428406006179 synthetase active site [active] 428406006180 NTP binding site [chemical binding]; other site 428406006181 metal binding site [ion binding]; metal-binding site 428406006182 TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named after...; Region: TGS_RelA_SpoT; cd01668 428406006183 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 428406006184 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence...; Region: YjgF_YER057c_UK114_like_2; cd06150 428406006185 homotrimer interaction site [polypeptide binding]; other site 428406006186 putative active site [active] 428406006187 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 428406006188 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 428406006189 3-hydroxybutyrate dehydrogenase; Provisional; Region: PRK12429 428406006190 d-3-hydroxybutyrate dehydrogenase (HBDH), classical (c) SDRs; Region: HBDH_SDR_c; cd08940 428406006191 NAD binding site [chemical binding]; other site 428406006192 homotetramer interface [polypeptide binding]; other site 428406006193 homodimer interface [polypeptide binding]; other site 428406006194 substrate binding site [chemical binding]; other site 428406006195 active site 428406006196 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 428406006197 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 428406006198 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 428406006199 PAS domain; Region: PAS_9; pfam13426 428406006200 putative active site [active] 428406006201 heme pocket [chemical binding]; other site 428406006202 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 428406006203 DNA binding residues [nucleotide binding] 428406006204 dimerization interface [polypeptide binding]; other site 428406006205 short chain dehydrogenase; Provisional; Region: PRK06949 428406006206 classical (c) SDRs; Region: SDR_c; cd05233 428406006207 NAD(P) binding site [chemical binding]; other site 428406006208 active site 428406006209 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 428406006210 hydroxyglutarate oxidase; Provisional; Region: PRK11728 428406006211 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 428406006212 Ferredoxin-like protein [Energy production and conversion]; Region: FixX; COG2440 428406006213 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 428406006214 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 428406006215 Tetramer interface [polypeptide binding]; other site 428406006216 active site 428406006217 FMN-binding site [chemical binding]; other site 428406006218 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 428406006219 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 428406006220 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406006221 putative substrate translocation pore; other site 428406006222 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 428406006223 putative acyl-acceptor binding pocket; other site 428406006224 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair_12; cd04625 428406006225 FOG: CBS domain [General function prediction only]; Region: COG0517 428406006226 O-acetylhomoserine aminocarboxypropyltransferase; Validated; Region: PRK08134 428406006227 CGS_like: Cystathionine gamma-synthase is a PLP dependent enzyme and catalyzes the committed step of methionine biosynthesis. This pathway is unique to microorganisms and plants, rendering the enzyme an attractive target for the development of...; Region: CGS_like; cd00614 428406006228 homodimer interface [polypeptide binding]; other site 428406006229 substrate-cofactor binding pocket; other site 428406006230 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406006231 catalytic residue [active] 428406006232 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 428406006233 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 428406006234 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 428406006235 Protein of unknown function (DUF962); Region: DUF962; cl01879 428406006236 Virulence factor BrkB; Region: Virul_fac_BrkB; cl07918 428406006237 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 428406006238 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 428406006239 Predicted membrane protein [Function unknown]; Region: COG3308 428406006240 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 428406006241 FAD binding domain; Region: FAD_binding_4; pfam01565 428406006242 Uncharacterized protein conserved in bacteria (DUF2077); Region: DUF2077; cl01370 428406006243 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 428406006244 ligand binding site [chemical binding]; other site 428406006245 type VI secretion protein IcmF; Region: VI_IcmF; TIGR03348 428406006246 Intracellular multiplication and human macrophage-killing; Region: IcmF-related; pfam06761 428406006247 Protein of unknown function (DUF1215); Region: DUF1215; pfam06744 428406006248 hypothetical protein; Provisional; Region: PRK08126 428406006249 Uncharacterized protein conserved in bacteria (DUF2077); Region: DUF2077; pfam09850 428406006250 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 428406006251 ligand binding site [chemical binding]; other site 428406006252 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3522 428406006253 Bacterial protein of unknown function (DUF876); Region: DUF876; pfam05936 428406006254 type VI secretion lipoprotein, VC_A0113 family; Region: VI_chp_3; TIGR03352 428406006255 PAAR motif; Region: PAAR_motif; pfam05488 428406006256 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 428406006257 Phage late control gene D protein (GPD); Region: Phage_GPD; pfam05954 428406006258 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 428406006259 Putative type VI secretion system Rhs element Vgr; Region: T6SS_Vgr; pfam13296 428406006260 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4253 428406006261 Protein of unknown function (DUF796); Region: DUF796; pfam05638 428406006262 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3517 428406006263 Protein of unknown function (DUF877); Region: DUF877; pfam05943 428406006264 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3516 428406006265 type VI secretion ATPase, ClpV1 family; Region: VI_ClpV1; TIGR03345 428406006266 Clp amino terminal domain; Region: Clp_N; pfam02861 428406006267 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406006268 Walker A motif; other site 428406006269 ATP binding site [chemical binding]; other site 428406006270 Walker B motif; other site 428406006271 arginine finger; other site 428406006272 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406006273 Walker A motif; other site 428406006274 ATP binding site [chemical binding]; other site 428406006275 Walker B motif; other site 428406006276 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 428406006277 Protein of avirulence locus involved in temperature-dependent protein secretion [General function prediction only]; Region: ImpE; COG4455 428406006278 ImpE protein; Region: ImpE; pfam07024 428406006279 Protein of unknown function (DUF3274); Region: DUF3274; pfam11678 428406006280 Gene 25-like lysozyme; Region: GPW_gp25; cl01403 428406006281 Type VI protein secretion system component VasA [Intracellular trafficking, secretion, and vesicular transport]; Region: COG3519 428406006282 Bacterial protein of unknown function (DUF879); Region: DUF879; pfam05947 428406006283 Protein of unknown function (DUF1305); Region: DUF1305; pfam06996 428406006284 type VI secretion-associated protein, ImpA family; Region: VI_chp_8; TIGR03363 428406006285 ImpA-related N-terminal; Region: ImpA-rel_N; pfam06812 428406006286 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 428406006287 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 428406006288 putative DNA binding site [nucleotide binding]; other site 428406006289 putative Zn2+ binding site [ion binding]; other site 428406006290 AsnC family; Region: AsnC_trans_reg; pfam01037 428406006291 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 428406006292 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 428406006293 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 428406006294 catalytic residue [active] 428406006295 Putative phosphatase (DUF442); Region: DUF442; cl17385 428406006296 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 428406006297 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 428406006298 putative DNA binding site [nucleotide binding]; other site 428406006299 putative Zn2+ binding site [ion binding]; other site 428406006300 AsnC family; Region: AsnC_trans_reg; pfam01037 428406006301 1-aminocyclopropane-1-carboxylate deaminase [Amino acid transport and metabolism]; Region: Acd; COG2515 428406006302 Aminocyclopropane-1-carboxylate deaminase (ACCD): Pyridoxal phosphate (PLP)-dependent enzyme which catalyzes the conversion of 1-aminocyclopropane-L-carboxylate (ACC), a precursor of the plant hormone ethylene, to alpha-ketobutyrate and ammonia; Region: ACCD; cd06449 428406006303 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406006304 catalytic residue [active] 428406006305 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 428406006306 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 428406006307 active site 428406006308 catalytic tetrad [active] 428406006309 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 428406006310 Old yellow enzyme (OYE)-related FMN binding domain, group 2. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as...; Region: OYE_like_2_FMN; cd04733 428406006311 putative active site [active] 428406006312 putative FMN binding site [chemical binding]; other site 428406006313 putative substrate binding site [chemical binding]; other site 428406006314 putative catalytic residue [active] 428406006315 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 428406006316 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 428406006317 DNA binding residues [nucleotide binding] 428406006318 Lysine efflux permease [General function prediction only]; Region: COG1279 428406006319 chromosome replication initiation inhibitor protein; Validated; Region: PRK03635 428406006320 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406006321 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 428406006322 dimerization interface [polypeptide binding]; other site 428406006323 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 428406006324 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 428406006325 dimerization interface [polypeptide binding]; other site 428406006326 putative DNA binding site [nucleotide binding]; other site 428406006327 putative Zn2+ binding site [ion binding]; other site 428406006328 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 428406006329 Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP_PGM_like; cd07067 428406006330 catalytic core [active] 428406006331 Putative hemolysin [General function prediction only]; Region: COG3176 428406006332 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 428406006333 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 428406006334 polyphosphate kinase; Provisional; Region: PRK05443 428406006335 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 428406006336 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 428406006337 Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C1_like; cd09165 428406006338 putative domain interface [polypeptide binding]; other site 428406006339 putative active site [active] 428406006340 catalytic site [active] 428406006341 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 428406006342 putative domain interface [polypeptide binding]; other site 428406006343 putative active site [active] 428406006344 catalytic site [active] 428406006345 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 428406006346 PAS domain; Region: PAS; smart00091 428406006347 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 428406006348 dimer interface [polypeptide binding]; other site 428406006349 phosphorylation site [posttranslational modification] 428406006350 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406006351 ATP binding site [chemical binding]; other site 428406006352 Mg2+ binding site [ion binding]; other site 428406006353 G-X-G motif; other site 428406006354 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 428406006355 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406006356 active site 428406006357 phosphorylation site [posttranslational modification] 428406006358 intermolecular recognition site; other site 428406006359 dimerization interface [polypeptide binding]; other site 428406006360 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 428406006361 DNA binding site [nucleotide binding] 428406006362 transcriptional regulator PhoU; Provisional; Region: PRK11115 428406006363 PhoU domain; Region: PhoU; pfam01895 428406006364 PhoU domain; Region: PhoU; pfam01895 428406006365 phosphate transporter ATP-binding protein; Provisional; Region: pstB; PRK10744 428406006366 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 428406006367 Walker A/P-loop; other site 428406006368 ATP binding site [chemical binding]; other site 428406006369 Q-loop/lid; other site 428406006370 ABC transporter signature motif; other site 428406006371 Walker B; other site 428406006372 D-loop; other site 428406006373 H-loop/switch region; other site 428406006374 phosphate transporter permease subunit PtsA; Provisional; Region: pstA; PRK11268 428406006375 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406006376 dimer interface [polypeptide binding]; other site 428406006377 conserved gate region; other site 428406006378 putative PBP binding loops; other site 428406006379 ABC-ATPase subunit interface; other site 428406006380 phosphate transporter permease subunit PstC; Provisional; Region: pstC; PRK11275 428406006381 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406006382 dimer interface [polypeptide binding]; other site 428406006383 conserved gate region; other site 428406006384 putative PBP binding loops; other site 428406006385 ABC-ATPase subunit interface; other site 428406006386 PBP superfamily domain; Region: PBP_like_2; cl17296 428406006387 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 428406006388 GlmM is a bacterial phosphoglucosamine mutase (PNGM) that belongs to the alpha-D-phosphohexomutase superfamily. It is required for the interconversion of glucosamine-6-phosphate and glucosamine-1-phosphate in the biosynthetic pathway of...; Region: GlmM; cd05802 428406006389 active site 428406006390 substrate binding site [chemical binding]; other site 428406006391 metal binding site [ion binding]; metal-binding site 428406006392 dihydropteroate synthase; Region: DHPS; TIGR01496 428406006393 DHPS subgroup of Pterin binding enzymes. DHPS (dihydropteroate synthase), a functional homodimer, catalyzes the condensation of p-aminobenzoic acid (pABA) in the de novo biosynthesis of folate, which is an essential cofactor in both nucleic acid and...; Region: DHPS; cd00739 428406006394 substrate binding pocket [chemical binding]; other site 428406006395 dimer interface [polypeptide binding]; other site 428406006396 inhibitor binding site; inhibition site 428406006397 ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]; Region: HflB; COG0465 428406006398 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406006399 Walker A motif; other site 428406006400 ATP binding site [chemical binding]; other site 428406006401 Walker B motif; other site 428406006402 arginine finger; other site 428406006403 Peptidase family M41; Region: Peptidase_M41; pfam01434 428406006404 FtsJ-like methyltransferase; Region: FtsJ; cl17430 428406006405 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 428406006406 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]; Region: COG1534 428406006407 Domain of unknown function (DUF4149); Region: DUF4149; pfam13664 428406006408 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 428406006409 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 428406006410 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 428406006411 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 428406006412 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 428406006413 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 428406006414 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 428406006415 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 428406006416 ATP-grasp domain; Region: ATP-grasp_4; cl17255 428406006417 Methylglyoxal synthase-like domain from type II glutamine-dependent carbamoyl phosphate synthetase (CSP). CSP, a CarA and CarB heterodimer, catalyzes the production of carbamoyl phosphate which is subsequently employed in the metabolic pathways...; Region: MGS_CPS_II; cd01424 428406006418 IMP binding site; other site 428406006419 dimer interface [polypeptide binding]; other site 428406006420 interdomain contacts; other site 428406006421 partial ornithine binding site; other site 428406006422 leucine export protein LeuE; Provisional; Region: PRK10958 428406006423 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 428406006424 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; smart01097 428406006425 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 428406006426 catalytic site [active] 428406006427 subunit interface [polypeptide binding]; other site 428406006428 propionyl-CoA synthetase; Provisional; Region: prpE; PRK10524 428406006429 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 428406006430 acyl-activating enzyme (AAE) consensus motif; other site 428406006431 AMP binding site [chemical binding]; other site 428406006432 active site 428406006433 CoA binding site [chemical binding]; other site 428406006434 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 428406006435 N-acetyl-D-glucosamine binding site [chemical binding]; other site 428406006436 catalytic residue [active] 428406006437 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 428406006438 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 428406006439 hydroxyacylglutathione hydrolase; Region: GSH_gloB; TIGR03413 428406006440 Methyltransferase domain; Region: Methyltransf_11; pfam08241 428406006441 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 428406006442 RNA/DNA hybrid binding site [nucleotide binding]; other site 428406006443 active site 428406006444 microbial_RNases. Ribonucleases (RNAses) cleave phosphodiester bonds in RNA and are essential for both non-specific RNA degradation and for numerous forms of RNA processing. The alignment contains fungal RNases (U2, T1, F1, Th, Pb, N1, and Ms) and...; Region: microbial_RNases; cl00212 428406006445 active site 428406006446 Endolysins and autolysins are found in viruses and bacteria, respectively. The ds DNA phages of eubacteria use endolysins or muralytic enzymes in conjunction with hollin, a small membrane protein, to degrade the peptidoglycan found in bacterial cell...; Region: endolysin_autolysin; cd00737 428406006447 catalytic residues [active] 428406006448 Protein of unknown function (DUF2589); Region: DUF2589; pfam11655 428406006449 Protein of unknown function (DUF2589); Region: DUF2589; pfam11655 428406006450 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 428406006451 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 428406006452 DNA binding residues [nucleotide binding] 428406006453 dimerization interface [polypeptide binding]; other site 428406006454 Protein of unknown function (DUF1488); Region: DUF1488; pfam07369 428406006455 SpoVR family protein; Provisional; Region: PRK11767 428406006456 Uncharacterized conserved protein [Function unknown]; Region: SpoVR; COG2719 428406006457 hypothetical protein; Provisional; Region: PRK05325 428406006458 PrkA family serine protein kinase; Provisional; Region: PRK15455 428406006459 PrkA serine protein kinase C-terminal domain; Region: PrkA; pfam06798 428406006460 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406006461 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406006462 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 428406006463 dimerization interface [polypeptide binding]; other site 428406006464 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 428406006465 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 428406006466 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 428406006467 Carbon monoxide dehydrogenase subunit G (CoxG); Region: CoxG; cd05018 428406006468 putative hydrophobic ligand binding site [chemical binding]; other site 428406006469 Aerobic-type carbon monoxide dehydrogenase, middle subunit CoxM/CutM homologs [Energy production and conversion]; Region: CoxM; COG1319 428406006470 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; smart01092 428406006471 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 428406006472 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 428406006473 catalytic loop [active] 428406006474 iron binding site [ion binding]; other site 428406006475 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 428406006476 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 428406006477 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 428406006478 Bacterial Bile acid CoA ligases and similar proteins; Region: BACL_like; cd05929 428406006479 acyl-activating enzyme (AAE) consensus motif; other site 428406006480 acyl-activating enzyme (AAE) consensus motif; other site 428406006481 putative AMP binding site [chemical binding]; other site 428406006482 putative active site [active] 428406006483 putative CoA binding site [chemical binding]; other site 428406006484 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 428406006485 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 428406006486 substrate binding site [chemical binding]; other site 428406006487 oxyanion hole (OAH) forming residues; other site 428406006488 trimer interface [polypeptide binding]; other site 428406006489 DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins; Region: DNA_pol_III_epsilon_Ecoli_like; cd06131 428406006490 active site 428406006491 catalytic site [active] 428406006492 substrate binding site [chemical binding]; other site 428406006493 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 428406006494 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 428406006495 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 428406006496 putative active site [active] 428406006497 putative substrate binding site [chemical binding]; other site 428406006498 putative cosubstrate binding site; other site 428406006499 catalytic site [active] 428406006500 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cl00447 428406006501 nudix motif; other site 428406006502 Aspartyl/asparaginyl beta-hydroxylase and related dioxygenases [Posttranslational modification, protein turnover, chaperones]; Region: COG3555 428406006503 The SYLF domain (also called DUF500), a novel lipid-binding module; Region: SYLF; cd11524 428406006504 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406006505 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406006506 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 428406006507 dimerization interface [polypeptide binding]; other site 428406006508 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 428406006509 FAD-NAD(P)-binding; Region: NAD_binding_9; pfam13454 428406006510 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 428406006511 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406006512 dimer interface [polypeptide binding]; other site 428406006513 conserved gate region; other site 428406006514 putative PBP binding loops; other site 428406006515 ABC-ATPase subunit interface; other site 428406006516 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 428406006517 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406006518 dimer interface [polypeptide binding]; other site 428406006519 conserved gate region; other site 428406006520 putative PBP binding loops; other site 428406006521 ABC-ATPase subunit interface; other site 428406006522 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 428406006523 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 428406006524 Walker A/P-loop; other site 428406006525 ATP binding site [chemical binding]; other site 428406006526 Q-loop/lid; other site 428406006527 ABC transporter signature motif; other site 428406006528 Walker B; other site 428406006529 D-loop; other site 428406006530 H-loop/switch region; other site 428406006531 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 428406006532 dipeptide transporter ATP-binding subunit; Provisional; Region: dppF; PRK11308 428406006533 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 428406006534 Walker A/P-loop; other site 428406006535 ATP binding site [chemical binding]; other site 428406006536 Q-loop/lid; other site 428406006537 ABC transporter signature motif; other site 428406006538 Walker B; other site 428406006539 D-loop; other site 428406006540 H-loop/switch region; other site 428406006541 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 428406006542 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 428406006543 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_2; cd08498 428406006544 Acyl-CoA thioester hydrolase/BAAT N-terminal region; Region: Bile_Hydr_Trans; pfam04775 428406006545 BAAT / Acyl-CoA thioester hydrolase C terminal; Region: BAAT_C; pfam08840 428406006546 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4950; cl17731 428406006547 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 428406006548 uncharacterized peroxidase-related enzyme; Region: peroxid_rel; TIGR01926 428406006549 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 428406006550 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 428406006551 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 428406006552 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 428406006553 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 428406006554 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 428406006555 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 428406006556 catalytic loop [active] 428406006557 iron binding site [ion binding]; other site 428406006558 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 428406006559 Predicted acyl esterases [General function prediction only]; Region: COG2936 428406006560 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 428406006561 X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain; Region: PepX_C; cl08482 428406006562 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 428406006563 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 428406006564 dimerization interface [polypeptide binding]; other site 428406006565 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 428406006566 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 428406006567 dimer interface [polypeptide binding]; other site 428406006568 putative CheW interface [polypeptide binding]; other site 428406006569 Protein of unknown function (DUF4239); Region: DUF4239; pfam14023 428406006570 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u4; cd11480 428406006571 probable sodium:solute symporter, VC_2705 subfamily; Region: Na_symport_lg; TIGR03648 428406006572 acetyl-CoA synthetase; Provisional; Region: PRK00174 428406006573 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 428406006574 active site 428406006575 CoA binding site [chemical binding]; other site 428406006576 acyl-activating enzyme (AAE) consensus motif; other site 428406006577 AMP binding site [chemical binding]; other site 428406006578 acetate binding site [chemical binding]; other site 428406006579 EamA-like transporter family; Region: EamA; pfam00892 428406006580 hypothetical protein; Provisional; Region: PRK05208 428406006581 Fumarate hydratase (Fumerase); Region: Fumerase; pfam05681 428406006582 Fumarase C-terminus; Region: Fumerase_C; pfam05683 428406006583 glutamate racemase; Provisional; Region: PRK00865 428406006584 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 428406006585 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 428406006586 Cupin domain; Region: Cupin_2; cl17218 428406006587 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK08270 428406006588 ATP cone domain; Region: ATP-cone; pfam03477 428406006589 Class III ribonucleotide reductase; Region: RNR_III; cd01675 428406006590 effector binding site; other site 428406006591 active site 428406006592 Zn binding site [ion binding]; other site 428406006593 Anaerobic ribonucleoside-triphosphate reductase; Region: NRDD; pfam13597 428406006594 anaerobic ribonucleoside-triphosphate reductase activating protein; Region: NrdG2; TIGR02495 428406006595 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 428406006596 FeS/SAM binding site; other site 428406006597 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 428406006598 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 428406006599 ligand binding site [chemical binding]; other site 428406006600 flexible hinge region; other site 428406006601 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 428406006602 putative switch regulator; other site 428406006603 non-specific DNA interactions [nucleotide binding]; other site 428406006604 DNA binding site [nucleotide binding] 428406006605 sequence specific DNA binding site [nucleotide binding]; other site 428406006606 putative cAMP binding site [chemical binding]; other site 428406006607 Uncharacterized conserved protein [Function unknown]; Region: COG4273 428406006608 SCP-2 sterol transfer family; Region: SCP2; cl01225 428406006609 putative protease; Provisional; Region: PRK15447 428406006610 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 428406006611 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 428406006612 Peptidase family U32; Region: Peptidase_U32; pfam01136 428406006613 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406006614 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 428406006615 Walker A motif; other site 428406006616 ATP binding site [chemical binding]; other site 428406006617 Walker B motif; other site 428406006618 arginine finger; other site 428406006619 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 428406006620 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406006621 Walker A motif; other site 428406006622 ATP binding site [chemical binding]; other site 428406006623 Walker B motif; other site 428406006624 arginine finger; other site 428406006625 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 428406006626 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 428406006627 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 428406006628 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 428406006629 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 428406006630 Hemin uptake protein hemP; Region: hemP; pfam10636 428406006631 Uncharacterized protein, possibly involved in utilization of glycolate and propanediol [General function prediction only]; Region: GlcG; COG3193 428406006632 phasin family protein; Region: phasin; TIGR01841 428406006633 nodulation ABC transporter NodI; Provisional; Region: PRK13537 428406006634 ATP-binding cassette domain of the lipid transporters, subfamily A; Region: ABC_subfamily_A; cd03263 428406006635 Walker A/P-loop; other site 428406006636 ATP binding site [chemical binding]; other site 428406006637 Q-loop/lid; other site 428406006638 ABC transporter signature motif; other site 428406006639 Walker B; other site 428406006640 D-loop; other site 428406006641 H-loop/switch region; other site 428406006642 ABC-2 type transporter; Region: ABC2_membrane; cl17235 428406006643 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 428406006644 amidophosphoribosyltransferase; Provisional; Region: PRK09246 428406006645 Glutamine amidotransferases class-II (GN-AT)_GPAT- type. This domain is found at the N-terminus of glutamine phosphoribosylpyrophosphate (Prpp) amidotransferase (GPATase) . The glutaminase domain catalyzes amide nitrogen transfer from glutamine to the...; Region: GPATase_N; cd00715 428406006646 active site 428406006647 tetramer interface [polypeptide binding]; other site 428406006648 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 428406006649 active site 428406006650 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 428406006651 Colicin V production protein; Region: Colicin_V; pfam02674 428406006652 Sporulation related domain; Region: SPOR; pfam05036 428406006653 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 428406006654 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 428406006655 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 428406006656 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 428406006657 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 428406006658 tryptophan synthase alpha subunit; Provisional; Region: trpA; CHL00200 428406006659 Ttryptophan synthase (TRPS) alpha subunit (TSA). TPRS is a bifunctional tetrameric enzyme (2 alpha and 2 beta subunits) that catalyzes the last two steps of L-tryptophan biosynthesis. Alpha and beta subunit catalyze two distinct reactions which are both...; Region: Tryptophan_synthase_alpha; cd04724 428406006660 substrate binding site [chemical binding]; other site 428406006661 active site 428406006662 catalytic residues [active] 428406006663 heterodimer interface [polypeptide binding]; other site 428406006664 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 428406006665 DNA methylase; Region: N6_N4_Mtase; pfam01555 428406006666 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 428406006667 Tryptophan synthase-beta: Trptophan synthase is a bifunctional enzyme that catalyses the last two steps in the biosynthesis of L-tryptophan via its alpha and beta reactions. In the alpha reaction, indole 3-glycerol phosphate is cleaved reversibly to...; Region: Trp-synth_B; cd06446 428406006668 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406006669 catalytic residue [active] 428406006670 Phosphoribosylanthranilate isomerase (PRAI) catalyzes the fourth step of the tryptophan biosynthesis, the conversion of N-(5'- phosphoribosyl)-anthranilate (PRA) to 1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate (CdRP). Most PRAIs are...; Region: PRAI; cd00405 428406006671 active site 428406006672 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 428406006673 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 428406006674 dimerization interface 3.5A [polypeptide binding]; other site 428406006675 active site 428406006676 Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimV; COG3170 428406006677 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 428406006678 Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimV; COG3170 428406006679 FimV C-terminal domain; Region: FimV_Cterm; TIGR03504 428406006680 aspartate-semialdehyde dehydrogenase; Reviewed; Region: PRK06598 428406006681 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 428406006682 3-isopropylmalate dehydrogenase; Provisional; Region: PRK00772 428406006683 tartrate dehydrogenase; Region: TTC; TIGR02089 428406006684 isopropylmalate isomerase small subunit; Provisional; Region: leuD; PRK01641 428406006685 Aconatase-like swivel domain of 3-isopropylmalate dehydratase and related uncharacterized proteins. 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate...; Region: IPMI_Swivel; cd01577 428406006686 substrate binding site [chemical binding]; other site 428406006687 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 428406006688 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 428406006689 substrate binding site [chemical binding]; other site 428406006690 ligand binding site [chemical binding]; other site 428406006691 Escherichia coli (Ec) citrate synthase (CS) GltA_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). The overall CS...; Region: EcCS_like; cd06114 428406006692 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 428406006693 dimer interface [polypeptide binding]; other site 428406006694 active site 428406006695 citrylCoA binding site [chemical binding]; other site 428406006696 NADH binding [chemical binding]; other site 428406006697 cationic pore residues; other site 428406006698 oxalacetate/citrate binding site [chemical binding]; other site 428406006699 coenzyme A binding site [chemical binding]; other site 428406006700 catalytic triad [active] 428406006701 Flavinator of succinate dehydrogenase; Region: Sdh5; cl01110 428406006702 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 428406006703 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 428406006704 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK07057 428406006705 L-aspartate oxidase; Provisional; Region: PRK06175 428406006706 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 428406006707 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase D (SdhD) subunit; SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. E. coli SQR, a member of this subfamily, reduces the...; Region: SQR_TypeC_SdhD; cd03494 428406006708 SdhC subunit interface [polypeptide binding]; other site 428406006709 proximal heme binding site [chemical binding]; other site 428406006710 cardiolipin binding site; other site 428406006711 Iron-sulfur protein interface; other site 428406006712 proximal quinone binding site [chemical binding]; other site 428406006713 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase C (SdhC) subunit; composed of bacterial SdhC and eukaryotic large cytochrome b binding (CybL) proteins. SQR catalyzes the oxidation of succinate to fumarate coupled to the...; Region: SQR_TypeC_SdhC; cd03499 428406006714 Iron-sulfur protein interface; other site 428406006715 proximal quinone binding site [chemical binding]; other site 428406006716 SdhD (CybS) interface [polypeptide binding]; other site 428406006717 proximal heme binding site [chemical binding]; other site 428406006718 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 428406006719 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 428406006720 DNA-binding site [nucleotide binding]; DNA binding site 428406006721 UTRA domain; Region: UTRA; pfam07702 428406006722 malate dehydrogenase; Provisional; Region: PRK05442 428406006723 Chloroplast-like malate dehydrogenases; Region: MDH_choloroplast_like; cd01338 428406006724 NAD(P) binding site [chemical binding]; other site 428406006725 dimer interface [polypeptide binding]; other site 428406006726 malate binding site [chemical binding]; other site 428406006727 Citrate lyase beta subunit [Carbohydrate transport and metabolism]; Region: CitE; COG2301 428406006728 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 428406006729 Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate...; Region: ICL_PEPM; cd00377 428406006730 tetramer interface [polypeptide binding]; other site 428406006731 active site 428406006732 Mg2+/Mn2+ binding site [ion binding]; other site 428406006733 aconitate hydratase; Provisional; Region: acnA; PRK12881 428406006734 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 428406006735 substrate binding site [chemical binding]; other site 428406006736 ligand binding site [chemical binding]; other site 428406006737 Aconitase A swivel domain. This is the major form of the TCA cycle enzyme aconitate hydratase, also known as aconitase and citrate hydro-lyase. It includes bacterial and archaeal aconitase A, and the eukaryotic cytosolic form of aconitase. This group...; Region: AcnA_IRP_Swivel; cd01580 428406006738 substrate binding site [chemical binding]; other site 428406006739 Protein of unknown function (DUF2863); Region: DUF2863; pfam11062 428406006740 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 428406006741 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_2; cd08498 428406006742 Predicted carboxypeptidase [Amino acid transport and metabolism]; Region: COG2866 428406006743 Peptidase M14-like domain of ATP/GTP binding proteins and cytosolic carboxypeptidases; uncharacterized bacterial subgroup; Region: M14_Nna1_like_1; cd06234 428406006744 putative active site [active] 428406006745 Zn binding site [ion binding]; other site 428406006746 hypothetical protein; Validated; Region: PRK02101 428406006747 PIN domain; Region: PIN_3; pfam13470 428406006748 methionine aminotransferase; Validated; Region: PRK09082 428406006749 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 428406006750 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406006751 homodimer interface [polypeptide binding]; other site 428406006752 catalytic residue [active] 428406006753 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 428406006754 Glutathione S-transferase (GST) family, N-terminal domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic...; Region: GST_N_family; cd00570 428406006755 C-terminal domain interface [polypeptide binding]; other site 428406006756 GSH binding site (G-site) [chemical binding]; other site 428406006757 dimer interface [polypeptide binding]; other site 428406006758 C-terminal, alpha helical domain of an unknown subfamily 9 of Glutathione S-transferases; Region: GST_C_9; cd10424 428406006759 putative N-terminal domain interface [polypeptide binding]; other site 428406006760 putative dimer interface [polypeptide binding]; other site 428406006761 putative substrate binding pocket (H-site) [chemical binding]; other site 428406006762 3-hydroxy-acyl-CoA dehydrogenase; Validated; Region: PRK08268 428406006763 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 428406006764 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 428406006765 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 428406006766 enoyl-CoA hydratase; Provisional; Region: PRK07511 428406006767 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 428406006768 substrate binding site [chemical binding]; other site 428406006769 oxyanion hole (OAH) forming residues; other site 428406006770 trimer interface [polypeptide binding]; other site 428406006771 Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP_PGM_like; cd07067 428406006772 catalytic core [active] 428406006773 Acyl-CoA dehydrogenase (ACAD) 10 and 11, N-terminal domain, and similar proteins. This subfamily is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs); Region: ACAD10_11_like; cd05154 428406006774 putative active site [active] 428406006775 putative substrate binding site [chemical binding]; other site 428406006776 ATP binding site [chemical binding]; other site 428406006777 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_9; cd07245 428406006778 dimer interface [polypeptide binding]; other site 428406006779 putative metal binding site [ion binding]; other site 428406006780 short chain dehydrogenase; Provisional; Region: PRK06500 428406006781 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 428406006782 NAD(P) binding site [chemical binding]; other site 428406006783 active site 428406006784 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406006785 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406006786 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 428406006787 putative effector binding pocket; other site 428406006788 dimerization interface [polypeptide binding]; other site 428406006789 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 428406006790 Uncharacterized bacterial subgroup of the Salmonella typhimurium Zn2+ transporter ZntB-like subfamily; Region: ZntB_u1; cd12834 428406006791 Cl binding site [ion binding]; other site 428406006792 oligomer interface [polypeptide binding]; other site 428406006793 leucine transcriptional activator; Reviewed; Region: leuO; PRK09508 428406006794 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406006795 The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold; Region: PBP2_Nitroaromatics_like; cd08417 428406006796 substrate binding pocket [chemical binding]; other site 428406006797 dimerization interface [polypeptide binding]; other site 428406006798 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 428406006799 CoenzymeA binding site [chemical binding]; other site 428406006800 subunit interaction site [polypeptide binding]; other site 428406006801 PHB binding site; other site 428406006802 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 428406006803 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 428406006804 active site 428406006805 GSH-dependent disulfide bond oxidoreductase; Provisional; Region: PRK13972 428406006806 GST_N family, Ure2p-like subfamily; composed of the Saccharomyces cerevisiae Ure2p and related GSTs. Ure2p is a regulator for nitrogen catabolism in yeast. It represses the expression of several gene products involved in the use of poor nitrogen sources...; Region: GST_N_Ure2p_like; cd03048 428406006807 C-terminal domain interface [polypeptide binding]; other site 428406006808 GSH binding site (G-site) [chemical binding]; other site 428406006809 dimer interface [polypeptide binding]; other site 428406006810 C-terminal, alpha helical domain of Escherichia coli YfcG Glutathione S-transferases and related uncharacterized proteins; Region: GST_C_YfcG_like; cd10291 428406006811 N-terminal domain interface [polypeptide binding]; other site 428406006812 putative dimer interface [polypeptide binding]; other site 428406006813 active site 428406006814 Putative protein-S-isoprenylcysteine methyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: STE14; COG2020 428406006815 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 428406006816 Urease accessory protein UreF [Posttranslational modification, protein turnover, chaperones]; Region: UreF; COG0830 428406006817 UreF; Region: UreF; pfam01730 428406006818 urease accessory protein UreE; Provisional; Region: ureE; PRK13263 428406006819 UreE urease accessory protein. UreE is a metallochaperone assisting the insertion of a Ni2+ ion in the active site of urease, an important step in the in vivo assembly of urease, an enzyme that hydrolyses urea into ammonia and carbamic acid. The...; Region: UreE; cd00571 428406006820 dimer interface [polypeptide binding]; other site 428406006821 catalytic residues [active] 428406006822 Urease alpha-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, fungi and plants. Their primary role is to allow the use of...; Region: Urease_alpha; cd00375 428406006823 subunit interactions [polypeptide binding]; other site 428406006824 urease subunit alpha; Reviewed; Region: ureC; PRK13207 428406006825 active site 428406006826 flap region; other site 428406006827 Urease beta-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use of...; Region: Urease_beta; cd00407 428406006828 gamma-beta subunit interface [polypeptide binding]; other site 428406006829 alpha-beta subunit interface [polypeptide binding]; other site 428406006830 Hydrogenase/urease accessory protein [Posttranslational modification, protein turnover, chaperones]; Region: HupE; COG2370 428406006831 Urease gamma-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use...; Region: Urease_gamma; cd00390 428406006832 alpha-gamma subunit interface [polypeptide binding]; other site 428406006833 beta-gamma subunit interface [polypeptide binding]; other site 428406006834 Urease accessory protein UreH [Posttranslational modification, protein turnover, chaperones]; Region: UreH; COG0829 428406006835 urea ABC transporter, ATP-binding protein UrtE; Region: urea_trans_UrtE; TIGR03410 428406006836 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 428406006837 Walker A/P-loop; other site 428406006838 ATP binding site [chemical binding]; other site 428406006839 Q-loop/lid; other site 428406006840 ABC transporter signature motif; other site 428406006841 Walker B; other site 428406006842 D-loop; other site 428406006843 H-loop/switch region; other site 428406006844 Uncharacterized ABC-type transport system, ATPase component [General function prediction only]; Region: COG4674 428406006845 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 428406006846 Walker A/P-loop; other site 428406006847 ATP binding site [chemical binding]; other site 428406006848 Q-loop/lid; other site 428406006849 ABC transporter signature motif; other site 428406006850 Walker B; other site 428406006851 D-loop; other site 428406006852 H-loop/switch region; other site 428406006853 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 428406006854 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 428406006855 TM-ABC transporter signature motif; other site 428406006856 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 428406006857 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 428406006858 TM-ABC transporter signature motif; other site 428406006859 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 428406006860 Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF); Region: PBP1_FmdD_like; cd06355 428406006861 putative ligand binding site [chemical binding]; other site 428406006862 NodN (nodulation factor N) contains a single hot dog fold similar to those of the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. Rhizobium and related species form nodules on the roots of their...; Region: NodN; cd03450 428406006863 putative active site [active] 428406006864 putative catalytic site [active] 428406006865 YdeM is a Bacillus subtilis protein that belongs to a family of prokaryotic proteins of unkown function. YdeM has sequence similarity to the hot-dog fold of (R)-specific enoyl-CoA hydratase. Other enzymes with this fold include the peroxisomal...; Region: YdeM; cd03454 428406006866 putative active site [active] 428406006867 putative catalytic site [active] 428406006868 pimeloyl-CoA dehydrogenase, small subunit; Region: pimD_small; TIGR03203 428406006869 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 428406006870 active site 428406006871 pimeloyl-CoA dehydrogenase, large subunit; Region: pimC_large; TIGR03204 428406006872 Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26; Region: ACAD_fadE6_17_26; cd01152 428406006873 FAD binding site [chemical binding]; other site 428406006874 substrate binding site [chemical binding]; other site 428406006875 catalytic base [active] 428406006876 Protein of unknown function (DUF1178); Region: DUF1178; pfam06676 428406006877 ADP-ribose pyrophosphatase (ADPRase) catalyzes the hydrolysis of ADP-ribose and a variety of additional ADP-sugar conjugates to AMP and ribose-5-phosphate. Like other members of the Nudix hydrolase superfamily, it requires a divalent cation, such as Mg2+; Region: ADPRase_NUDT5; cd03424 428406006878 dimer interface [polypeptide binding]; other site 428406006879 ADP-ribose binding site [chemical binding]; other site 428406006880 active site 428406006881 nudix motif; other site 428406006882 metal binding site [ion binding]; metal-binding site 428406006883 Protein of unknown function (DUF2818); Region: DUF2818; pfam10993 428406006884 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 428406006885 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 428406006886 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 428406006887 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 428406006888 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 428406006889 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 428406006890 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 428406006891 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 428406006892 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 428406006893 NADH dehydrogenase subunit J; Provisional; Region: PRK06433 428406006894 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 428406006895 4Fe-4S binding domain; Region: Fer4; cl02805 428406006896 4Fe-4S binding domain; Region: Fer4; pfam00037 428406006897 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 428406006898 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 428406006899 NADH dehydrogenase subunit G; Validated; Region: PRK09129 428406006900 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 428406006901 catalytic loop [active] 428406006902 iron binding site [ion binding]; other site 428406006903 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 428406006904 MopB_NDH-1_NuoG2: The second domain of the NuoG subunit of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1), found in beta- and gammaproteobacteria. The NDH-1 is the first energy-transducting complex in the respiratory chain and functions as...; Region: MopB_NDH-1_NuoG2; cd02772 428406006905 Molybdopterin-Binding, C-terminal (MopB_CT) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum-...; Region: MopB_CT; cd02775 428406006906 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 428406006907 SLBB domain; Region: SLBB; pfam10531 428406006908 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 428406006909 NADH dehydrogenase subunit E; Validated; Region: PRK07539 428406006910 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes; Region: TRX_Fd_NuoE; cd03064 428406006911 putative dimer interface [polypeptide binding]; other site 428406006912 [2Fe-2S] cluster binding site [ion binding]; other site 428406006913 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 428406006914 NADH dehydrogenase subunit D; Validated; Region: PRK06075 428406006915 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 428406006916 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 428406006917 NADH dehydrogenase subunit B; Validated; Region: PRK06411 428406006918 NADH:ubiquinone oxidoreductase subunit A; Validated; Region: PRK06602 428406006919 Preprotein translocase SecG subunit; Region: SecG; pfam03840 428406006920 Triosephosphate isomerase (TIM) is a glycolytic enzyme that catalyzes the interconversion of dihydroxyacetone phosphate and D-glyceraldehyde-3-phosphate. The reaction is very efficient and requires neither cofactors nor metal ions. TIM, usually...; Region: TIM; cd00311 428406006921 triosephosphate isomerase; Provisional; Region: PRK14567 428406006922 substrate binding site [chemical binding]; other site 428406006923 dimer interface [polypeptide binding]; other site 428406006924 catalytic triad [active] 428406006925 putative NAD(P)H quinone oxidoreductase, PIG3 family; Region: quinone_pig3; TIGR02824 428406006926 PIG3 p53-inducible quinone oxidoreductase; Region: p53_inducible_oxidoreductase; cd05276 428406006927 NAD(P) binding site [chemical binding]; other site 428406006928 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 428406006929 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 428406006930 RNase E interface [polypeptide binding]; other site 428406006931 trimer interface [polypeptide binding]; other site 428406006932 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 428406006933 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 428406006934 RNase E interface [polypeptide binding]; other site 428406006935 trimer interface [polypeptide binding]; other site 428406006936 active site 428406006937 Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to...; Region: PNPase_KH; cd02393 428406006938 putative nucleic acid binding region [nucleotide binding]; other site 428406006939 G-X-X-G motif; other site 428406006940 S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA; Region: S1_PNPase; cd04472 428406006941 RNA binding site [nucleotide binding]; other site 428406006942 domain interface; other site 428406006943 Ribosomal protein S15 (prokaryotic)_S13 (eukaryotic) binds the central domain of 16S rRNA and is required for assembly of the small ribosomal subunit and for intersubunit association, thus representing a key element in the assembly of the whole ribosome; Region: Ribosomal_S15p_S13e; cd00353 428406006944 16S/18S rRNA binding site [nucleotide binding]; other site 428406006945 S13e-L30e interaction site [polypeptide binding]; other site 428406006946 25S rRNA binding site [nucleotide binding]; other site 428406006947 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 428406006948 Periplasmic solute-binding domain of active transport proteins; Region: PBP1_SBP_like_3; cd06329 428406006949 putative ligand binding site [chemical binding]; other site 428406006950 2-isopropylmalate synthase; Validated; Region: PRK00915 428406006951 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 428406006952 active site 428406006953 catalytic residues [active] 428406006954 metal binding site [ion binding]; metal-binding site 428406006955 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 428406006956 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 428406006957 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 428406006958 phosphatidylserine decarboxylase; Provisional; Region: PRK05305 428406006959 ketol-acid reductoisomerase; Provisional; Region: PRK05479 428406006960 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 428406006961 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 428406006962 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 428406006963 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 428406006964 putative valine binding site [chemical binding]; other site 428406006965 dimer interface [polypeptide binding]; other site 428406006966 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 428406006967 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK06965 428406006968 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 428406006969 PYR/PP interface [polypeptide binding]; other site 428406006970 dimer interface [polypeptide binding]; other site 428406006971 TPP binding site [chemical binding]; other site 428406006972 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 428406006973 Thiamine pyrophosphate (TPP) family, Acetohydroxyacid synthase (AHAS) subfamily, TPP-binding module; composed of proteins similar to the large catalytic subunit of AHAS. AHAS catalyzes the condensation of two molecules of pyruvate to give the...; Region: TPP_AHAS; cd02015 428406006974 TPP-binding site [chemical binding]; other site 428406006975 dimer interface [polypeptide binding]; other site 428406006976 RNA polymerase factor sigma-70; Validated; Region: PRK09047 428406006977 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 428406006978 DNA binding residues [nucleotide binding] 428406006979 Protein of unknown function (DUF3619); Region: DUF3619; pfam12279 428406006980 Protein of unknown function (DUF3106); Region: DUF3106; pfam11304 428406006981 RDD family; Region: RDD; pfam06271 428406006982 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 428406006983 PGAP1-like protein; Region: PGAP1; pfam07819 428406006984 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 428406006985 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 428406006986 putative active site [active] 428406006987 putative metal binding site [ion binding]; other site 428406006988 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 428406006989 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can...; Region: GT1_like_2; cd03814 428406006990 Diacylglycerol kinase [Cell envelope biogenesis, outer membrane]; Region: DgkA; COG0818 428406006991 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 428406006992 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 428406006993 Bacterial transcriptional repressor; Region: TetR; pfam13972 428406006994 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 428406006995 Bacterial protein of unknown function (DUF924); Region: DUF924; pfam06041 428406006996 Truncated hemoglobins (trHbs) are a family of oxygen-binding heme proteins found in cyanobacteria, eubacteria, unicellular eukaryotes, and plants. The truncated hemoglobins have a characteristic two-over-two alpha helical folding pattern that is distinct...; Region: Trunc_globin; cd00454 428406006997 apolar tunnel; other site 428406006998 heme binding site [chemical binding]; other site 428406006999 dimerization interface [polypeptide binding]; other site 428406007000 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3127 428406007001 FtsX-like permease family; Region: FtsX; pfam02687 428406007002 N-terminal domain of molybdenum-binding protein [General function prediction only]; Region: ModE; COG2005 428406007003 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406007004 Periplasmic molybdate-binding protein/domain [Inorganic ion transport and metabolism]; Region: COG1910 428406007005 ABC-type tungstate transport system, permease component [Coenzyme metabolism]; Region: TupB; COG2998 428406007006 PBP superfamily domain; Region: PBP_like_2; pfam12849 428406007007 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406007008 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406007009 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold; Region: PBP2_DntR_like_4; cd08463 428406007010 putative substrate binding pocket [chemical binding]; other site 428406007011 putative dimerization interface [polypeptide binding]; other site 428406007012 xanthine dehydrogenase, small subunit; Region: xanthine_xdhA; TIGR02963 428406007013 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 428406007014 catalytic loop [active] 428406007015 iron binding site [ion binding]; other site 428406007016 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 428406007017 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; pfam03450 428406007018 xanthine dehydrogenase, molybdopterin binding subunit; Region: xanthine_xdhB; TIGR02965 428406007019 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 428406007020 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 428406007021 XdhC and CoxI family; Region: XdhC_CoxI; pfam02625 428406007022 xanthine dehydrogenase accessory protein XdhC; Region: xanthine_xdhC; TIGR02964 428406007023 XdhC Rossmann domain; Region: XdhC_C; pfam13478 428406007024 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Add; COG1816 428406007025 Adenosine deaminase (ADA) is a monomeric zinc dependent enzyme which catalyzes the irreversible hydrolytic deamination of both adenosine, as well as desoxyadenosine, to ammonia and inosine or desoxyinosine, respectively. ADA plays an important role in...; Region: ADA; cd01320 428406007026 active site 428406007027 purine riboside binding site [chemical binding]; other site 428406007028 guanine deaminase; Provisional; Region: PRK09228 428406007029 Guanine deaminase (GDEase). Guanine deaminase is an aminohydrolase responsible for the conversion of guanine to xanthine and ammonia, the first step to utilize guanine as a nitrogen source. This reaction also removes the guanine base from the pool and...; Region: GDEase; cd01303 428406007030 active site 428406007031 Predicted membrane protein [Function unknown]; Region: COG2119 428406007032 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 428406007033 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 428406007034 type VI secretion system Vgr family protein; Region: VI_Rhs_Vgr; TIGR03361 428406007035 Phage late control gene D protein (GPD); Region: Phage_GPD; pfam05954 428406007036 Phage-related baseplate assembly protein; Region: Phage_base_V; pfam04717 428406007037 Putative type VI secretion system Rhs element Vgr; Region: T6SS_Vgr; pfam13296 428406007038 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4253 428406007039 Protein of unknown function (DUF989); Region: DUF989; pfam06181 428406007040 Predicted membrane protein [Function unknown]; Region: COG3748 428406007041 Cytochrome c; Region: Cytochrom_C; pfam00034 428406007042 HIUase (5-hydroxyisourate hydrolase) catalyzes the second step in a three-step ureide pathway in which 5-hydroxyisourate (HIU), a product of the uricase (urate oxidase) reaction, is hydrolyzed to 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU); Region: TLP_HIUase; cd05822 428406007043 active site 428406007044 homotetramer interface [polypeptide binding]; other site 428406007045 Transcriptional regulators [Transcription]; Region: GntR; COG1802 428406007046 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 428406007047 DNA-binding site [nucleotide binding]; DNA binding site 428406007048 FCD domain; Region: FCD; pfam07729 428406007049 xanthine permease; Region: pbuX; TIGR03173 428406007050 hydroxydechloroatrazine ethylaminohydrolase; Reviewed; Region: PRK08203 428406007051 TRZ/ATZ family contains enzymes from the atrazine degradation pathway and related hydrolases. Atrazine, a chlorinated herbizide, can be catabolized by a variety of different bacteria. The first three steps of the atrazine dehalogenation pathway are...; Region: ATZ_TRZ_like; cd01298 428406007052 active site 428406007053 putative substrate binding pocket [chemical binding]; other site 428406007054 putative urate catabolism protein; Region: uraD_N-term-dom; TIGR03212 428406007055 Catalytic domain of bacterial PuuE allantoinases, Schizosaccharomyces pombe chitin deacetylase 1 (SpCDA1), and similar proteins; Region: CE4_PuuE_SpCDA1; cd10977 428406007056 active site 428406007057 catalytic site [active] 428406007058 tetramer interface [polypeptide binding]; other site 428406007059 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3195 428406007060 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 428406007061 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 428406007062 eyelet of channel; other site 428406007063 trimer interface [polypeptide binding]; other site 428406007064 malic enzyme; Reviewed; Region: PRK12862 428406007065 Malic enzyme, N-terminal domain; Region: malic; pfam00390 428406007066 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 428406007067 putative NAD(P) binding site [chemical binding]; other site 428406007068 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 428406007069 Domain of unknown function (DUF4136); Region: DUF4136; pfam13590 428406007070 aminopeptidase N; Provisional; Region: pepN; PRK14015 428406007071 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_1; cd09600 428406007072 active site 428406007073 Zn binding site [ion binding]; other site 428406007074 Fructose-1,6-bisphosphatase, an enzyme that catalyzes the hydrolysis of fructose-1,6-biphosphate into fructose-6-phosphate and is critical in gluconeogenesis pathway. The alignment model also includes chloroplastic FBPases and sedoheptulose-1; Region: FBPase; cd00354 428406007075 AMP binding site [chemical binding]; other site 428406007076 metal binding site [ion binding]; metal-binding site 428406007077 active site 428406007078 LysM domain/BON superfamily protein; Provisional; Region: PRK11198 428406007079 BON domain; Region: BON; pfam04972 428406007080 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 428406007081 Poly(3-hydroxybutyrate) depolymerase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: LpqC; COG3509 428406007082 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 428406007083 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406007084 The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 428406007085 dimerization interface [polypeptide binding]; other site 428406007086 substrate binding pocket [chemical binding]; other site 428406007087 phosphonate utilization associated putative membrane protein; Region: phn_DUF6; TIGR03340 428406007088 Multidrug resistance efflux transporter; Region: EmrE; pfam13536 428406007089 transcription elongation factor GreB; Reviewed; Region: greB; PRK01885 428406007090 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 428406007091 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 428406007092 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 428406007093 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 428406007094 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 428406007095 Zn2+ binding site [ion binding]; other site 428406007096 Mg2+ binding site [ion binding]; other site 428406007097 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 428406007098 synthetase active site [active] 428406007099 NTP binding site [chemical binding]; other site 428406007100 metal binding site [ion binding]; metal-binding site 428406007101 TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named after...; Region: TGS_RelA_SpoT; cd01668 428406007102 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 428406007103 DNA-directed RNA polymerase subunit omega; Reviewed; Region: rpoZ; PRK00392 428406007104 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 428406007105 Guanosine monophosphate kinase (GMPK, EC 2.7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine...; Region: GMPK; cd00071 428406007106 catalytic site [active] 428406007107 G-X2-G-X-G-K; other site 428406007108 hypothetical protein; Provisional; Region: PRK11820 428406007109 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 428406007110 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 428406007111 Protein kinase domain; Region: Pkinase; pfam00069 428406007112 Catalytic domain of Protein Kinases; Region: PKc; cd00180 428406007113 active site 428406007114 ATP binding site [chemical binding]; other site 428406007115 substrate binding site [chemical binding]; other site 428406007116 activation loop (A-loop); other site 428406007117 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cd00143 428406007118 active site 428406007119 ribonuclease PH; Reviewed; Region: rph; PRK00173 428406007120 Ribonuclease PH; Region: RNase_PH_bact; cd11362 428406007121 hexamer interface [polypeptide binding]; other site 428406007122 active site 428406007123 NTPase/HAM1. This family consists of the HAM1 protein and pyrophosphate-releasing xanthosine/ inosine triphosphatase. HAM1 protects the cell against mutagenesis by the base analog 6-N-hydroxylaminopurine (HAP) in E. Coli and S. cerevisiae. A...; Region: HAM1; cd00515 428406007124 active site 428406007125 dimerization interface [polypeptide binding]; other site 428406007126 coproporphyrinogen III oxidase; Provisional; Region: PRK08898 428406007127 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 428406007128 FeS/SAM binding site; other site 428406007129 HemN C-terminal domain; Region: HemN_C; pfam06969 428406007130 PAS domain S-box; Region: sensory_box; TIGR00229 428406007131 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 428406007132 putative active site [active] 428406007133 heme pocket [chemical binding]; other site 428406007134 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 428406007135 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 428406007136 DNA binding residues [nucleotide binding] 428406007137 dimerization interface [polypeptide binding]; other site 428406007138 Protein of unknown function (DUF2968); Region: DUF2968; pfam11180 428406007139 Pyroglutamyl peptidase (PGP) type I, also known as pyrrolidone carboxyl peptidase (pcp) type I: Enzymes responsible for cleaving pyroglutamate (pGlu) from the N-terminal end of specialized proteins. The N-terminal pGlu protects these proteins from...; Region: Peptidase_C15; cd00501 428406007140 putative substrate binding pocket [chemical binding]; other site 428406007141 AC domain interface; other site 428406007142 catalytic triad [active] 428406007143 AB domain interface; other site 428406007144 interchain disulfide; other site 428406007145 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 428406007146 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; cl15441 428406007147 Predicted membrane protein [Function unknown]; Region: COG3817 428406007148 Protein of unknown function (DUF979); Region: DUF979; pfam06166 428406007149 Predicted membrane protein [Function unknown]; Region: COG3819 428406007150 Escherichia coli putative lactam utilization protein YbgL and similar proteins; Region: LamB_YcsF_YbgL_like; cd10800 428406007151 putative active site [active] 428406007152 Allophanate hydrolase subunit 2 [Amino acid transport and metabolism]; Region: DUR1; COG1984 428406007153 Allophanate hydrolase subunit 1; Region: AHS1; smart00796 428406007154 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]; Region: DUR1; COG2049 428406007155 bicyclomycin/multidrug efflux system; Provisional; Region: PRK11102 428406007156 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406007157 putative substrate translocation pore; other site 428406007158 ABC-type uncharacterized transport systems, ATPase components [General function prediction only]; Region: COG3845 428406007159 First domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_I; cd03216 428406007160 Walker A/P-loop; other site 428406007161 ATP binding site [chemical binding]; other site 428406007162 Q-loop/lid; other site 428406007163 ABC transporter signature motif; other site 428406007164 Walker B; other site 428406007165 D-loop; other site 428406007166 H-loop/switch region; other site 428406007167 Second domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_II; cd03215 428406007168 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 428406007169 Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette; Region: TM_PBP1_transp_TpRbsC_like; cd06580 428406007170 TM-ABC transporter signature motif; other site 428406007171 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 428406007172 Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette; Region: TM_PBP1_transp_TpRbsC_like; cd06580 428406007173 TM-ABC transporter signature motif; other site 428406007174 Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein [General function prediction only]; Region: Med; COG1744 428406007175 Periplasmic binding domain of the basic membrane lipoprotein Med in Bacillus and its close homologs from other bacteria and Archaea; Region: PBP1_BmpA_Med_like; cd06353 428406007176 putative ligand binding site [chemical binding]; other site 428406007177 Uncharacterized conserved protein [Function unknown]; Region: COG3339 428406007178 quinone oxidoreductase, NADPH-dependent; Provisional; Region: PRK10754 428406007179 Quinone oxidoreductase (QOR); Region: QOR2; cd05286 428406007180 NADP binding site [chemical binding]; other site 428406007181 dimer interface [polypeptide binding]; other site 428406007182 Methylglyoxal synthase catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The first part of the catalytic mechanism is believed to be similar to TIM (triosephosphate isomerase) in that both enzymes utilize DHAP to...; Region: MGS; cd01422 428406007183 active site 428406007184 dimer interfaces [polypeptide binding]; other site 428406007185 catalytic residues [active] 428406007186 short chain dehydrogenase; Provisional; Region: PRK08339 428406007187 putative beta-ketoacyl acyl carrier protein [ACP] reductase (BKR)-like, SDR; Region: BKR_like_SDR_like; cd05344 428406007188 putative NAD(P) binding site [chemical binding]; other site 428406007189 putative active site [active] 428406007190 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 428406007191 EamA-like transporter family; Region: EamA; pfam00892 428406007192 EamA-like transporter family; Region: EamA; pfam00892 428406007193 uncharacterized nucleobase-cation-symport-1 (NCS1) transporter subfamily, YbbW-like; solute-binding domain; Region: SLC-NCS1sbd_YbbW-like; cd11485 428406007194 Permease for cytosine/purines, uracil, thiamine, allantoin; Region: Transp_cyt_pur; pfam02133 428406007195 Na binding site [ion binding]; other site 428406007196 putative substrate binding site [chemical binding]; other site 428406007197 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 428406007198 active site 428406007199 Bacterial protein of unknown function (DUF853); Region: DUF853; pfam05872 428406007200 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406007201 Walker A motif; other site 428406007202 ATP binding site [chemical binding]; other site 428406007203 Walker B motif; other site 428406007204 hypothetical protein; Validated; Region: PRK00110 428406007205 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 428406007206 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 428406007207 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 428406007208 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 428406007209 coproporphyrinogen III oxidase; Provisional; Region: PRK05330 428406007210 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; pfam01218 428406007211 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 428406007212 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 428406007213 active site 428406007214 (T/H)XGH motif; other site 428406007215 Uncharacterized homolog of plant Iojap protein [Function unknown]; Region: COG0799 428406007216 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 428406007217 Maf-like protein; Region: Maf; pfam02545 428406007218 Nucleotide binding protein Maf. Maf has been implicated in inhibition of septum formation in eukaryotes, bacteria and archaea, but homologs in B.subtilis and S.cerevisiae are nonessential for cell division. Maf has been predicted to be a nucleotide- or...; Region: Maf; cd00555 428406007219 active site 428406007220 dimer interface [polypeptide binding]; other site 428406007221 ribonuclease G; Provisional; Region: PRK11712 428406007222 S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and...; Region: S1_RNase_E; cd04453 428406007223 homodimer interface [polypeptide binding]; other site 428406007224 oligonucleotide binding site [chemical binding]; other site 428406007225 benzoate transport; Region: 2A0115; TIGR00895 428406007226 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406007227 putative substrate translocation pore; other site 428406007228 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406007229 2-dehydropantoate 2-reductase; Reviewed; Region: PRK06522 428406007230 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 428406007231 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 428406007232 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 428406007233 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 428406007234 NAD(P) binding site [chemical binding]; other site 428406007235 catalytic residues [active] 428406007236 benzoylformate decarboxylase; Reviewed; Region: PRK07092 428406007237 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 428406007238 PYR/PP interface [polypeptide binding]; other site 428406007239 dimer interface [polypeptide binding]; other site 428406007240 TPP binding site [chemical binding]; other site 428406007241 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 428406007242 Thiamine pyrophosphate (TPP) family, BFDC subfamily, TPP-binding module; composed of proteins similar to Pseudomonas putida benzoylformate decarboxylase (BFDC). P. putida BFDC plays a role in the mandelate pathway, catalyzing the conversion of...; Region: TPP_BFDC; cd02002 428406007243 TPP-binding site [chemical binding]; other site 428406007244 dimer interface [polypeptide binding]; other site 428406007245 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406007246 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406007247 The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold; Region: PBP2_GbpR; cd08435 428406007248 putative dimerization interface [polypeptide binding]; other site 428406007249 uncharacterized peroxidase-related enzyme; Region: peroxid_rel; TIGR01926 428406007250 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 428406007251 lipid A export permease/ATP-binding protein MsbA; Region: MsbA_lipidA; TIGR02203 428406007252 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 428406007253 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 428406007254 Walker A/P-loop; other site 428406007255 ATP binding site [chemical binding]; other site 428406007256 Q-loop/lid; other site 428406007257 ABC transporter signature motif; other site 428406007258 Walker B; other site 428406007259 D-loop; other site 428406007260 H-loop/switch region; other site 428406007261 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of...; Region: Glyco_transf_25; cd06532 428406007262 Predicted glycosyltransferases [General function prediction only]; Region: COG1216 428406007263 N-terminal domain of Chondroitin polymerase functions as a GalNAc transferase; Region: GT2_Chondriotin_Pol_N; cd06420 428406007264 Substrate binding site; other site 428406007265 metal-binding site 428406007266 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 428406007267 putative metal binding site; other site 428406007268 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 428406007269 O-Antigen ligase; Region: Wzy_C; pfam04932 428406007270 This family is most closely related to the GT1 family of glycosyltransferases and named after YqgM in Bacillus licheniformis about which little is known. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to...; Region: GT1_YqgM_like; cd03801 428406007271 Glycosyltransferase Family 4; Region: Glyco_transf_4; pfam13439 428406007272 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 428406007273 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 428406007274 putative active site [active] 428406007275 putative PHP Thumb interface [polypeptide binding]; other site 428406007276 DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains...; Region: DnaE_OBF; cd04485 428406007277 generic binding surface II; other site 428406007278 generic binding surface I; other site 428406007279 rhodanese superfamily protein; Provisional; Region: PRK05320 428406007280 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 428406007281 active site residue [active] 428406007282 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 428406007283 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 428406007284 Pirin-related protein [General function prediction only]; Region: COG1741 428406007285 Pirin; Region: Pirin; pfam02678 428406007286 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11074 428406007287 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406007288 The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold; Region: PBP2_HupR; cd08431 428406007289 putative dimerization interface [polypeptide binding]; other site 428406007290 Glutamyl- and glutaminyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]; Region: GlnS; COG0008 428406007291 glutamyl-queuosine tRNA(Asp) synthetase; Region: queuosine_YadB; TIGR03838 428406007292 active site 428406007293 HIGH motif; other site 428406007294 nucleotide binding site [chemical binding]; other site 428406007295 active site 428406007296 KMSKS motif; other site 428406007297 DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif; Region: DEADc; cd00268 428406007298 DEAD-like helicases superfamily; Region: DEXDc; smart00487 428406007299 ATP binding site [chemical binding]; other site 428406007300 Mg++ binding site [ion binding]; other site 428406007301 motif III; other site 428406007302 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 428406007303 nucleotide binding region [chemical binding]; other site 428406007304 ATP-binding site [chemical binding]; other site 428406007305 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 428406007306 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 428406007307 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 428406007308 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 428406007309 acyl-CoA synthetase; Validated; Region: PRK06178 428406007310 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 428406007311 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 428406007312 ATP-grasp domain; Region: ATP-grasp_4; cl17255 428406007313 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 428406007314 Biotin carboxyl carrier protein [Lipid metabolism]; Region: AccB; COG0511 428406007315 The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase; Region: biotinyl_domain; cd06850 428406007316 carboxyltransferase (CT) interaction site; other site 428406007317 biotinylation site [posttranslational modification]; other site 428406007318 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 428406007319 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 428406007320 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 428406007321 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 428406007322 Outer membrane protein W [Cell envelope biogenesis, outer membrane]; Region: OmpW; COG3047 428406007323 Protein of unknown function (DUF2957); Region: DUF2957; pfam11170 428406007324 Protein of unknown function (DUF2957); Region: DUF2957; pfam11170 428406007325 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 428406007326 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 428406007327 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 428406007328 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 428406007329 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 428406007330 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 428406007331 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 428406007332 DNA binding residues [nucleotide binding] 428406007333 DNA primase; Validated; Region: dnaG; PRK05667 428406007334 CHC2 zinc finger; Region: zf-CHC2; pfam01807 428406007335 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 428406007336 TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG. Primases synthesize RNA primers for the initiation of DNA replication. DnaG...; Region: TOPRIM_DnaG_primases; cd03364 428406007337 active site 428406007338 metal binding site [ion binding]; metal-binding site 428406007339 interdomain interaction site; other site 428406007340 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 428406007341 DNA primase DnaG DnaB-binding; Region: DnaG_DnaB_bind; pfam08278 428406007342 Yqey-like protein; Region: YqeY; pfam09424 428406007343 HI0933-like protein; Region: HI0933_like; pfam03486 428406007344 UGMP family protein; Validated; Region: PRK09604 428406007345 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 428406007346 putative GTP cyclohydrolase; Provisional; Region: PRK13674 428406007347 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 428406007348 Thiamine pyrophosphate (TPP) family, DXS subfamily, TPP-binding module; 1-Deoxy-D-xylulose-5-phosphate synthase (DXS) is a regulatory enzyme of the mevalonate-independent pathway involved in terpenoid biosynthesis. Terpeniods are plant natural products...; Region: TPP_DXS; cd02007 428406007349 TPP-binding site; other site 428406007350 Pyrimidine (PYR) binding domain of 1-deoxy-D-xylulose-5-phosphate synthase (DXS), transketolase (TK), and related proteins; Region: TPP_PYR_DXS_TK_like; cd07033 428406007351 PYR/PP interface [polypeptide binding]; other site 428406007352 dimer interface [polypeptide binding]; other site 428406007353 TPP binding site [chemical binding]; other site 428406007354 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 428406007355 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 428406007356 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 428406007357 substrate binding pocket [chemical binding]; other site 428406007358 chain length determination region; other site 428406007359 substrate-Mg2+ binding site; other site 428406007360 catalytic residues [active] 428406007361 aspartate-rich region 1; other site 428406007362 active site lid residues [active] 428406007363 aspartate-rich region 2; other site 428406007364 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 428406007365 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 428406007366 Rieske non-heme iron oxygenase (RO) family, N-terminal Rieske domain of the oxygenase alpha subunit; The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable...; Region: Rieske_RO_Alpha_N; cd03469 428406007367 [2Fe-2S] cluster binding site [ion binding]; other site 428406007368 C-terminal catalytic domain of the oxygenase alpha subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases; Region: RHO_alpha_C; cd00680 428406007369 alpha subunit interface [polypeptide binding]; other site 428406007370 active site 428406007371 substrate binding site [chemical binding]; other site 428406007372 Fe binding site [ion binding]; other site 428406007373 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 428406007374 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 428406007375 Thiosulfate sulfurtransferase (TST), N-terminal, inactive domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the 1st repeat, which does not contain the catalytically active Cys residue. The role of the 1st repeat is uncertain, but it...; Region: TST_Repeat_1; cd01448 428406007376 active site residue [active] 428406007377 Thiosulfate sulfurtransferase (TST), C-terminal, catalytic domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the second repeat. Only the second repeat contains the catalytically active Cys residue; Region: TST_Repeat_2; cd01449 428406007378 active site residue [active] 428406007379 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428 428406007380 ZIP Zinc transporter; Region: Zip; pfam02535 428406007381 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 428406007382 BAAT / Acyl-CoA thioester hydrolase C terminal; Region: BAAT_C; pfam08840 428406007383 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 428406007384 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 428406007385 K+-transporting ATPase, c chain; Region: KdpC; cl00944 428406007386 DNA polymerase I; Provisional; Region: PRK05755 428406007387 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 428406007388 active site 428406007389 metal binding site 1 [ion binding]; metal-binding site 428406007390 putative 5' ssDNA interaction site; other site 428406007391 metal binding site 3; metal-binding site 428406007392 metal binding site 2 [ion binding]; metal-binding site 428406007393 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 428406007394 putative DNA binding site [nucleotide binding]; other site 428406007395 putative metal binding site [ion binding]; other site 428406007396 DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases; Region: DNA_polA_I_Ecoli_like_exo; cd06139 428406007397 active site 428406007398 catalytic site [active] 428406007399 substrate binding site [chemical binding]; other site 428406007400 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 428406007401 active site 428406007402 DNA binding site [nucleotide binding] 428406007403 catalytic site [active] 428406007404 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]; Region: COG1611 428406007405 Putative homoserine kinase type II (protein kinase fold) [General function prediction only]; Region: COG2334 428406007406 Homoserine Kinase, type II. Homoserine kinase is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and...; Region: HomoserineK_II; cd05153 428406007407 putative active site [active] 428406007408 putative substrate binding site [chemical binding]; other site 428406007409 ATP binding site [chemical binding]; other site 428406007410 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 428406007411 Part of AAA domain; Region: AAA_19; pfam13245 428406007412 Family description; Region: UvrD_C_2; pfam13538 428406007413 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 428406007414 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 428406007415 active site 428406007416 HIGH motif; other site 428406007417 nucleotide binding site [chemical binding]; other site 428406007418 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 428406007419 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 428406007420 active site 428406007421 KMSKS motif; other site 428406007422 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 428406007423 tRNA binding surface [nucleotide binding]; other site 428406007424 anticodon binding site; other site 428406007425 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 428406007426 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 428406007427 dTDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]; Region: RfbA; COG1209 428406007428 active site 428406007429 tetramer interface; other site 428406007430 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the...; Region: S1_IF1; cd04451 428406007431 rRNA binding site [nucleotide binding]; other site 428406007432 predicted 30S ribosome binding site; other site 428406007433 Predicted extracellular endo alpha-1,4 polygalactosaminidase or related polysaccharide hydrolase [Carbohydrate transport and metabolism]; Region: COG2342 428406007434 4-hydroxybenzoate 3-monooxygenase; Validated; Region: PRK08243 428406007435 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 428406007436 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406007437 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406007438 The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold; Region: PBP2_DntR_NahR_LinR_like; cd08459 428406007439 substrate binding pocket [chemical binding]; other site 428406007440 dimerization interface [polypeptide binding]; other site 428406007441 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 428406007442 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 428406007443 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 428406007444 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 428406007445 Walker A/P-loop; other site 428406007446 ATP binding site [chemical binding]; other site 428406007447 Q-loop/lid; other site 428406007448 ABC transporter signature motif; other site 428406007449 Walker B; other site 428406007450 D-loop; other site 428406007451 H-loop/switch region; other site 428406007452 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 428406007453 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 428406007454 Walker A/P-loop; other site 428406007455 ATP binding site [chemical binding]; other site 428406007456 Q-loop/lid; other site 428406007457 ABC transporter signature motif; other site 428406007458 Walker B; other site 428406007459 D-loop; other site 428406007460 H-loop/switch region; other site 428406007461 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 428406007462 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 428406007463 TM-ABC transporter signature motif; other site 428406007464 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 428406007465 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 428406007466 TM-ABC transporter signature motif; other site 428406007467 4-carboxymuconolactone decarboxylase; Region: decarb_PcaC; TIGR02425 428406007468 3-oxoadipate enol-lactonase; Region: protocat_pcaD; TIGR02427 428406007469 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 428406007470 3-carboxy-cis,cis-muconate cycloisomerase; Provisional; Region: PRK09053 428406007471 prokaryotic 3-carboxy-cis,cis-muconate cycloisomerase (CMLE)_like; Region: pCLME; cd01597 428406007472 tetramer interface [polypeptide binding]; other site 428406007473 active site 428406007474 beta-ketoadipyl CoA thiolase; Validated; Region: PRK09050 428406007475 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 428406007476 dimer interface [polypeptide binding]; other site 428406007477 active site 428406007478 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 428406007479 3-oxoacid CoA-transferase, A subunit; Region: pcaI_scoA_fam; TIGR02429 428406007480 beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family; Region: pcaR_pcaU; TIGR02431 428406007481 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 428406007482 Bacterial transcriptional regulator; Region: IclR; pfam01614 428406007483 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 428406007484 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 428406007485 substrate binding pocket [chemical binding]; other site 428406007486 membrane-bound complex binding site; other site 428406007487 hinge residues; other site 428406007488 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 428406007489 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406007490 dimer interface [polypeptide binding]; other site 428406007491 conserved gate region; other site 428406007492 putative PBP binding loops; other site 428406007493 ABC-ATPase subunit interface; other site 428406007494 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 428406007495 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406007496 dimer interface [polypeptide binding]; other site 428406007497 conserved gate region; other site 428406007498 putative PBP binding loops; other site 428406007499 ABC-ATPase subunit interface; other site 428406007500 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 428406007501 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 428406007502 Walker A/P-loop; other site 428406007503 ATP binding site [chemical binding]; other site 428406007504 Q-loop/lid; other site 428406007505 ABC transporter signature motif; other site 428406007506 Walker B; other site 428406007507 D-loop; other site 428406007508 H-loop/switch region; other site 428406007509 glutamate and aspartate transporter subunit; Provisional; Region: PRK10797 428406007510 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 428406007511 substrate binding pocket [chemical binding]; other site 428406007512 membrane-bound complex binding site; other site 428406007513 hinge residues; other site 428406007514 D-amino acid dehydrogenase small subunit; Validated; Region: PRK00711 428406007515 Predicted membrane protein [Function unknown]; Region: COG4267 428406007516 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can...; Region: GT1_like_3; cd03813 428406007517 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 428406007518 poly-beta-1,6 N-acetyl-D-glucosamine export porin PgaA; Region: PGA_TPR_OMP; TIGR03939 428406007519 Predicted integral membrane protein [Function unknown]; Region: COG5616 428406007520 Tetratricopeptide repeat; Region: TPR_15; pfam13429 428406007521 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 428406007522 Domain of unknown function DUF21; Region: DUF21; pfam01595 428406007523 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the CorC_HlyC domain. CorC_HlyC is a transporter associated domain. This small domain is found in Na+/H+ antiporters, in proteins involved in...; Region: CBS_pair_CorC_HlyC_assoc; cd04590 428406007524 Transporter associated domain; Region: CorC_HlyC; smart01091 428406007525 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 428406007526 Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB; Region: HTH_YyaN; cd01109 428406007527 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 428406007528 DNA binding residues [nucleotide binding] 428406007529 Type I phosphodiesterase / nucleotide pyrophosphatase; Region: Phosphodiest; pfam01663 428406007530 Type I phosphodiesterase / nucleotide pyrophosphatase; Region: Phosphodiest; pfam01663 428406007531 Outer membrane protein V [Cell envelope biogenesis, outer membrane]; Region: OmpV; COG3713 428406007532 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 428406007533 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 428406007534 substrate binding pocket [chemical binding]; other site 428406007535 membrane-bound complex binding site; other site 428406007536 hinge residues; other site 428406007537 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 428406007538 Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]; Region: AcoR; COG3284 428406007539 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406007540 Walker A motif; other site 428406007541 ATP binding site [chemical binding]; other site 428406007542 Walker B motif; other site 428406007543 arginine finger; other site 428406007544 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 428406007545 proline iminopeptidase, Neisseria-type subfamily; Region: pro_imino_pep_1; TIGR01249 428406007546 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 428406007547 coenzyme PQQ synthesis protein PqqA; Provisional; Region: pqqA; PRK00284 428406007548 pyrroloquinoline quinone biosynthesis protein PqqB; Provisional; Region: PRK05184 428406007549 coenzyme PQQ biosynthesis protein B; Region: PQQ_syn_pqqB; TIGR02108 428406007550 pyrroloquinoline quinone biosynthesis protein PqqC; Provisional; Region: PRK05157 428406007551 Coenzyme PQQ synthesis protein D (PqqD); Region: PqqD; pfam05402 428406007552 pyrroloquinoline quinone biosynthesis protein PqqE; Provisional; Region: PRK05301 428406007553 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 428406007554 FeS/SAM binding site; other site 428406007555 radical SAM additional 4Fe4S-binding SPASM domain; Region: rSAM_more_4Fe4S; TIGR04085 428406007556 Cytochrome c; Region: Cytochrom_C; cl11414 428406007557 PQQ-dependent dehydrogenase, methanol/ethanol family; Region: PQQ_enz_alc_DH; TIGR03075 428406007558 Ethanol dehydrogenase, a bacterial quinoprotein (PQQ-dependent type I alcohol dehydrogenase); Region: PQQ_ADH_I; cd10277 428406007559 dimer interface [polypeptide binding]; other site 428406007560 Trp docking motif [polypeptide binding]; other site 428406007561 active site 428406007562 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 428406007563 PQQ-dependent catabolism-associated beta-propeller protein; Region: PQQ_ABC_repeats; TIGR03866 428406007564 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 428406007565 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 428406007566 WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from...; Region: WD40; cl02567 428406007567 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 428406007568 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 428406007569 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 428406007570 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 428406007571 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 428406007572 NAD(P) binding site [chemical binding]; other site 428406007573 catalytic residues [active] 428406007574 Sulfur oxidation protein SoxY; Region: SoxY; pfam13501 428406007575 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 428406007576 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 428406007577 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 428406007578 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 428406007579 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 428406007580 trimer interface [polypeptide binding]; other site 428406007581 eyelet of channel; other site 428406007582 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 428406007583 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LCLAT1-like; Region: LPLAT_LCLAT1-like; cd07990 428406007584 putative acyl-acceptor binding pocket; other site 428406007585 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 428406007586 Uncharacterized membrane-anchored protein conserved in bacteria [Function unknown]; Region: COG4705 428406007587 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 428406007588 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 428406007589 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 428406007590 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 428406007591 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 428406007592 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 428406007593 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 428406007594 hydroxyacylglutathione hydrolase; Region: GSH_gloB; TIGR03413 428406007595 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 428406007596 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 428406007597 dimer interface [polypeptide binding]; other site 428406007598 active site 428406007599 metal binding site [ion binding]; metal-binding site 428406007600 glutathione binding site [chemical binding]; other site 428406007601 Uncharacterized protein related to arylsulfate sulfotransferase involved in siderophore biosynthesis [General function prediction only]; Region: COG4321 428406007602 Choline dehydrogenase and related flavoproteins [Amino acid transport and metabolism]; Region: BetA; COG2303 428406007603 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 428406007604 Gluconate 2-dehydrogenase subunit 3; Region: Gluconate_2-dh3; pfam13618 428406007605 Cytochrome c; Region: Cytochrom_C; cl11414 428406007606 Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is...; Region: Heme_Cu_Oxidase_I; cl00275 428406007607 Low-spin heme binding site [chemical binding]; other site 428406007608 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 428406007609 D-pathway; other site 428406007610 Putative water exit pathway; other site 428406007611 Binuclear center (active site) [active] 428406007612 K-pathway; other site 428406007613 Putative proton exit pathway; other site 428406007614 Cytochrome C oxidase, mono-heme subunit/FixO; Region: FixO; cl01130 428406007615 Cytochrome c; Region: Cytochrom_C; pfam00034 428406007616 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 428406007617 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 428406007618 SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c...; Region: SCO; cd02968 428406007619 Cu(I) binding site [ion binding]; other site 428406007620 Zonular occludens toxin (Zot); Region: Zot; cl17485 428406007621 multiple promoter invertase; Provisional; Region: mpi; PRK13413 428406007622 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 428406007623 catalytic residues [active] 428406007624 catalytic nucleophile [active] 428406007625 Presynaptic Site I dimer interface [polypeptide binding]; other site 428406007626 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 428406007627 Synaptic Flat tetramer interface [polypeptide binding]; other site 428406007628 Synaptic Site I dimer interface [polypeptide binding]; other site 428406007629 DNA binding site [nucleotide binding] 428406007630 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cl17393 428406007631 DNA-binding interface [nucleotide binding]; DNA binding site 428406007632 seryl-tRNA synthetase; Provisional; Region: PRK05431 428406007633 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 428406007634 Seryl-tRNA synthetase (SerRS) class II core catalytic domain. SerRS is responsible for the attachment of serine to the 3' OH group of ribose of the appropriate tRNA. This domain It is primarily responsible for ATP-dependent formation of the enzyme...; Region: SerRS_core; cd00770 428406007635 dimer interface [polypeptide binding]; other site 428406007636 active site 428406007637 motif 1; other site 428406007638 motif 2; other site 428406007639 motif 3; other site 428406007640 recombination factor protein RarA; Reviewed; Region: PRK13342 428406007641 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406007642 Walker A motif; other site 428406007643 ATP binding site [chemical binding]; other site 428406007644 Walker B motif; other site 428406007645 arginine finger; other site 428406007646 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 428406007647 metabolite-proton symporter; Region: 2A0106; TIGR00883 428406007648 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406007649 putative substrate translocation pore; other site 428406007650 Agmatinase-like family includes proclavaminic acid amidinohydrolase; Region: Agmatinase_PAH; cd11592 428406007651 agmatinase; Region: agmatinase; TIGR01230 428406007652 oligomer interface [polypeptide binding]; other site 428406007653 putative active site [active] 428406007654 Mn binding site [ion binding]; other site 428406007655 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406007656 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406007657 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 428406007658 dimerization interface [polypeptide binding]; other site 428406007659 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 428406007660 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 428406007661 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 428406007662 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 428406007663 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 428406007664 thioredoxin reductase; Provisional; Region: PRK10262 428406007665 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 428406007666 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 428406007667 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 428406007668 Smr domain; Region: Smr; pfam01713 428406007669 Predicted membrane protein [Function unknown]; Region: COG2860 428406007670 UPF0126 domain; Region: UPF0126; pfam03458 428406007671 UPF0126 domain; Region: UPF0126; pfam03458 428406007672 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 428406007673 Nitrogen regulatory protein P-II; Region: P-II; smart00938 428406007674 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 428406007675 S-adenosylmethionine binding site [chemical binding]; other site 428406007676 NAD synthetase; Provisional; Region: PRK13981 428406007677 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 428406007678 multimer interface [polypeptide binding]; other site 428406007679 active site 428406007680 catalytic triad [active] 428406007681 protein interface 1 [polypeptide binding]; other site 428406007682 NAD+ synthase is a homodimer, which catalyzes the final step in de novo nicotinamide adenine dinucleotide (NAD+) biosynthesis, an amide transfer from either ammonia or glutamine to nicotinic acid adenine dinucleotide (NaAD). The conversion of NaAD to NAD...; Region: NAD_synthase; cd00553 428406007683 homodimer interface [polypeptide binding]; other site 428406007684 NAD binding pocket [chemical binding]; other site 428406007685 ATP binding pocket [chemical binding]; other site 428406007686 Mg binding site [ion binding]; other site 428406007687 active-site loop [active] 428406007688 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; cl17497 428406007689 Protein of unknown function, DUF482; Region: DUF482; pfam04339 428406007690 Inorganic pyrophosphatase. These enzymes hydrolyze inorganic pyrophosphate (PPi) to two molecules of orthophosphates (Pi). The reaction requires bivalent cations. The enzymes in general exist as homooligomers; Region: pyrophosphatase; cd00412 428406007691 dimer interface [polypeptide binding]; other site 428406007692 substrate binding site [chemical binding]; other site 428406007693 metal binding sites [ion binding]; metal-binding site 428406007694 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 428406007695 Uncharacterized Saccharopolyspora spinosa aldehyde dehydrogenase (AAS00426)-like; Region: ALDH_AAS00426; cd07109 428406007696 NAD(P) binding site [chemical binding]; other site 428406007697 catalytic residues [active] 428406007698 catalytic residues [active] 428406007699 putative beta-ketoacyl acyl carrier protein [ACP] reductase (BKR), subgroup 3, classical (c) SDR; Region: BKR_3_SDR_c; cd05345 428406007700 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK07231 428406007701 putative NAD(P) binding site [chemical binding]; other site 428406007702 active site 428406007703 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406007704 D-galactonate transporter; Region: 2A0114; TIGR00893 428406007705 putative substrate translocation pore; other site 428406007706 heme biosynthesis-associated TPR protein; Region: TPR_hemY_coli; TIGR00540 428406007707 HemY protein N-terminus; Region: HemY_N; pfam07219 428406007708 bifunctional uroporphyrinogen-III synthetase/uroporphyrin-III C-methyltransferase; Reviewed; Region: PRK06975 428406007709 Uroporphyrinogen-III synthase (HemD) catalyzes the asymmetrical cyclization of tetrapyrrole (linear) to uroporphyrinogen-III, the fourth step in the biosynthesis of heme. This ubiquitous enzyme is present in eukaryotes, bacteria and archaea. Mutations in...; Region: HemD; cd06578 428406007710 active site 428406007711 putative uroporphyrinogen III C-methyltransferase; Provisional; Region: PRK10920 428406007712 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 428406007713 Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12. HMBS catalyzes the conversion of...; Region: HMBS; cl17708 428406007714 domain interfaces; other site 428406007715 active site 428406007716 phosphoenolpyruvate carboxylase; Reviewed; Region: PRK00009 428406007717 Phosphoenolpyruvate carboxylase [Energy production and conversion]; Region: Ppc; COG2352 428406007718 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406007719 Major Facilitator Superfamily; Region: MFS_1; pfam07690 428406007720 putative substrate translocation pore; other site 428406007721 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406007722 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406007723 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406007724 LysR substrate binding domain; Region: LysR_substrate; pfam03466 428406007725 dimerization interface [polypeptide binding]; other site 428406007726 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 428406007727 dinuclear metal binding motif [ion binding]; other site 428406007728 RNA polymerase sigma factor; Provisional; Region: PRK12514 428406007729 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 428406007730 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 428406007731 DNA binding residues [nucleotide binding] 428406007732 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5343 428406007733 Anti-sigma-K factor rskA; Region: RskA; pfam10099 428406007734 argininosuccinate lyase; Provisional; Region: PRK00855 428406007735 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 428406007736 active sites [active] 428406007737 tetramer interface [polypeptide binding]; other site 428406007738 Orn/Lys/Arg decarboxylase, N-terminal domain; Region: OKR_DC_1_N; pfam03709 428406007739 Arginine/lysine/ornithine decarboxylases [Amino acid transport and metabolism]; Region: LdcC; COG1982 428406007740 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 428406007741 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 428406007742 catalytic residue [active] 428406007743 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 428406007744 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 428406007745 trimer interface [polypeptide binding]; other site 428406007746 active site 428406007747 FdhD/NarQ family; Region: FdhD-NarQ; pfam02634 428406007748 Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the...; Region: Cu-Zn_Superoxide_Dismutase; cd00305 428406007749 Cu/Zn superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodC; COG2032 428406007750 E-class dimer interface [polypeptide binding]; other site 428406007751 P-class dimer interface [polypeptide binding]; other site 428406007752 active site 428406007753 Cu2+ binding site [ion binding]; other site 428406007754 Zn2+ binding site [ion binding]; other site 428406007755 Cytochrome b subunit of formate dehydrogenase [Energy production and conversion]; Region: FdnI; COG2864 428406007756 formate dehydrogenase, gamma subunit; Region: formate-DH-gamm; TIGR01583 428406007757 Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]; Region: HybA; COG0437 428406007758 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 428406007759 Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the...; Region: MopB_Formate-Dh-Na-like; cd02752 428406007760 [4Fe-4S] binding site [ion binding]; other site 428406007761 molybdopterin cofactor binding site; other site 428406007762 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 428406007763 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 428406007764 Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the...; Region: MopB_CT_Formate-Dh-Na-like; cd02792 428406007765 molybdopterin cofactor binding site; other site 428406007766 Uncharacterized component of anaerobic dehydrogenases [General function prediction only]; Region: TorD; COG3381 428406007767 4Fe-4S dicluster domain; Region: Fer4_10; pfam13237 428406007768 4Fe-4S binding domain; Region: Fer4; pfam00037 428406007769 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 428406007770 4Fe-4S binding domain; Region: Fer4; pfam00037 428406007771 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 428406007772 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 428406007773 Protein of unknown function (DUF3306); Region: DUF3306; pfam11748 428406007774 Protein of unknown function (DUF3305); Region: DUF3305; pfam11749 428406007775 antiporter inner membrane protein; Provisional; Region: PRK11670 428406007776 Domain of unknown function DUF59; Region: DUF59; pfam01883 428406007777 MRP (Multiple Resistance and pH adaptation) is a homologue of the Fer4_NifH superfamily. Like the other members of the superfamily, MRP contains a ATP-binding domain at the N-termini. It is found in bacteria as a membrane-spanning protein and functions...; Region: MRP-like; cd02037 428406007778 Walker A motif; other site 428406007779 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 428406007780 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 428406007781 ligand binding site [chemical binding]; other site 428406007782 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 428406007783 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 428406007784 active site 428406007785 HIGH motif; other site 428406007786 KMSKS motif; other site 428406007787 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 428406007788 tRNA binding surface [nucleotide binding]; other site 428406007789 anticodon binding site; other site 428406007790 tRNA-binding-domain-containing Escherichia coli methionyl-tRNA synthetase (EcMetRS)-like proteins. This family includes EcMetRS and Aquifex aeolicus Trbp111 (AaTrbp111). This domain has general tRNA binding properties. MetRS aminoacylates methionine...; Region: tRNA_bind_EcMetRS_like; cd02800 428406007791 dimer interface [polypeptide binding]; other site 428406007792 putative tRNA-binding site [nucleotide binding]; other site 428406007793 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2911 428406007794 Family of unknown function (DUF490); Region: DUF490; pfam04357 428406007795 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 428406007796 Surface antigen; Region: Bac_surface_Ag; pfam01103 428406007797 Protein of unknown function (DUF3460); Region: DUF3460; pfam11943 428406007798 Rec8/ScpA/Scc1-like protein (kleisin family) [Replication, recombination, and repair]; Region: scpA; COG1354 428406007799 pantoate--beta-alanine ligase; Region: panC; TIGR00018 428406007800 Pantoate-beta-alanine ligase; Region: PanC; cd00560 428406007801 active site 428406007802 ATP-binding site [chemical binding]; other site 428406007803 pantoate-binding site; other site 428406007804 HXXH motif; other site 428406007805 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 428406007806 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 428406007807 P-loop; other site 428406007808 Magnesium ion binding site [ion binding]; other site 428406007809 cobyric acid synthase; Provisional; Region: PRK00784 428406007810 Dethiobiotin synthetase [Coenzyme metabolism]; Region: BioD; COG0132 428406007811 Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ); Region: GATase1_CobQ; cd01750 428406007812 catalytic triad [active] 428406007813 Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU). CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a...; Region: CobU; cd00544 428406007814 homotrimer interface [polypeptide binding]; other site 428406007815 Walker A motif; other site 428406007816 GTP binding site [chemical binding]; other site 428406007817 Walker B motif; other site 428406007818 cobalamin biosynthesis protein; Provisional; Region: cobD; PRK01209 428406007819 putative threonine-phosphate decarboxylase; Provisional; Region: PRK06959 428406007820 L-threonine-O-3-phosphate decarboxylase; Region: L_thr_O3P_dcar; TIGR01140 428406007821 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 428406007822 catalytic residue [active] 428406007823 vitamin B12-transporter protein BtuF; Provisional; Region: PRK03379 428406007824 Cobalamin binding protein BtuF. These proteins have been shown to function as initial receptors in ABC transport of vitamin B12 (cobalamin) in eubacterial and some archaeal species. They belong to the TroA superfamily of helical backbone metal receptor...; Region: BtuF; cd01144 428406007825 cobalamin binding residues [chemical binding]; other site 428406007826 putative BtuC binding residues; other site 428406007827 dimer interface [polypeptide binding]; other site 428406007828 Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP_PGM_like; cd07067 428406007829 catalytic core [active] 428406007830 cobalamin synthase; Reviewed; Region: cobS; PRK00235 428406007831 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 428406007832 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 428406007833 putative dimer interface [polypeptide binding]; other site 428406007834 active site pocket [active] 428406007835 putative cataytic base [active] 428406007836 ATP:corrinoid adenosyltransferase [Coenzyme metabolism]; Region: BtuR; COG2109 428406007837 ATP:corrinoid adenosyltransferase BtuR/CobO/CobP. This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer; Region: CobA_CobO_BtuR; cd00561 428406007838 homodimer interface [polypeptide binding]; other site 428406007839 Walker A motif; other site 428406007840 ATP binding site [chemical binding]; other site 428406007841 hydroxycobalamin binding site [chemical binding]; other site 428406007842 Walker B motif; other site 428406007843 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 428406007844 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 428406007845 Walker A/P-loop; other site 428406007846 ATP binding site [chemical binding]; other site 428406007847 Q-loop/lid; other site 428406007848 ABC transporter signature motif; other site 428406007849 Walker B; other site 428406007850 D-loop; other site 428406007851 H-loop/switch region; other site 428406007852 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 428406007853 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 428406007854 ABC-ATPase subunit interface; other site 428406007855 dimer interface [polypeptide binding]; other site 428406007856 putative PBP binding regions; other site 428406007857 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 428406007858 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 428406007859 N-terminal plug; other site 428406007860 ligand-binding site [chemical binding]; other site 428406007861 Domain of unknown function (DUF1875); Region: DUF1875; pfam08961 428406007862 Cell division protein ZapA; Region: ZapA; pfam05164 428406007863 Uncharacterized conserved protein [Function unknown]; Region: COG2947 428406007864 Protein of unknown function (DUF541); Region: SIMPL; cl01077 428406007865 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 428406007866 DNA-binding transcriptional activator XapR; Provisional; Region: PRK09986 428406007867 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406007868 The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved in the biosynthesis of isoleucine, leucine and valine; contains type 2 periplasmic binding fold; Region: PBP2_IlvR; cd08453 428406007869 putative dimerization interface [polypeptide binding]; other site 428406007870 putative substrate binding pocket [chemical binding]; other site 428406007871 dihydroxy-acid dehydratase; Provisional; Region: PRK00911 428406007872 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; pfam04364 428406007873 multifunctional aminopeptidase A; Provisional; Region: PRK00913 428406007874 Cytosol aminopeptidase family, N-terminal and catalytic domains. Family M17 contains zinc- and manganese-dependent exopeptidases ( EC 3.4.11.1), including leucine aminopeptidase. They catalyze removal of amino acids from the N-terminus of a protein and...; Region: Peptidase_M17; cd00433 428406007875 interface (dimer of trimers) [polypeptide binding]; other site 428406007876 Substrate-binding/catalytic site; other site 428406007877 Zn-binding sites [ion binding]; other site 428406007878 Predicted permeases [General function prediction only]; Region: COG0795 428406007879 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 428406007880 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 428406007881 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 428406007882 Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), N-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a cobaltochelatase; Region: CbiX_SirB_N; cd03416 428406007883 putative active site [active] 428406007884 5-carboxymethyl-2-hydroxymuconate isomerase (CHMI) is a trimeric enzyme catalyzing the isomerization of the unsaturated ketone 5-(carboxymethyl)-2-hydroxymuconate to 5-(carboxymethyl)-2-oxo-3-hexene-1,6-dionate. This is one step in the...; Region: CHMI; cd00580 428406007885 putative substrate binding pocket [chemical binding]; other site 428406007886 trimer interface [polypeptide binding]; other site 428406007887 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 428406007888 active site 428406007889 SAM binding site [chemical binding]; other site 428406007890 homodimer interface [polypeptide binding]; other site 428406007891 GTPases - Sulfate adenylate transferase subunit 1 [Inorganic ion transport and metabolism]; Region: CysN; COG2895 428406007892 CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; Region: CysN_ATPS; cd04166 428406007893 CysD dimerization site [polypeptide binding]; other site 428406007894 G1 box; other site 428406007895 putative GEF interaction site [polypeptide binding]; other site 428406007896 GTP/Mg2+ binding site [chemical binding]; other site 428406007897 Switch I region; other site 428406007898 G2 box; other site 428406007899 G3 box; other site 428406007900 Switch II region; other site 428406007901 G4 box; other site 428406007902 G5 box; other site 428406007903 CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN...; Region: CysN_NodQ_II; cd03695 428406007904 TCysN_NoDQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN...; Region: CysN_NoDQ_III; cd04095 428406007905 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 428406007906 This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. A highly...; Region: PAPS_reductase; cd01713 428406007907 Active Sites [active] 428406007908 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes [Amino acid transport and metabolism / Coenzyme metabolism]; Region: CysH; COG0175 428406007909 This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. A highly...; Region: PAPS_reductase; cd01713 428406007910 Active Sites [active] 428406007911 Bacterial protein of unknown function (DUF934); Region: DUF934; pfam06073 428406007912 Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism]; Region: CysI; COG0155 428406007913 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 428406007914 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 428406007915 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 428406007916 transcriptional regulator CysB-like protein; Reviewed; Region: PRK12684 428406007917 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406007918 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 428406007919 substrate binding site [chemical binding]; other site 428406007920 dimerization interface [polypeptide binding]; other site 428406007921 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 428406007922 Type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids; Region: PBP1_ABC-type_HAAT_like; cd06333 428406007923 putative ligand binding site [chemical binding]; other site 428406007924 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 428406007925 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 428406007926 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 428406007927 active site 428406007928 DNA binding site [nucleotide binding] 428406007929 Int/Topo IB signature motif; other site 428406007930 Predicted chitinase [General function prediction only]; Region: COG3179 428406007931 catalytic residue [active] 428406007932 Acyltransferase family; Region: Acyl_transf_3; pfam01757 428406007933 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]; Region: COG3620 428406007934 GDSL-like Lipase/Acylhydrolase family; Region: Lipase_GDSL_2; pfam13472 428406007935 active site 428406007936 catalytic triad [active] 428406007937 oxyanion hole [active] 428406007938 Protein of unknown function (DUF2612); Region: DUF2612; pfam11041 428406007939 Baseplate J-like protein; Region: Baseplate_J; cl01294 428406007940 phage tail tape measure protein, TP901 family, core region; Region: tape_meas_TP901; TIGR01760 428406007941 virion protein; Provisional; Region: V; PHA02564 428406007942 Protein of unknown function (DUF3277); Region: DUF3277; pfam11681 428406007943 Protein of unknown function (DUF3383); Region: DUF3383; pfam11863 428406007944 Protein of unknown function (DUF4054); Region: DUF4054; pfam13262 428406007945 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4834 428406007946 Uncharacterized protein conserved in bacteria (DUF2184); Region: DUF2184; pfam09950 428406007947 Uncharacterized protein conserved in bacteria (DUF2213); Region: DUF2213; pfam09979 428406007948 Phage Mu protein F like protein; Region: Phage_Mu_F; cl10072 428406007949 phage-related protein, HI1409 family; Region: phge_rel_HI1409; TIGR01555 428406007950 Protein of unknown function (DUF1073); Region: DUF1073; pfam06381 428406007951 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5410 428406007952 Terminase-like family; Region: Terminase_6; pfam03237 428406007953 Phage-related terminase [General function prediction only]; Region: COG5362; cl02216 428406007954 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 428406007955 Protein of unknown function (DUF2591); Region: DUF2591; pfam10765 428406007956 Protein of unknown function (DUF968); Region: DUF968; pfam06147 428406007957 Protein of unknown function (DUF1367); Region: DUF1367; pfam07105 428406007958 HNH endonuclease; Region: HNH_3; pfam13392 428406007959 HNH endonuclease; Region: HNH_3; pfam13392 428406007960 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 428406007961 DNA-binding interface [nucleotide binding]; DNA binding site 428406007962 replicative DNA helicase; Region: DnaB; TIGR00665 428406007963 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 428406007964 DnaB helicase C terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a...; Region: DnaB_C; cd00984 428406007965 Walker A motif; other site 428406007966 ATP binding site [chemical binding]; other site 428406007967 Walker B motif; other site 428406007968 DNA binding loops [nucleotide binding] 428406007969 MarR family; Region: MarR_2; cl17246 428406007970 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 428406007971 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 428406007972 non-specific DNA binding site [nucleotide binding]; other site 428406007973 salt bridge; other site 428406007974 sequence-specific DNA binding site [nucleotide binding]; other site 428406007975 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 428406007976 non-specific DNA binding site [nucleotide binding]; other site 428406007977 sequence-specific DNA binding site [nucleotide binding]; other site 428406007978 salt bridge; other site 428406007979 Predicted transcriptional regulator [Transcription]; Region: COG2932 428406007980 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC...; Region: S24_LexA-like; cd06529 428406007981 Catalytic site [active] 428406007982 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 428406007983 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 428406007984 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 428406007985 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 428406007986 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 428406007987 KTSC domain; Region: KTSC; pfam13619 428406007988 YqaJ-like viral recombinase domain; Region: YqaJ; pfam09588 428406007989 restriction alleviation protein, Lar family; Region: anti_R_Lar; TIGR03655 428406007990 Helix-turn-helix domain; Region: HTH_17; cl17695 428406007991 dihydroxy-acid dehydratase; Provisional; Region: PRK12448 428406007992 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 428406007993 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 428406007994 active site 428406007995 catalytic tetrad [active] 428406007996 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 428406007997 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406007998 putative substrate translocation pore; other site 428406007999 Transcriptional regulators [Transcription]; Region: MarR; COG1846 428406008000 MarR family; Region: MarR_2; pfam12802 428406008001 CLC voltage-gated chloride channel. The ClC chloride channels catalyse the selective flow of Cl- ions across cell membranes, thereby regulating electrical excitation in skeletal muscle and the flow of salt and water across epithelial barriers. This...; Region: Voltage_gated_ClC; cd00400 428406008002 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 428406008003 Cl- selectivity filter; other site 428406008004 Cl- binding residues [ion binding]; other site 428406008005 pore gating glutamate residue; other site 428406008006 dimer interface [polypeptide binding]; other site 428406008007 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with either the SpoIVFB domain (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) or the chloride channel protein EriC; Region: CBS_pair_SpoIVFB_EriC_assoc; cd04612 428406008008 FOG: CBS domain [General function prediction only]; Region: COG0517 428406008009 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 428406008010 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 428406008011 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 428406008012 metal binding site [ion binding]; metal-binding site 428406008013 active site 428406008014 I-site; other site 428406008015 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 428406008016 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 428406008017 NAD(P) binding site [chemical binding]; other site 428406008018 active site 428406008019 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 428406008020 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 428406008021 catalytic loop [active] 428406008022 iron binding site [ion binding]; other site 428406008023 NAD(P)H dependent flavin oxidoreductases use flavin as a substrate in mediating electron transfer from iron complexes or iron proteins. Structurally similar to ferredoxin reductases, but with only 15% sequence identity, flavin reductases reduce FAD, FMN; Region: flavin_oxioreductase; cd06189 428406008024 FAD binding pocket [chemical binding]; other site 428406008025 FAD binding motif [chemical binding]; other site 428406008026 phosphate binding motif [ion binding]; other site 428406008027 beta-alpha-beta structure motif; other site 428406008028 NAD binding pocket [chemical binding]; other site 428406008029 acetylornithine transaminase protein; Provisional; Region: argD; PRK03715 428406008030 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 428406008031 inhibitor-cofactor binding pocket; inhibition site 428406008032 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406008033 catalytic residue [active] 428406008034 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 428406008035 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 428406008036 Coenzyme A binding pocket [chemical binding]; other site 428406008037 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 428406008038 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 428406008039 Walker A/P-loop; other site 428406008040 ATP binding site [chemical binding]; other site 428406008041 Q-loop/lid; other site 428406008042 ABC transporter signature motif; other site 428406008043 Walker B; other site 428406008044 D-loop; other site 428406008045 H-loop/switch region; other site 428406008046 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 428406008047 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 428406008048 Walker A/P-loop; other site 428406008049 ATP binding site [chemical binding]; other site 428406008050 Q-loop/lid; other site 428406008051 ABC transporter signature motif; other site 428406008052 Walker B; other site 428406008053 D-loop; other site 428406008054 H-loop/switch region; other site 428406008055 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 428406008056 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 428406008057 TM-ABC transporter signature motif; other site 428406008058 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 428406008059 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 428406008060 TM-ABC transporter signature motif; other site 428406008061 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 428406008062 Type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine); Region: PBP1_ABC_LIVBP_like; cd06342 428406008063 dimerization interface [polypeptide binding]; other site 428406008064 ligand binding site [chemical binding]; other site 428406008065 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism]; Region: lytB; COG0761 428406008066 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 428406008067 FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]; Region: SlpA; COG1047 428406008068 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 428406008069 hypothetical protein; Reviewed; Region: PRK00024 428406008070 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 428406008071 MPN+ (JAMM) motif; other site 428406008072 Zinc-binding site [ion binding]; other site 428406008073 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 428406008074 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 428406008075 L-aspartate oxidase; Provisional; Region: PRK09077 428406008076 L-aspartate oxidase; Provisional; Region: PRK06175 428406008077 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 428406008078 nicotinate-nucleotide pyrophosphorylase; Provisional; Region: PRK06978 428406008079 Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase), also called nicotinate-nucleotide pyrophosphorylase, is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid (QA) with...; Region: QPRTase; cd01572 428406008080 dimerization interface [polypeptide binding]; other site 428406008081 active site 428406008082 quinolinate synthetase; Provisional; Region: PRK09375 428406008083 The Delta9 Fatty Acid Desaturase (Delta9-FADS)-like CD includes the delta-9 and delta-11 acyl CoA desaturases found in various eukaryotes including vertebrates, insects, higher plants, and fungi. The delta-9 acyl-lipid desaturases are found in a wide...; Region: Delta9-FADS-like; cd03505 428406008084 Fatty acid desaturase; Region: FA_desaturase; pfam00487 428406008085 Di-iron ligands [ion binding]; other site 428406008086 Transposase; Region: DDE_Tnp_ISL3; pfam01610 428406008087 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: COG3264 428406008088 Mechanosensitive ion channel; Region: MS_channel; pfam00924 428406008089 Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar proteins; Region: PLDc_Nuc; cd09170 428406008090 PLD-like domain; Region: PLDc_2; pfam13091 428406008091 putative active site [active] 428406008092 catalytic site [active] 428406008093 ribosomal RNA small subunit methyltransferase RsmB; Region: rsmB; TIGR00563 428406008094 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 428406008095 S-adenosylmethionine binding site [chemical binding]; other site 428406008096 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 428406008097 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 428406008098 active site 428406008099 substrate binding site [chemical binding]; other site 428406008100 cosubstrate binding site; other site 428406008101 catalytic site [active] 428406008102 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 428406008103 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406008104 active site 428406008105 phosphorylation site [posttranslational modification] 428406008106 intermolecular recognition site; other site 428406008107 dimerization interface [polypeptide binding]; other site 428406008108 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 428406008109 DNA binding residues [nucleotide binding] 428406008110 dimerization interface [polypeptide binding]; other site 428406008111 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 428406008112 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 428406008113 dimer interface [polypeptide binding]; other site 428406008114 phosphorylation site [posttranslational modification] 428406008115 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406008116 ATP binding site [chemical binding]; other site 428406008117 Mg2+ binding site [ion binding]; other site 428406008118 G-X-G motif; other site 428406008119 Response regulator receiver domain; Region: Response_reg; pfam00072 428406008120 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406008121 active site 428406008122 phosphorylation site [posttranslational modification] 428406008123 intermolecular recognition site; other site 428406008124 dimerization interface [polypeptide binding]; other site 428406008125 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 428406008126 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 428406008127 active site 428406008128 Riboflavin kinase; Region: Flavokinase; smart00904 428406008129 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 428406008130 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 428406008131 active site 428406008132 HIGH motif; other site 428406008133 nucleotide binding site [chemical binding]; other site 428406008134 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 428406008135 active site 428406008136 KMSKS motif; other site 428406008137 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 428406008138 tRNA binding surface [nucleotide binding]; other site 428406008139 anticodon binding site; other site 428406008140 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 428406008141 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 428406008142 lipoprotein signal peptidase; Provisional; Region: PRK14787 428406008143 Uncharacterized conserved protein [Function unknown]; Region: COG1434 428406008144 YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been...; Region: YdcF-like; cd06259 428406008145 putative active site [active] 428406008146 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 428406008147 Flavoprotein; Region: Flavoprotein; pfam02441 428406008148 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 428406008149 luciferase family oxidoreductase, group 1; Region: oxido_grp_1; TIGR03558 428406008150 Flavin-utilizing monoxygenases; Region: Flavin_utilizing_monoxygenases; cl07892 428406008151 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 428406008152 trimer interface [polypeptide binding]; other site 428406008153 active site 428406008154 ATP-dependent Clp protease ATP-binding subunit clpA; Region: ClpA; TIGR02639 428406008155 Clp amino terminal domain; Region: Clp_N; pfam02861 428406008156 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406008157 Walker A motif; other site 428406008158 ATP binding site [chemical binding]; other site 428406008159 Walker B motif; other site 428406008160 arginine finger; other site 428406008161 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406008162 Walker A motif; other site 428406008163 ATP binding site [chemical binding]; other site 428406008164 Walker B motif; other site 428406008165 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 428406008166 Uncharacterized conserved protein [Function unknown]; Region: COG2127 428406008167 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 428406008168 DNA-binding site [nucleotide binding]; DNA binding site 428406008169 RNA-binding motif; other site 428406008170 Domain of unknown function (DUF4126); Region: DUF4126; pfam13548 428406008171 isocitrate dehydrogenase; Validated; Region: PRK07362 428406008172 isocitrate dehydrogenase; Reviewed; Region: PRK07006 428406008173 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 428406008174 active site 428406008175 metal binding site [ion binding]; metal-binding site 428406008176 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 428406008177 di-heme enzyme, MXAN_0977 family; Region: MXAN_0977_Heme2; TIGR04039 428406008178 Uncharacterized ACR, COG1430; Region: DUF192; pfam02643 428406008179 Metal-dependent hydrolases of the beta-lactamase superfamily III [General function prediction only]; Region: ElaC; COG1234 428406008180 Predicted periplasmic protein [General function prediction only]; Region: COG3895 428406008181 Membrane-bound lysozyme-inhibitor of c-type lysozyme; Region: MliC; pfam09864 428406008182 DNA-binding transcriptional regulator LysR; Provisional; Region: PRK11013 428406008183 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406008184 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 428406008185 dimerization interface [polypeptide binding]; other site 428406008186 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406008187 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406008188 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 428406008189 putative effector binding pocket; other site 428406008190 dimerization interface [polypeptide binding]; other site 428406008191 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 428406008192 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406008193 putative substrate translocation pore; other site 428406008194 Predicted membrane protein [Function unknown]; Region: COG2259 428406008195 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406008196 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406008197 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_2; cd08427 428406008198 putative dimerization interface [polypeptide binding]; other site 428406008199 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 428406008200 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 428406008201 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406008202 citrate-proton symporter; Provisional; Region: PRK15075 428406008203 putative substrate translocation pore; other site 428406008204 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 428406008205 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 428406008206 dimer interface [polypeptide binding]; other site 428406008207 active site 428406008208 catalytic residue [active] 428406008209 Predicted metalloprotease [General function prediction only]; Region: COG2321 428406008210 Putative neutral zinc metallopeptidase; Region: Zn_peptidase; pfam04228 428406008211 glucose-1-dehydrogenase; Provisional; Region: PRK06947 428406008212 classical (c) SDRs; Region: SDR_c; cd05233 428406008213 NAD(P) binding site [chemical binding]; other site 428406008214 active site 428406008215 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Ada; COG2169 428406008216 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 428406008217 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 428406008218 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 428406008219 AlkA N-terminal domain; Region: AlkA_N; pfam06029 428406008220 3-methyl-adenine DNA glycosylase II; Provisional; Region: PRK10308 428406008221 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 428406008222 minor groove reading motif; other site 428406008223 helix-hairpin-helix signature motif; other site 428406008224 substrate binding pocket [chemical binding]; other site 428406008225 active site 428406008226 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 428406008227 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 428406008228 The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases...; Region: ATase; cd06445 428406008229 DNA binding site [nucleotide binding] 428406008230 active site 428406008231 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 428406008232 EamA-like transporter family; Region: EamA; pfam00892 428406008233 EamA-like transporter family; Region: EamA; pfam00892 428406008234 HipA N-terminal domain; Region: Couple_hipA; cl11853 428406008235 HipA-like N-terminal domain; Region: HipA_N; pfam07805 428406008236 HipA-like C-terminal domain; Region: HipA_C; pfam07804 428406008237 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like6; cd05664 428406008238 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 428406008239 metal binding site [ion binding]; metal-binding site 428406008240 putative dimer interface [polypeptide binding]; other site 428406008241 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 428406008242 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 428406008243 substrate binding pocket [chemical binding]; other site 428406008244 membrane-bound complex binding site; other site 428406008245 hinge residues; other site 428406008246 Predicted secreted protein [Function unknown]; Region: COG5445 428406008247 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 428406008248 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 428406008249 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 428406008250 Zn2+ binding site [ion binding]; other site 428406008251 Mg2+ binding site [ion binding]; other site 428406008252 Periplasmic glycine betaine/choline-binding (lipo)protein of an ABC-type transport system (osmoprotectant binding protein) [Cell envelope biogenesis, outer membrane]; Region: OpuBC; COG1732 428406008253 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406008254 dimer interface [polypeptide binding]; other site 428406008255 conserved gate region; other site 428406008256 ABC-ATPase subunit interface; other site 428406008257 H+/gluconate symporter and related permeases [Carbohydrate transport and metabolism / Amino acid transport and metabolism]; Region: GntT; COG2610 428406008258 metabolite-proton symporter; Region: 2A0106; TIGR00883 428406008259 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406008260 putative substrate translocation pore; other site 428406008261 CC3(TIP30)-like, atypical (a) SDRs; Region: CC3_like_SDR_a; cd05250 428406008262 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 428406008263 NAD binding site [chemical binding]; other site 428406008264 active site 428406008265 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 428406008266 IHF dimer interface [polypeptide binding]; other site 428406008267 IHF - DNA interface [nucleotide binding]; other site 428406008268 HutD; Region: HutD; pfam05962 428406008269 Formimidoylglutamase or HutE; Region: Formimidoylglutamase; cd09988 428406008270 putative active site [active] 428406008271 putative metal binding site [ion binding]; other site 428406008272 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 428406008273 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 428406008274 Walker A/P-loop; other site 428406008275 ATP binding site [chemical binding]; other site 428406008276 Q-loop/lid; other site 428406008277 ABC transporter signature motif; other site 428406008278 Walker B; other site 428406008279 D-loop; other site 428406008280 H-loop/switch region; other site 428406008281 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family; Region: HEQRo_perm_3TM; TIGR01726 428406008282 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406008283 ABC-ATPase subunit interface; other site 428406008284 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 428406008285 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 428406008286 substrate binding pocket [chemical binding]; other site 428406008287 membrane-bound complex binding site; other site 428406008288 hinge residues; other site 428406008289 Transcriptional regulator [Transcription]; Region: IclR; COG1414 428406008290 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 428406008291 Bacterial transcriptional regulator; Region: IclR; pfam01614 428406008292 SnoaL-like polyketide cyclase; Region: SnoaL; pfam07366 428406008293 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the...; Region: S2P-M50_like_2; cd06160 428406008294 Peptidase family M50; Region: Peptidase_M50; pfam02163 428406008295 active site 428406008296 putative substrate binding region [chemical binding]; other site 428406008297 superoxide dismutase; Provisional; Region: PRK10543 428406008298 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 428406008299 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 428406008300 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 428406008301 ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a...; Region: ExoVII_LU_OBF; cd04489 428406008302 generic binding surface II; other site 428406008303 generic binding surface I; other site 428406008304 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 428406008305 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 428406008306 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 428406008307 tetraacyldisaccharide 4'-kinase; Provisional; Region: PRK01906 428406008308 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 428406008309 Uncharacterized conserved protein [Function unknown]; Region: COG2835 428406008310 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 428406008311 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 428406008312 Ligand binding site; other site 428406008313 oligomer interface; other site 428406008314 adenylate kinase; Reviewed; Region: adk; PRK00279 428406008315 Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP). This enzyme is required for the biosynthesis of ADP and is essential for...; Region: ADK; cd01428 428406008316 AMP-binding site [chemical binding]; other site 428406008317 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 428406008318 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK08217 428406008319 17hydroxysteroid dehydrogenase type 10 (HSD10)-like, classical (c) SDRs; Region: HSD10-like_SDR_c; cd05371 428406008320 NAD binding site [chemical binding]; other site 428406008321 homodimer interface [polypeptide binding]; other site 428406008322 homotetramer interface [polypeptide binding]; other site 428406008323 active site 428406008324 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406008325 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406008326 TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_4; cd08440 428406008327 putative dimerization interface [polypeptide binding]; other site 428406008328 Predicted Na+-dependent transporter [General function prediction only]; Region: COG0385 428406008329 SBF-like CPA transporter family (DUF4137); Region: DUF4137; pfam13593 428406008330 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 428406008331 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 428406008332 Coenzyme A binding pocket [chemical binding]; other site 428406008333 AMIN domain; Region: AMIN; pfam11741 428406008334 N-acetylmuramoyl-L-alanine amidase or MurNAc-LAA (also known as peptidoglycan aminohydrolase, NAMLA amidase, NAMLAA, Amidase 3, and peptidoglycan amidase; EC 3.5.1.28) is an autolysin that hydrolyzes the amide bond between N-acetylmuramoyl and L-amino...; Region: MurNAc-LAA; cd02696 428406008335 active site 428406008336 metal binding site [ion binding]; metal-binding site 428406008337 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 428406008338 epoxyqueuosine reductase; Region: TIGR00276 428406008339 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 428406008340 Chalcone-flavanone isomerase; Region: Chalcone; cl03589 428406008341 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl17792 428406008342 methylated-DNA--protein-cysteine methyltransferase; Provisional; Region: PRK00901 428406008343 The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases...; Region: ATase; cd06445 428406008344 DNA binding site [nucleotide binding] 428406008345 active site 428406008346 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 428406008347 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 428406008348 active site 428406008349 DNA binding site [nucleotide binding] 428406008350 Int/Topo IB signature motif; other site 428406008351 This CD includes cysteinyl-tRNA(Pro) deacylases from Haemophilus influenzae and Escherichia coli and other related bacterial proteins. These trans-acting, single-domain proteins are homologs of ProX and also the cis-acting prolyl-tRNA synthetase (ProRS)...; Region: YbaK_deacylase; cd00002 428406008352 putative deacylase active site [active] 428406008353 putative glycerol-3-phosphate acyltransferase PlsY; Provisional; Region: PRK00220 428406008354 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 428406008355 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 428406008356 conserved cys residue [active] 428406008357 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 428406008358 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 428406008359 Protein related to penicillin acylase [General function prediction only]; Region: COG2366 428406008360 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a...; Region: Ntn_hydrolase; cl00467 428406008361 Cephalosporin acylase (CA) belongs to a family of beta-lactam acylases that includes penicillin G acylase (PGA) and aculeacin A acylase. PGA and CA are crucial for the production of backbone chemicals like 6-aminopenicillanic acid and...; Region: Ntn_CA; cd01936 428406008362 active site 428406008363 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a...; Region: Ntn_hydrolase; cl00467 428406008364 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1666 428406008365 Proteins similar to Escherichia coli YajQ; Region: YajQ_like; cd11740 428406008366 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK00046 428406008367 FAD binding domain; Region: FAD_binding_4; pfam01565 428406008368 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 428406008369 Protein of unknown function (DUF1255); Region: DUF1255; pfam06865 428406008370 argininosuccinate synthase; Validated; Region: PRK05370 428406008371 argininosuccinate synthase; Provisional; Region: PRK13820 428406008372 ornithine carbamoyltransferase; Provisional; Region: PRK00779 428406008373 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 428406008374 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 428406008375 Protein of unknown function (DUF3579); Region: DUF3579; pfam12112 428406008376 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 428406008377 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 428406008378 Uncharacterized conserved protein [Function unknown]; Region: COG2912 428406008379 Transglutaminase-like superfamily; Region: Transglut_core2; pfam13369 428406008380 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 428406008381 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 428406008382 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 428406008383 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406008384 ATP binding site [chemical binding]; other site 428406008385 Mg2+ binding site [ion binding]; other site 428406008386 G-X-G motif; other site 428406008387 MutL_Trans_MutL: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to Escherichia coli MutL. EcMutL belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second...; Region: MutL_Trans_MutL; cd03482 428406008388 ATP binding site [chemical binding]; other site 428406008389 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 428406008390 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 428406008391 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 428406008392 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 428406008393 Coenzyme A binding pocket [chemical binding]; other site 428406008394 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3826 428406008395 alpha-ketoglutarate-dependent dioxygenase AlkB; Provisional; Region: PRK15401 428406008396 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]; Region: AlkA; COG0122 428406008397 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 428406008398 minor groove reading motif; other site 428406008399 helix-hairpin-helix signature motif; other site 428406008400 substrate binding pocket [chemical binding]; other site 428406008401 active site 428406008402 Periplasmic nitrate reductase protein NapE; Region: NapE; pfam06796 428406008403 NapD protein; Region: NapD; pfam03927 428406008404 nitrate reductase catalytic subunit; Provisional; Region: PRK13532 428406008405 Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol...; Region: MopB_Nitrate-R-NapA-like; cd02754 428406008406 [4Fe-4S] binding site [ion binding]; other site 428406008407 molybdopterin cofactor binding site; other site 428406008408 Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol...; Region: MopB_CT_Nitrate-R-NapA-like; cd02791 428406008409 molybdopterin cofactor binding site; other site 428406008410 Nitrate reductase cytochrome c-type subunit (NapB); Region: NapB; pfam03892 428406008411 periplasmic nitrate (or nitrite) reductase c-type cytochrome, NapC/NirT family; Region: napC_nirT; TIGR02161 428406008412 NapC/NirT cytochrome c family, N-terminal region; Region: Cytochrom_NNT; pfam03264 428406008413 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13538 428406008414 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 428406008415 Walker A/P-loop; other site 428406008416 ATP binding site [chemical binding]; other site 428406008417 Q-loop/lid; other site 428406008418 ABC transporter signature motif; other site 428406008419 Walker B; other site 428406008420 D-loop; other site 428406008421 H-loop/switch region; other site 428406008422 ABC-type transport system involved in cytochrome c biogenesis, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CcmB; COG2386 428406008423 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 428406008424 cytochrome c-type biogenesis protein CcmE; Reviewed; Region: PRK13254 428406008425 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: CcmF; COG1138 428406008426 TlpA-like family, DsbE (also known as CcmG and CycY) subfamily; DsbE is a membrane-anchored, periplasmic TRX-like reductase containing a CXXC motif that specifically donates reducing equivalents to apocytochrome c via CcmH, another cytochrome c...; Region: TlpA_like_DsbE; cd03010 428406008427 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 428406008428 catalytic residues [active] 428406008429 central insert; other site 428406008430 Cytochrome C biogenesis protein; Region: CcmH; pfam03918 428406008431 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: COG4235 428406008432 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional; Region: PRK15435 428406008433 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 428406008434 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 428406008435 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 428406008436 The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases...; Region: ATase; cd06445 428406008437 DNA binding site [nucleotide binding] 428406008438 active site 428406008439 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 428406008440 PurM (Aminoimidazole Ribonucleotide [AIR] synthetase), one of eleven enzymes required for purine biosynthesis, catalyzes the conversion of formylglycinamide ribonucleotide (FGAM) and ATP to AIR, ADP, and Pi, the fifth step in de novo purine biosynthesis; Region: PurM; cd02196 428406008441 dimerization interface [polypeptide binding]; other site 428406008442 putative ATP binding site [chemical binding]; other site 428406008443 Domain of unknown function DUF20; Region: UPF0118; pfam01594 428406008444 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 428406008445 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 428406008446 DnaA regulatory inactivator Hda; Validated; Region: PRK08903 428406008447 Walker A motif; other site 428406008448 ATP binding site [chemical binding]; other site 428406008449 Walker B motif; other site 428406008450 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 428406008451 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 428406008452 poly(A) polymerase; Region: pcnB; TIGR01942 428406008453 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 428406008454 active site 428406008455 NTP binding site [chemical binding]; other site 428406008456 metal binding triad [ion binding]; metal-binding site 428406008457 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 428406008458 Polymerase A arginine-rich C-terminus; Region: PolyA_pol_arg_C; pfam12626 428406008459 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK). Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and amino acids as well as formyl-tRNA. Mammalian cells are able to utilize pre-formed folates after...; Region: HPPK; cd00483 428406008460 catalytic center binding site [active] 428406008461 ATP binding site [chemical binding]; other site 428406008462 Deoxynucleoside kinases [Nucleotide transport and metabolism]; Region: COG1428 428406008463 Deoxyribonucleoside kinase (dNK) catalyzes the phosphorylation of deoxyribonucleosides to yield corresponding monophosphates (dNMPs). This family consists of various deoxynucleoside kinases including deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC 2.7.1; Region: dNK; cd01673 428406008464 Substrate-binding site [chemical binding]; other site 428406008465 Substrate specificity [chemical binding]; other site 428406008466 Ketopantoate hydroxymethyltransferase (KPHMT) is the first enzyme in the pantothenate biosynthesis pathway. Ketopantoate hydroxymethyltransferase (KPHMT) catalyzes the first committed step in the biosynthesis of pantothenate (vitamin B5), which is a...; Region: KPHMT-like; cd06557 428406008467 oligomerization interface [polypeptide binding]; other site 428406008468 active site 428406008469 metal binding site [ion binding]; metal-binding site 428406008470 ABC-type tungstate transport system, periplasmic component [Coenzyme metabolism]; Region: TupA; COG4662 428406008471 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 428406008472 cobalt transport protein ATP-binding subunit; Region: cbiO; TIGR01166 428406008473 Walker A/P-loop; other site 428406008474 ATP binding site [chemical binding]; other site 428406008475 Q-loop/lid; other site 428406008476 ABC transporter signature motif; other site 428406008477 Walker B; other site 428406008478 D-loop; other site 428406008479 H-loop/switch region; other site 428406008480 aminodeoxychorismate synthase; Provisional; Region: PRK07508 428406008481 chorismate binding enzyme; Region: Chorismate_bind; cl10555 428406008482 PyridoxaL 5'-Phosphate Dependent Enzymes class IV (PLPDE_IV). This D-amino acid superfamily, one of five classes of PLPDE, consists of branched-chain amino acid aminotransferases (BCAT), D-amino acid transferases (DAAT), and...; Region: PLPDE_IV; cl00224 428406008483 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 428406008484 substrate-cofactor binding pocket; other site 428406008485 homodimer interface [polypeptide binding]; other site 428406008486 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406008487 catalytic residue [active] 428406008488 chaperone protein DnaJ; Provisional; Region: PRK10767 428406008489 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s; Region: DnaJ; cd06257 428406008490 HSP70 interaction site [polypeptide binding]; other site 428406008491 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 428406008492 Zn binding sites [ion binding]; other site 428406008493 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 428406008494 dimer interface [polypeptide binding]; other site 428406008495 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 428406008496 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 428406008497 nucleotide binding site [chemical binding]; other site 428406008498 The outer membrane phospholipase A (OMPLA) is an integral membrane enzyme that catalyses the hydrolysis of acylester bonds in phospholipids using calcium as a cofactor. The enzyme has a fold of transmembrane beta-barrels and is widespread among...; Region: OMPLA; cd00541 428406008499 substrate binding site [chemical binding]; other site 428406008500 dimerization interface [polypeptide binding]; other site 428406008501 active site 428406008502 calcium binding site [ion binding]; other site 428406008503 nucleoside diphosphate kinase regulator; Provisional; Region: PRK05753 428406008504 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 428406008505 TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains. Group I TRX is a small ancient protein that alter the redox...; Region: TRX_family; cd02947 428406008506 catalytic residues [active] 428406008507 Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: GrpE; COG0576 428406008508 GrpE is the adenine nucleotide exchange factor of DnaK (Hsp70)-type ATPases. The GrpE dimer binds to the ATPase domain of Hsp70 catalyzing the dissociation of ADP, which enables rebinding of ATP, one step in the Hsp70 reaction cycle in protein folding; Region: GrpE; cd00446 428406008509 dimer interface [polypeptide binding]; other site 428406008510 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 428406008511 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cd00165 428406008512 RNA binding surface [nucleotide binding]; other site 428406008513 ferrochelatase; Reviewed; Region: hemH; PRK00035 428406008514 Ferrochelatase, N-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is...; Region: Ferrochelatase_N; cd03411 428406008515 C-terminal domain interface [polypeptide binding]; other site 428406008516 active site 428406008517 Ferrochelatase, C-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is...; Region: Ferrochelatase_C; cd00419 428406008518 active site 428406008519 N-terminal domain interface [polypeptide binding]; other site 428406008520 imidazolonepropionase; Validated; Region: PRK09356 428406008521 Imidazolonepropionase/imidazolone-5-propionate hydrolase (Imidazolone-5PH) catalyzes the third step in the histidine degradation pathway, the hydrolysis of (S)-3-(5-oxo-4,5-dihydro-3H-imidazol-4-yl)propanoate to N-formimidoyl-L-glutamate. In bacteria; Region: Imidazolone-5PH; cd01296 428406008522 active site 428406008523 Formimidoylglutamase or HutE; Region: Formimidoylglutamase; cd09988 428406008524 putative active site [active] 428406008525 putative metal binding site [ion binding]; other site 428406008526 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 428406008527 active sites [active] 428406008528 tetramer interface [polypeptide binding]; other site 428406008529 urocanate hydratase; Provisional; Region: PRK05414 428406008530 histidine utilization repressor, proteobacterial; Region: his_ut_repres; TIGR02018 428406008531 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 428406008532 DNA-binding site [nucleotide binding]; DNA binding site 428406008533 UTRA domain; Region: UTRA; pfam07702 428406008534 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 428406008535 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406008536 dimer interface [polypeptide binding]; other site 428406008537 conserved gate region; other site 428406008538 putative PBP binding loops; other site 428406008539 ABC-ATPase subunit interface; other site 428406008540 ABC-type taurine transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG4525 428406008541 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 428406008542 Walker A/P-loop; other site 428406008543 ATP binding site [chemical binding]; other site 428406008544 Q-loop/lid; other site 428406008545 ABC transporter signature motif; other site 428406008546 Walker B; other site 428406008547 D-loop; other site 428406008548 H-loop/switch region; other site 428406008549 ABC-type taurine transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: TauA; COG4521 428406008550 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 428406008551 substrate binding pocket [chemical binding]; other site 428406008552 membrane-bound complex binding site; other site 428406008553 hinge residues; other site 428406008554 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 428406008555 Winged helix-turn-helix transcription repressor, HrcA DNA-binding; Region: HrcA_DNA-bdg; pfam03444 428406008556 NAD(+)/NADH kinase family protein; Provisional; Region: ppnK; PRK02155 428406008557 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK02231 428406008558 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 428406008559 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 428406008560 Walker A/P-loop; other site 428406008561 ATP binding site [chemical binding]; other site 428406008562 Q-loop/lid; other site 428406008563 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 428406008564 ABC transporter signature motif; other site 428406008565 Walker B; other site 428406008566 D-loop; other site 428406008567 H-loop/switch region; other site 428406008568 Peptidase S8 family domain, uncharacterized subfamily 13; Region: Peptidases_S8_13; cd07496 428406008569 active site 428406008570 catalytic triad [active] 428406008571 Peptidase S8 family domain, uncharacterized subfamily 13; Region: Peptidases_S8_13; cd07496 428406008572 active site 428406008573 catalytic triad [active] 428406008574 rhomboid family GlyGly-CTERM serine protease; Region: rhom_GG_sort; TIGR03902 428406008575 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed; Region: PRK11072 428406008576 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 428406008577 metal binding triad; other site 428406008578 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 428406008579 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 428406008580 metal binding triad; other site 428406008581 Predicted membrane protein [Function unknown]; Region: COG3164 428406008582 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 428406008583 nitrilase; Region: PLN02798 428406008584 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 428406008585 putative active site [active] 428406008586 catalytic triad [active] 428406008587 dimer interface [polypeptide binding]; other site 428406008588 protease TldD; Provisional; Region: tldD; PRK10735 428406008589 phospho-2-dehydro-3-deoxyheptonate aldolase; Validated; Region: PRK09261 428406008590 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 428406008591 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 428406008592 Mechanosensitive ion channel; Region: MS_channel; pfam00924 428406008593 ATP:cob(I)alamin adenosyltransferase; Region: PduO_Nterm; TIGR00636 428406008594 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 428406008595 FAD binding domain; Region: FAD_binding_4; pfam01565 428406008596 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 428406008597 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406008598 The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 428406008599 dimerization interface [polypeptide binding]; other site 428406008600 substrate binding pocket [chemical binding]; other site 428406008601 glycolate oxidase subunit GlcD; Provisional; Region: PRK11230 428406008602 FAD binding domain; Region: FAD_binding_4; pfam01565 428406008603 glycolate oxidase FAD binding subunit; Provisional; Region: glcE; PRK11282 428406008604 FAD binding domain; Region: FAD_binding_4; pfam01565 428406008605 glycolate oxidase iron-sulfur subunit; Provisional; Region: glcF; PRK11274 428406008606 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 428406008607 Cysteine-rich domain; Region: CCG; pfam02754 428406008608 Cysteine-rich domain; Region: CCG; pfam02754 428406008609 Putative effector of murein hydrolase LrgA [General function prediction only]; Region: COG1380 428406008610 Putative effector of murein hydrolase [Cell envelope biogenesis, outer membrane]; Region: LrgB; COG1346 428406008611 N-terminal domain of Streptomyces griseus SgaA (suppression of growth disturbance caused by A-factor at a high concentration under high osmolality during early growth phase), and similar domains; Region: SgaA_N_like; cd07247 428406008612 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 428406008613 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG3837 428406008614 Predicted transcriptional regulator [Transcription]; Region: COG2378 428406008615 HTH domain; Region: HTH_11; pfam08279 428406008616 WYL domain; Region: WYL; pfam13280 428406008617 Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue per...; Region: GSH_Peroxidase; cd00340 428406008618 catalytic residues [active] 428406008619 dimer interface [polypeptide binding]; other site 428406008620 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 428406008621 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 428406008622 Walker A motif; other site 428406008623 ATP binding site [chemical binding]; other site 428406008624 Walker B motif; other site 428406008625 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 428406008626 Pilus retraction ATPase PilT. PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism...; Region: PilT; cd01131 428406008627 Walker A motif; other site 428406008628 ATP binding site [chemical binding]; other site 428406008629 Walker B motif; other site 428406008630 Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins; Region: PLPDE_III_Yggs_like; cd06824 428406008631 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 428406008632 catalytic residue [active] 428406008633 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 428406008634 pyrroline-5-carboxylate reductase; Region: proC; TIGR00112 428406008635 4-hydroxybenzoate octaprenyltransferase; Reviewed; Region: ubiA; PRK12848 428406008636 UbiA prenyltransferase family; Region: UbiA; pfam01040 428406008637 catalase/hydroperoxidase HPI(I); Provisional; Region: PRK15061 428406008638 N-terminal catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_1; cd00649 428406008639 dimer interface [polypeptide binding]; other site 428406008640 active site 428406008641 heme binding site [chemical binding]; other site 428406008642 C-terminal non-catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_2; cd08200 428406008643 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 428406008644 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 428406008645 dimerization interface [polypeptide binding]; other site 428406008646 DPS ferroxidase diiron center [ion binding]; other site 428406008647 ion pore; other site 428406008648 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406008649 Walker A motif; other site 428406008650 ATP binding site [chemical binding]; other site 428406008651 Walker B motif; other site 428406008652 arginine finger; other site 428406008653 Phage protein Gp37/Gp68; Region: Gp37_Gp68; pfam07505 428406008654 SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]; Region: LexA; COG1974 428406008655 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC...; Region: S24_LexA-like; cd06529 428406008656 Catalytic site [active] 428406008657 TniQ; Region: TniQ; pfam06527 428406008658 Bacterial TniB protein; Region: TniB; pfam05621 428406008659 AAA domain; Region: AAA_22; pfam13401 428406008660 Integrase core domain; Region: rve; pfam00665 428406008661 Mu transposase, C-terminal; Region: Mu-transpos_C; pfam09299 428406008662 TnsA endonuclease N terminal; Region: Tn7_Tnp_TnsA_N; pfam08722 428406008663 TnsA endonuclease C terminal; Region: Tn7_Tnp_TnsA_C; pfam08721 428406008664 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 428406008665 cation diffusion facilitator family transporter; Region: CDF; TIGR01297 428406008666 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 428406008667 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 428406008668 dimerization interface [polypeptide binding]; other site 428406008669 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 428406008670 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 428406008671 dimer interface [polypeptide binding]; other site 428406008672 phosphorylation site [posttranslational modification] 428406008673 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406008674 ATP binding site [chemical binding]; other site 428406008675 Mg2+ binding site [ion binding]; other site 428406008676 G-X-G motif; other site 428406008677 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 428406008678 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406008679 active site 428406008680 phosphorylation site [posttranslational modification] 428406008681 intermolecular recognition site; other site 428406008682 dimerization interface [polypeptide binding]; other site 428406008683 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 428406008684 DNA binding residues [nucleotide binding] 428406008685 dimerization interface [polypeptide binding]; other site 428406008686 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 428406008687 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 428406008688 HlyD family secretion protein; Region: HlyD_3; pfam13437 428406008689 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 428406008690 Mn2+ and Fe2+ transporters of the NRAMP family [Inorganic ion transport and metabolism]; Region: MntH; COG1914 428406008691 Natural resistance-associated macrophage protein; Region: Nramp; pfam01566 428406008692 Carbohydrate-selective porin, OprB family; Region: OprB; pfam04966 428406008693 Transcriptional regulators RcnR and FrmR, and related domains; this domain family was previously known as part of DUF156; Region: RcnR-FrmR-like_DUF156; cd10153 428406008694 putative metal binding site [ion binding]; other site 428406008695 putative homodimer interface [polypeptide binding]; other site 428406008696 putative homotetramer interface [polypeptide binding]; other site 428406008697 putative homodimer-homodimer interface [polypeptide binding]; other site 428406008698 putative allosteric switch controlling residues; other site 428406008699 Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]; Region: CzcD; COG1230 428406008700 Cation efflux family; Region: Cation_efflux; cl00316 428406008701 Ca2+/Na+ antiporter [Inorganic ion transport and metabolism]; Region: ECM27; COG0530 428406008702 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 428406008703 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 428406008704 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406008705 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406008706 The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_OxyR; cd08411 428406008707 dimerization interface [polypeptide binding]; other site 428406008708 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 428406008709 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 428406008710 putative active site [active] 428406008711 putative metal binding site [ion binding]; other site 428406008712 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 428406008713 GAF domain; Region: GAF; pfam01590 428406008714 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 428406008715 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 428406008716 metal binding site [ion binding]; metal-binding site 428406008717 active site 428406008718 I-site; other site 428406008719 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 428406008720 RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a...; Region: RecG_wedge_OBF; cd04488 428406008721 generic binding surface II; other site 428406008722 ssDNA binding site; other site 428406008723 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 428406008724 ATP binding site [chemical binding]; other site 428406008725 putative Mg++ binding site [ion binding]; other site 428406008726 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 428406008727 nucleotide binding region [chemical binding]; other site 428406008728 ATP-binding site [chemical binding]; other site 428406008729 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 428406008730 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 428406008731 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 428406008732 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 428406008733 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 428406008734 SecD export protein N-terminal TM region; Region: SecD-TM1; pfam13721 428406008735 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 428406008736 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 428406008737 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 428406008738 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 428406008739 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 428406008740 Protein export membrane protein; Region: SecD_SecF; pfam02355 428406008741 Uncharacterized conserved protein [Function unknown]; Region: COG2353 428406008742 YceI-like domain; Region: YceI; smart00867 428406008743 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 428406008744 adenylosuccinate lyase; Provisional; Region: PRK09285 428406008745 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 428406008746 tetramer interface [polypeptide binding]; other site 428406008747 active site 428406008748 putative glutathione S-transferase; Provisional; Region: PRK10357 428406008749 GST_N family, unknown subfamily 3; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of...; Region: GST_N_3; cd03049 428406008750 putative C-terminal domain interface [polypeptide binding]; other site 428406008751 putative GSH binding site (G-site) [chemical binding]; other site 428406008752 putative dimer interface [polypeptide binding]; other site 428406008753 C-terminal, alpha helical domain of an unknown subfamily 6 of Glutathione S-transferases; Region: GST_C_6; cd03205 428406008754 dimer interface [polypeptide binding]; other site 428406008755 N-terminal domain interface [polypeptide binding]; other site 428406008756 putative substrate binding pocket (H-site) [chemical binding]; other site 428406008757 Glutamate synthase domain 2 [Amino acid transport and metabolism]; Region: GltB; COG0069 428406008758 Glutamate synthase (GltS) FMN-binding domain. GltS is a complex iron-sulfur flavoprotein that catalyzes the reductive synthesis of L-glutamate from 2-oxoglutarate and L-glutamine via intramolecular channelling of ammonia, a reaction in the plant, yeast...; Region: GltS_FMN; cd02808 428406008759 active site 428406008760 FMN binding site [chemical binding]; other site 428406008761 substrate binding site [chemical binding]; other site 428406008762 3Fe-4S cluster binding site [ion binding]; other site 428406008763 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 428406008764 tRNA methyl transferase. This family represents tRNA(5-methylaminomethyl-2-thiouridine)-methyltransferase which is involved in the biosynthesis of the modified nucleoside 5-methylaminomethyl-2-thiouridine present in the wobble position of some tRNAs; Region: tRNA_Me_trans; cd01998 428406008765 Contains a crystal structure of the Nudix hydrolase from Nitrosomonas europaea, which has an unknown function. In general, members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes...; Region: Nudix_Hydrolase_2; cd03675 428406008766 nudix motif; other site 428406008767 Rubrum transdehydrogenase NAD-binding and catalytic domains; Region: Rubrum_tdh; cd05304 428406008768 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 428406008769 ligand binding site [chemical binding]; other site 428406008770 homodimer interface [polypeptide binding]; other site 428406008771 NAD(P) binding site [chemical binding]; other site 428406008772 trimer interface B [polypeptide binding]; other site 428406008773 trimer interface A [polypeptide binding]; other site 428406008774 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 428406008775 tetramerization interface [polypeptide binding]; other site 428406008776 active site 428406008777 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 428406008778 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; COG1282 428406008779 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 428406008780 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406008781 active site 428406008782 phosphorylation site [posttranslational modification] 428406008783 intermolecular recognition site; other site 428406008784 dimerization interface [polypeptide binding]; other site 428406008785 Methyltransferase domain; Region: Methyltransf_25; pfam13649 428406008786 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 428406008787 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 428406008788 dimer interface [polypeptide binding]; other site 428406008789 phosphorylation site [posttranslational modification] 428406008790 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406008791 ATP binding site [chemical binding]; other site 428406008792 G-X-G motif; other site 428406008793 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 428406008794 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406008795 active site 428406008796 phosphorylation site [posttranslational modification] 428406008797 intermolecular recognition site; other site 428406008798 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 428406008799 dimerization interface [polypeptide binding]; other site 428406008800 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 428406008801 dimer interface [polypeptide binding]; other site 428406008802 phosphorylation site [posttranslational modification] 428406008803 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406008804 ATP binding site [chemical binding]; other site 428406008805 Mg2+ binding site [ion binding]; other site 428406008806 G-X-G motif; other site 428406008807 Response regulator receiver domain; Region: Response_reg; pfam00072 428406008808 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406008809 active site 428406008810 phosphorylation site [posttranslational modification] 428406008811 intermolecular recognition site; other site 428406008812 dimerization interface [polypeptide binding]; other site 428406008813 Predicted N6-adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0116 428406008814 THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Region: THUMP_AdoMetMT; cd11715 428406008815 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 428406008816 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 428406008817 Uncharacterized protein family (UPF0093); Region: UPF0093; cl00863 428406008818 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 428406008819 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 428406008820 putative catalytic cysteine [active] 428406008821 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK05574 428406008822 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 428406008823 Lipopolysaccharide-assembly; Region: LptE; cl01125 428406008824 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 428406008825 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 428406008826 HIGH motif; other site 428406008827 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 428406008828 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 428406008829 active site 428406008830 KMSKS motif; other site 428406008831 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 428406008832 tRNA binding surface [nucleotide binding]; other site 428406008833 dihydrodipicolinate reductase; Provisional; Region: PRK00048 428406008834 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 428406008835 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 428406008836 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 428406008837 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 428406008838 ferric uptake regulator; Provisional; Region: fur; PRK09462 428406008839 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 428406008840 metal binding site 2 [ion binding]; metal-binding site 428406008841 putative DNA binding helix; other site 428406008842 metal binding site 1 [ion binding]; metal-binding site 428406008843 dimer interface [polypeptide binding]; other site 428406008844 structural Zn2+ binding site [ion binding]; other site 428406008845 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406008846 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406008847 The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold; Region: PBP2_LeuO; cd08466 428406008848 putative substrate binding pocket [chemical binding]; other site 428406008849 putative dimerization interface [polypeptide binding]; other site 428406008850 Neurotransmitter-gated ion-channel transmembrane region; Region: Neur_chan_memb; pfam02932 428406008851 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 428406008852 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; pfam00044 428406008853 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 428406008854 transketolase; Reviewed; Region: PRK12753 428406008855 Thiamine pyrophosphate (TPP) family, Transketolase (TK) subfamily, TPP-binding module; TK catalyzes the transfer of a two-carbon unit from ketose phosphates to aldose phosphates. In heterotrophic organisms, TK provides a link between glycolysis and the...; Region: TPP_TK; cd02012 428406008856 TPP-binding site [chemical binding]; other site 428406008857 dimer interface [polypeptide binding]; other site 428406008858 Pyrimidine (PYR) binding domain of 1-deoxy-D-xylulose-5-phosphate synthase (DXS), transketolase (TK), and related proteins; Region: TPP_PYR_DXS_TK_like; cd07033 428406008859 PYR/PP interface [polypeptide binding]; other site 428406008860 dimer interface [polypeptide binding]; other site 428406008861 TPP binding site [chemical binding]; other site 428406008862 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 428406008863 galactonate dehydratase; Provisional; Region: PRK14017 428406008864 D-galactonate dehydratase catalyses the dehydration of galactonate to 2-keto-3-deoxygalactnate (KDGal), as part of the D-galactonate nonphosphorolytic catabolic Entner-Doudoroff pathway. D-galactonate dehydratase belongs to the enolase superfamily of...; Region: D-galactonate_dehydratase; cd03325 428406008865 putative active site pocket [active] 428406008866 putative metal binding site [ion binding]; other site 428406008867 2-dehydro-3-deoxy-6-phosphogalactonate aldolase; Reviewed; Region: PRK09140 428406008868 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 428406008869 active site 428406008870 intersubunit interface [polypeptide binding]; other site 428406008871 catalytic residue [active] 428406008872 short chain dehydrogenase; Provisional; Region: PRK07063 428406008873 classical (c) SDRs; Region: SDR_c; cd05233 428406008874 NAD(P) binding site [chemical binding]; other site 428406008875 active site 428406008876 aldose 1-epimerase, similar to Escherichia coli YphB; Region: Aldose_epim_Ec_YphB; cd09021 428406008877 active site 428406008878 catalytic residues [active] 428406008879 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 428406008880 Strictosidine synthase; Region: Str_synth; pfam03088 428406008881 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 428406008882 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 428406008883 TM-ABC transporter signature motif; other site 428406008884 L-arabinose transporter ATP-binding protein; Provisional; Region: araG; PRK11288 428406008885 First domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_I; cd03216 428406008886 Walker A/P-loop; other site 428406008887 ATP binding site [chemical binding]; other site 428406008888 Q-loop/lid; other site 428406008889 ABC transporter signature motif; other site 428406008890 Walker B; other site 428406008891 D-loop; other site 428406008892 H-loop/switch region; other site 428406008893 Second domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_II; cd03215 428406008894 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: RbsB; COG1879 428406008895 Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily; Region: PBP1_arabinose_binding; cd01540 428406008896 ligand binding site [chemical binding]; other site 428406008897 2-keto-3-deoxy-galactonokinase [Carbohydrate transport and metabolism]; Region: DgoK; COG3734 428406008898 2-keto-3-deoxy-galactonokinase; Region: DGOK; pfam05035 428406008899 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 428406008900 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 428406008901 trimer interface [polypeptide binding]; other site 428406008902 eyelet of channel; other site 428406008903 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 428406008904 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406008905 The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold; Region: PBP2_GcdR_TrpI_HvrB_AmpR_like; cd08432 428406008906 dimerization interface [polypeptide binding]; other site 428406008907 substrate binding pocket [chemical binding]; other site 428406008908 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_8; cd07246 428406008909 putative dimer interface [polypeptide binding]; other site 428406008910 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 428406008911 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385 428406008912 RNA methyltransferase, RsmE family; Region: TIGR00046 428406008913 Bacterial protein of unknown function (DUF937); Region: DUF937; cl01528 428406008914 pca operon transcription factor PcaQ; Region: TF_pcaQ; TIGR02424 428406008915 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406008916 The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold; Region: PBP2_GbpR; cd08435 428406008917 putative dimerization interface [polypeptide binding]; other site 428406008918 dihydroxy-acid dehydratase; Validated; Region: PRK06131 428406008919 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 428406008920 Dihydrodipicolinate synthase family; Region: DHDPS-like; cd00408 428406008921 inhibitor site; inhibition site 428406008922 active site 428406008923 dimer interface [polypeptide binding]; other site 428406008924 catalytic residue [active] 428406008925 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 428406008926 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 428406008927 Periplasmic binding proteins and sugar binding domain of LacI family; Region: Peripla_BP_1; pfam00532 428406008928 Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily; Region: PBP1_arabinose_binding; cd01540 428406008929 ligand binding site [chemical binding]; other site 428406008930 L-arabinose transporter ATP-binding protein; Provisional; Region: araG; PRK11288 428406008931 First domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_I; cd03216 428406008932 Walker A/P-loop; other site 428406008933 ATP binding site [chemical binding]; other site 428406008934 Q-loop/lid; other site 428406008935 ABC transporter signature motif; other site 428406008936 Walker B; other site 428406008937 D-loop; other site 428406008938 H-loop/switch region; other site 428406008939 Second domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_II; cd03215 428406008940 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 428406008941 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 428406008942 TM-ABC transporter signature motif; other site 428406008943 Barstar_evA4336-like contains uncharacterized sequences similar to the uncharacterized, predicted RNAase inhibitor evA4336 found in Azoarcus sp. EvN1. This is a subfamily of the Barstar family of RNAase inhibitors. Barstar is an intracellular inhibitor...; Region: Barstar_evA4336-like; cd05141 428406008944 putative RNAase interaction site [polypeptide binding]; other site 428406008945 RNase_Sa. Ribonucleases first isolated from Streptomyces aureofaciens. In general, ribonucleases cleave phosphodiester bonds in RNA and are essential for both non-specific RNA degradation and for numerous forms of RNA processing. RNAse Sa is a guanylate...; Region: RNase_Sa; cd00607 428406008946 active site 428406008947 barstar interaction site; other site 428406008948 malic enzyme; Reviewed; Region: PRK12862 428406008949 Malic enzyme, N-terminal domain; Region: malic; pfam00390 428406008950 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 428406008951 putative NAD(P) binding site [chemical binding]; other site 428406008952 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 428406008953 thiamine monophosphate kinase; Provisional; Region: PRK05731 428406008954 ThiL (Thiamine-monophosphate kinase) plays a dual role in de novo biosynthesis and in salvage of exogenous thiamine. Thiamine salvage occurs in two steps, with thiamine kinase catalyzing the formation of thiamine phosphate, and ThiL catalyzing the...; Region: ThiL; cd02194 428406008955 ATP binding site [chemical binding]; other site 428406008956 dimerization interface [polypeptide binding]; other site 428406008957 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 428406008958 tetramer interfaces [polypeptide binding]; other site 428406008959 binuclear metal-binding site [ion binding]; other site 428406008960 Uncharacterized protein (competence- and mitomycin-induced) [General function prediction only]; Region: CinA; COG1546 428406008961 Orotidine 5'-phosphate decarboxylase (ODCase) is a dimeric enzyme that decarboxylates orotidine 5'-monophosphate (OMP) to form uridine 5'-phosphate (UMP), an essential step in the pyrimidine biosynthetic pathway. In mammals, UMP synthase...; Region: OMP_decarboxylase_like; cd04725 428406008962 active site 428406008963 dimer interface [polypeptide binding]; other site 428406008964 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 428406008965 Escherichia coli Mg2+ transporter CorA_like subgroup; Region: EcCorA-like_1; cd12835 428406008966 Cl binding site [ion binding]; other site 428406008967 oligomer interface [polypeptide binding]; other site 428406008968 monofunctional biosynthetic peptidoglycan transglycosylase; Provisional; Region: mtgA; PRK00056 428406008969 monofunctional biosynthetic peptidoglycan transglycosylase; Region: mono_pep_trsgly; TIGR02070 428406008970 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 428406008971 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 428406008972 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 428406008973 shikimate binding site; other site 428406008974 NAD(P) binding site [chemical binding]; other site 428406008975 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 428406008976 TonB C terminal; Region: TonB_2; pfam13103 428406008977 This domain is the catalytic domain of ribonuclease II; Region: RNB; smart00955 428406008978 RNB domain; Region: RNB; pfam00773 428406008979 4-hydroxybenzoate synthetase (chorismate lyase) [Coenzyme metabolism]; Region: UbiC; COG3161 428406008980 Predicted esterase [General function prediction only]; Region: COG3150 428406008981 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 428406008982 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase; Region: mpl; TIGR01081 428406008983 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 428406008984 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 428406008985 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 428406008986 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a...; Region: TlpA_like_family; cd02966 428406008987 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 428406008988 catalytic residues [active] 428406008989 Dehydroquinase (DHQase), type II. Dehydroquinase (or 3-dehydroquinate dehydratase) catalyzes the reversible dehydration of 3-dehydroquinate to form 3-dehydroshikimate. This reaction is part of two metabolic pathways: the biosynthetic shikimate pathway...; Region: DHQase_II; cd00466 428406008990 Dehydroquinase class II; Region: DHquinase_II; pfam01220 428406008991 trimer interface [polypeptide binding]; other site 428406008992 active site 428406008993 dimer interface [polypeptide binding]; other site 428406008994 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 428406008995 The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase; Region: biotinyl_domain; cd06850 428406008996 carboxyltransferase (CT) interaction site; other site 428406008997 biotinylation site [posttranslational modification]; other site 428406008998 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 428406008999 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 428406009000 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 428406009001 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 428406009002 Ribosomal protein L11 methyltransferase (PrmA); Region: PrmA; pfam06325 428406009003 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 428406009004 S-adenosylmethionine binding site [chemical binding]; other site 428406009005 Protein of unknown function (DUF3426); Region: DUF3426; pfam11906 428406009006 Peroxiredoxin (PRX) family, Atypical 2-cys PRX subfamily; composed of PRXs containing peroxidatic and resolving cysteines, similar to the homodimeric thiol specific antioxidant (TSA) protein also known as TRX-dependent thiol peroxidase (Tpx). Tpx is a...; Region: PRX_Atyp2cys; cd03014 428406009007 dimer interface [polypeptide binding]; other site 428406009008 catalytic triad [active] 428406009009 peroxidatic and resolving cysteines [active] 428406009010 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 428406009011 Ribokinase-like subgroup A. Found in bacteria and archaea, this subgroup is part of the ribokinase/pfkB superfamily. Its oligomerization state is unknown at this time; Region: ribokinase_group_A; cd01942 428406009012 substrate binding site [chemical binding]; other site 428406009013 ATP binding site [chemical binding]; other site 428406009014 Outer membrane lipoprotein [Cell envelope biogenesis, outer membrane]; Region: SlyB; COG3133 428406009015 Uncharacterized protein conserved in bacteria (DUF2147); Region: DUF2147; pfam09917 428406009016 Cache domain; Region: Cache_2; pfam08269 428406009017 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 428406009018 dimer interface [polypeptide binding]; other site 428406009019 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 428406009020 putative CheW interface [polypeptide binding]; other site 428406009021 Threonine/homoserine efflux transporter [Amino acid transport and metabolism]; Region: rhtA; COG5006 428406009022 Peptidase M14-like domain; uncharacterized subfamily; Region: M14-like_6; cd06233 428406009023 putative active site [active] 428406009024 Zn binding site [ion binding]; other site 428406009025 ribonucleotide-diphosphate reductase subunit beta; Provisional; Region: nrdF2; PRK13966 428406009026 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 428406009027 dimer interface [polypeptide binding]; other site 428406009028 putative radical transfer pathway; other site 428406009029 diiron center [ion binding]; other site 428406009030 tyrosyl radical; other site 428406009031 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK07207 428406009032 ATP cone domain; Region: ATP-cone; pfam03477 428406009033 Class I ribonucleotide reductase; Region: RNR_I; cd01679 428406009034 active site 428406009035 dimer interface [polypeptide binding]; other site 428406009036 catalytic residues [active] 428406009037 effector binding site; other site 428406009038 R2 peptide binding site; other site 428406009039 phospholipase C, phosphocholine-specific, Pseudomonas-type; Region: PC_PLC; TIGR03396 428406009040 Phosphoesterase family; Region: Phosphoesterase; pfam04185 428406009041 Domain of unknown function (DUF756); Region: DUF756; pfam05506 428406009042 Domain of unknown function (DUF756); Region: DUF756; pfam05506 428406009043 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 428406009044 Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20...; Region: PGRP; cd06583 428406009045 amidase catalytic site [active] 428406009046 Zn binding residues [ion binding]; other site 428406009047 substrate binding site [chemical binding]; other site 428406009048 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 428406009049 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406009050 active site 428406009051 phosphorylation site [posttranslational modification] 428406009052 intermolecular recognition site; other site 428406009053 dimerization interface [polypeptide binding]; other site 428406009054 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406009055 Walker A motif; other site 428406009056 ATP binding site [chemical binding]; other site 428406009057 Walker B motif; other site 428406009058 arginine finger; other site 428406009059 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 428406009060 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 428406009061 putative active site [active] 428406009062 heme pocket [chemical binding]; other site 428406009063 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 428406009064 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 428406009065 dimer interface [polypeptide binding]; other site 428406009066 phosphorylation site [posttranslational modification] 428406009067 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406009068 ATP binding site [chemical binding]; other site 428406009069 Mg2+ binding site [ion binding]; other site 428406009070 G-X-G motif; other site 428406009071 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 428406009072 signal recognition particle protein; Provisional; Region: PRK10867 428406009073 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 428406009074 The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes. SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The...; Region: SRP; cd03115 428406009075 P loop; other site 428406009076 GTP binding site [chemical binding]; other site 428406009077 Signal peptide binding domain; Region: SRP_SPB; pfam02978 428406009078 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 428406009079 active site 428406009080 MarC family integral membrane protein; Region: MarC; cl00919 428406009081 Prolyl 4-hydroxylase alpha subunit homologues; Region: P4Hc; smart00702 428406009082 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 428406009083 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 428406009084 N-acetyl-D-glucosamine binding site [chemical binding]; other site 428406009085 catalytic residue [active] 428406009086 prolyl-tRNA synthetase; Provisional; Region: PRK09194 428406009087 Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: ProRS_core_prok; cd00779 428406009088 dimer interface [polypeptide binding]; other site 428406009089 motif 1; other site 428406009090 active site 428406009091 motif 2; other site 428406009092 INS is an amino acid-editing domain inserted (INS) into the bacterial class II prolyl-tRNA synthetase (ProRS) however, this CD is not exclusively bacterial. It is also found at the N-terminus of the eukaryotic/archaea-like ProRS's of yeasts and...; Region: ProRS-INS; cd04334 428406009093 putative deacylase active site [active] 428406009094 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 428406009095 active site 428406009096 motif 3; other site 428406009097 ProRS Prolyl-anticodon binding domain, short version found predominantly in bacteria. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding; Region: ProRS_anticodon_short; cd00861 428406009098 anticodon binding site; other site 428406009099 Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the Nudix hydrolase superfamily. Members of this family are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant...; Region: Ap4A_hydrolase_plant_like; cd03671 428406009100 putative active site [active] 428406009101 Ap4A binding site [chemical binding]; other site 428406009102 nudix motif; other site 428406009103 putative metal binding site [ion binding]; other site 428406009104 CNP1-like family; Region: CNP1; pfam08750 428406009105 gamma-glutamyl kinase; Provisional; Region: PRK05429 428406009106 AAK_G5K_ProB: Glutamate-5-kinase (G5K) catalyzes glutamate-dependent ATP cleavage; G5K transfers the terminal phosphoryl group of ATP to the gamma-carboxyl group of glutamate, in the first and controlling step of proline (and, in mammals, ornithine)...; Region: AAK_G5K_ProB; cd04242 428406009107 nucleotide binding site [chemical binding]; other site 428406009108 homotetrameric interface [polypeptide binding]; other site 428406009109 putative phosphate binding site [ion binding]; other site 428406009110 putative allosteric binding site; other site 428406009111 PUA domain; Region: PUA; pfam01472 428406009112 GTPase CgtA; Reviewed; Region: obgE; PRK12299 428406009113 GTP1/OBG; Region: GTP1_OBG; pfam01018 428406009114 Obg GTPase; Region: Obg; cd01898 428406009115 G1 box; other site 428406009116 GTP/Mg2+ binding site [chemical binding]; other site 428406009117 Switch I region; other site 428406009118 G2 box; other site 428406009119 G3 box; other site 428406009120 Switch II region; other site 428406009121 G4 box; other site 428406009122 G5 box; other site 428406009123 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 428406009124 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 428406009125 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 428406009126 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 428406009127 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 428406009128 substrate binding pocket [chemical binding]; other site 428406009129 chain length determination region; other site 428406009130 substrate-Mg2+ binding site; other site 428406009131 catalytic residues [active] 428406009132 aspartate-rich region 1; other site 428406009133 active site lid residues [active] 428406009134 aspartate-rich region 2; other site 428406009135 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 428406009136 active site 428406009137 DNA binding site [nucleotide binding] 428406009138 Int/Topo IB signature motif; other site 428406009139 Protein of unknown function DUF262; Region: DUF262; pfam03235 428406009140 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 428406009141 HNH endonuclease; Region: HNH_2; pfam13391 428406009142 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 428406009143 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 428406009144 AAA domain; Region: AAA_21; pfam13304 428406009145 Walker A/P-loop; other site 428406009146 ATP binding site [chemical binding]; other site 428406009147 Q-loop/lid; other site 428406009148 ABC transporter signature motif; other site 428406009149 TOPRIM_OLD: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in bacterial and archaeal nucleases of the OLD (overcome lysogenization defect) family. The bacteriophage P2 OLD protein, which has DNase as well as...; Region: TOPRIM_OLD; cd01026 428406009150 putative active site [active] 428406009151 putative metal-binding site [ion binding]; other site 428406009152 Transposase; Region: HTH_Tnp_1; cl17663 428406009153 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 428406009154 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 428406009155 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 428406009156 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; pfam13005 428406009157 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 428406009158 IS66 C-terminal element; Region: DDE_Tnp_IS66_C; pfam13817 428406009159 Methyltransferase domain; Region: Methyltransf_26; pfam13659 428406009160 DEAD-like helicases superfamily; Region: DEXDc; smart00487 428406009161 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 428406009162 ATP binding site [chemical binding]; other site 428406009163 putative Mg++ binding site [ion binding]; other site 428406009164 Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]; Region: SrmB; COG0513 428406009165 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 428406009166 nucleotide binding region [chemical binding]; other site 428406009167 ATP-binding site [chemical binding]; other site 428406009168 Distinct helicase family with a unique C-terminal domain including a metal-binding cysteine cluster [General function prediction only]; Region: COG1205 428406009169 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 428406009170 ATP binding site [chemical binding]; other site 428406009171 putative Mg++ binding site [ion binding]; other site 428406009172 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 428406009173 ATP-binding site [chemical binding]; other site 428406009174 Domain of unknown function (DUF1998); Region: DUF1998; pfam09369 428406009175 Superfamily of nucleases including Short Patch Repair (Vsr) Endonucleases, archaeal Holliday junction resolvases, MutH methy-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and...; Region: Restriction_endonuclease_like; cl00277 428406009176 Phage integrase, N-terminal; Region: Integrase_l_N; pfam12834 428406009177 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 428406009178 active site 428406009179 catalytic residues [active] 428406009180 DNA binding site [nucleotide binding] 428406009181 Int/Topo IB signature motif; other site 428406009182 Protein of unknown function (DUF1311); Region: DUF1311; pfam07007 428406009183 Protein of unknown function (DUF1444); Region: DUF1444; cl02011 428406009184 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 428406009185 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 428406009186 non-specific DNA binding site [nucleotide binding]; other site 428406009187 salt bridge; other site 428406009188 sequence-specific DNA binding site [nucleotide binding]; other site 428406009189 Plasmid replication region DNA-binding N-term; Region: KfrA_N; pfam11740 428406009190 Helix-turn-helix domain; Region: HTH_17; pfam12728 428406009191 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 428406009192 Domain of unknown function DUF21; Region: DUF21; pfam01595 428406009193 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the CorC_HlyC domain. CorC_HlyC is a transporter associated domain. This small domain is found in Na+/H+ antiporters, in proteins involved in...; Region: CBS_pair_CorC_HlyC_assoc; cd04590 428406009194 Transporter associated domain; Region: CorC_HlyC; smart01091 428406009195 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 428406009196 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 428406009197 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 428406009198 Walker A motif; other site 428406009199 ATP binding site [chemical binding]; other site 428406009200 Walker B motif; other site 428406009201 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 428406009202 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 428406009203 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 428406009204 Type II secretory pathway, prepilin signal peptidase PulO and related peptidases [Cell motility and secretion / Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: PulO; COG1989 428406009205 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 428406009206 Type IV leader peptidase family; Region: Peptidase_A24; pfam01478 428406009207 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 428406009208 Dephospho-coenzyme A kinase (DPCK, EC 2.7.1.24) catalyzes the phosphorylation of dephosphocoenzyme A (dCoA) to yield CoA, which is the final step in CoA biosynthesis; Region: DPCK; cd02022 428406009209 CoA-binding site [chemical binding]; other site 428406009210 ATP-binding [chemical binding]; other site 428406009211 hypothetical protein; Provisional; Region: PRK05287 428406009212 Domain of unknown function (DUF329); Region: DUF329; pfam03884 428406009213 The MutT pyrophosphohydrolase is a prototypical Nudix hydrolase that catalyzes the hydrolysis of nucleoside and deoxynucleoside triphosphates (NTPs and dNTPs) by substitution at a beta-phosphorus to yield a nucleotide monophosphate (NMP) and inorganic...; Region: MutT_pyrophosphohydrolase; cd03425 428406009214 active site 428406009215 8-oxo-dGMP binding site [chemical binding]; other site 428406009216 nudix motif; other site 428406009217 metal binding site [ion binding]; metal-binding site 428406009218 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG2607 428406009219 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406009220 Walker A motif; other site 428406009221 ATP binding site [chemical binding]; other site 428406009222 Walker B motif; other site 428406009223 Ornithine acetyltransferase (OAT) family; also referred to as ArgJ. OAT catalyzes the first and fifth steps in arginine biosynthesis, coupling acetylation of glutamate with deacetylation of N-acetylornithine, which allows recycling of the acetyl group in...; Region: OAT; cd02152 428406009224 heterotetramer interface [polypeptide binding]; other site 428406009225 active site pocket [active] 428406009226 cleavage site 428406009227 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 428406009228 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 428406009229 SEC-C motif; Region: SEC-C; pfam02810 428406009230 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 428406009231 Peptidase family M23; Region: Peptidase_M23; pfam01551 428406009232 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 428406009233 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 428406009234 Peroxiredoxin (PRX) family, PRX5-like subfamily; members are similar to the human protein, PRX5, a homodimeric TRX peroxidase, widely expressed in tissues and found cellularly in mitochondria, peroxisomes and the cytosol. The cellular location of PRX5...; Region: PRX5_like; cd03013 428406009235 catalytic triad [active] 428406009236 dimer interface [polypeptide binding]; other site 428406009237 cell division protein FtsZ; Validated; Region: PRK09330 428406009238 FtsZ is a GTPase that is similar to the eukaryotic tubulins and is essential for cell division in prokaryotes. FtsZ is capable of polymerizing in a GTP-driven process into structures similar to those formed by tubulin. FtsZ forms a ring-shaped septum at...; Region: FtsZ_type1; cd02201 428406009239 nucleotide binding site [chemical binding]; other site 428406009240 SulA interaction site; other site 428406009241 cell division protein FtsA; Region: ftsA; TIGR01174 428406009242 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 428406009243 nucleotide binding site [chemical binding]; other site 428406009244 Cell division protein FtsA; Region: FtsA; pfam14450 428406009245 Cell division septal protein [Cell envelope biogenesis, outer membrane]; Region: FtsQ; COG1589 428406009246 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 428406009247 Cell division protein FtsQ; Region: FtsQ; pfam03799 428406009248 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 428406009249 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 428406009250 ATP-grasp domain; Region: ATP-grasp_4; cl17255 428406009251 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 428406009252 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 428406009253 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 428406009254 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 428406009255 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 428406009256 MurG is an N-acetylglucosaminyltransferase, the last enzyme involved in the intracellular phase of peptidoglycan biosynthesis. It transfers N-acetyl-D-glucosamine (GlcNAc) from UDP-GlcNAc to the C4 hydroxyl of a lipid-linked N-acetylmuramoyl pentapeptide...; Region: GT1_MurG; cd03785 428406009257 active site 428406009258 homodimer interface [polypeptide binding]; other site 428406009259 cell division protein FtsW; Region: ftsW; TIGR02614 428406009260 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK02006 428406009261 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 428406009262 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 428406009263 Phospho-N-acetylmuramoyl-pentapeptide-transferase (mraY) is an enzyme responsible for the formation of the first lipid intermediate in the synthesis of bacterial cell wall peptidoglycan. It catalyzes the formation of...; Region: GT_MraY; cd06852 428406009264 Mg++ binding site [ion binding]; other site 428406009265 putative catalytic motif [active] 428406009266 putative substrate binding site [chemical binding]; other site 428406009267 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 428406009268 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 428406009269 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 428406009270 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 428406009271 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 428406009272 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 428406009273 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 428406009274 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 428406009275 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 428406009276 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 428406009277 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 428406009278 Cell division protein FtsL; Region: FtsL; cl11433 428406009279 MraW methylase family; Region: Methyltransf_5; cl17771 428406009280 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 428406009281 cell division protein MraZ; Reviewed; Region: PRK00326 428406009282 MraZ protein; Region: MraZ; pfam02381 428406009283 MraZ protein; Region: MraZ; pfam02381 428406009284 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 428406009285 diiron binding motif [ion binding]; other site 428406009286 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 428406009287 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 428406009288 trimer interface [polypeptide binding]; other site 428406009289 eyelet of channel; other site 428406009290 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406009291 metabolite-proton symporter; Region: 2A0106; TIGR00883 428406009292 putative substrate translocation pore; other site 428406009293 hypothetical protein; Provisional; Region: PRK09256 428406009294 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 428406009295 Predicted membrane protein, hemolysin III homolog [General function prediction only]; Region: COG1272 428406009296 channel protein, hemolysin III family; Region: hlyIII; TIGR01065 428406009297 Long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07059 428406009298 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 428406009299 acyl-activating enzyme (AAE) consensus motif; other site 428406009300 putative AMP binding site [chemical binding]; other site 428406009301 putative active site [active] 428406009302 putative CoA binding site [chemical binding]; other site 428406009303 Predicted aminopeptidase (DUF2265); Region: DUF2265; pfam10023 428406009304 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 428406009305 The MopB_3 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. These members...; Region: MopB_3; cd02766 428406009306 putative [4Fe-4S] binding site [ion binding]; other site 428406009307 putative molybdopterin cofactor binding site [chemical binding]; other site 428406009308 The MopB_CT_3 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the...; Region: MopB_CT_3; cd02786 428406009309 putative molybdopterin cofactor binding site; other site 428406009310 Transcriptional regulators [Transcription]; Region: PurR; COG1609 428406009311 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 428406009312 DNA binding site [nucleotide binding] 428406009313 domain linker motif; other site 428406009314 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors; Region: PBP1_LacI_like_4; cd06280 428406009315 putative dimerization interface [polypeptide binding]; other site 428406009316 putative ligand binding site [chemical binding]; other site 428406009317 PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_fru; cd00211 428406009318 active site 428406009319 phosphorylation site [posttranslational modification] 428406009320 Histidine-containing phosphocarrier protein (HPr)-like proteins. HPr is a central component of the bacterial phosphoenolpyruvate sugar phosphotransferase system (PTS). The PTS catalyses the phosphorylation of sugar substrates during their translocation...; Region: PTS-HPr_like; cd00367 428406009321 dimerization domain swap beta strand [polypeptide binding]; other site 428406009322 regulatory protein interface [polypeptide binding]; other site 428406009323 active site 428406009324 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 428406009325 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 428406009326 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 428406009327 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 428406009328 Fructose-1-phosphate kinase and related fructose-6-phosphate kinase (PfkB) [Carbohydrate transport and metabolism]; Region: FruK; COG1105 428406009329 1-phosphofructokinase (FruK), minor 6-phosphofructokinase (pfkB) and related sugar kinases. FruK plays an important role in the predominant pathway for fructose utilisation.This group also contains tagatose-6-phophate kinase, an enzyme of the tagatose...; Region: FruK_PfkB_like; cd01164 428406009330 putative substrate binding site [chemical binding]; other site 428406009331 putative ATP binding site [chemical binding]; other site 428406009332 PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA and...; Region: PTS_IIB_fructose; cd05569 428406009333 active site 428406009334 P-loop; other site 428406009335 phosphorylation site [posttranslational modification] 428406009336 Phosphotransferase system, fructose-specific IIC component [Carbohydrate transport and metabolism]; Region: FruA; cl17425 428406009337 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 428406009338 Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins; Region: PBP1_STKc_like; cd06326 428406009339 putative ligand binding site [chemical binding]; other site 428406009340 acetylornithine deacetylase; Provisional; Region: PRK07522 428406009341 M20 Peptidase acetylornithine deacetylase; Region: M20_ArgE; cd03894 428406009342 metal binding site [ion binding]; metal-binding site 428406009343 putative dimer interface [polypeptide binding]; other site 428406009344 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 428406009345 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like1; cd05666 428406009346 metal binding site [ion binding]; metal-binding site 428406009347 putative dimer interface [polypeptide binding]; other site 428406009348 enoyl-CoA hydratase; Provisional; Region: PRK05862 428406009349 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 428406009350 substrate binding site [chemical binding]; other site 428406009351 oxyanion hole (OAH) forming residues; other site 428406009352 trimer interface [polypeptide binding]; other site 428406009353 enoyl-CoA hydratase; Provisional; Region: PRK08140 428406009354 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 428406009355 substrate binding site [chemical binding]; other site 428406009356 oxyanion hole (OAH) forming residues; other site 428406009357 trimer interface [polypeptide binding]; other site 428406009358 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 428406009359 CoenzymeA binding site [chemical binding]; other site 428406009360 subunit interaction site [polypeptide binding]; other site 428406009361 PHB binding site; other site 428406009362 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 428406009363 phenylacetate-CoA ligase; Region: PA_CoA_ligase; TIGR02155 428406009364 acyl-activating enzyme (AAE) consensus motif; other site 428406009365 AMP binding site [chemical binding]; other site 428406009366 active site 428406009367 CoA binding site [chemical binding]; other site 428406009368 Membrane-bound lytic murein transglycosylase [Cell envelope biogenesis, outer membrane]; Region: MltA; COG2821 428406009369 MltA specific insert domain; Region: MltA; smart00925 428406009370 3D domain; Region: 3D; pfam06725 428406009371 CO2+/MG2+ efflux protein ApaG; Reviewed; Region: apaG; PRK05461 428406009372 Ribulose-5-phosphate 3-epimerase (RPE). This enzyme catalyses the interconversion of D-ribulose 5-phosphate (Ru5P) into D-xylulose 5-phosphate, as part of the Calvin cycle (reductive pentose phosphate pathway) in chloroplasts and in the oxidative pentose...; Region: RPE; cd00429 428406009373 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 428406009374 substrate binding site [chemical binding]; other site 428406009375 hexamer interface [polypeptide binding]; other site 428406009376 metal binding site [ion binding]; metal-binding site 428406009377 phosphoglycolate phosphatase; Provisional; Region: PRK13222 428406009378 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 428406009379 motif II; other site 428406009380 anthranilate synthase component I; Provisional; Region: PRK13565 428406009381 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 428406009382 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 428406009383 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 428406009384 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 428406009385 glutamine binding [chemical binding]; other site 428406009386 catalytic triad [active] 428406009387 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 428406009388 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 428406009389 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 428406009390 Indole-3-glycerol phosphate synthase (IGPS); an enzyme in the tryptophan biosynthetic pathway, catalyzing the ring closure reaction of 1-(o-carboxyphenylamino)-1-deoxyribulose-5-phosphate (CdRP) to indole-3-glycerol phosphate (IGP), accompanied by the...; Region: IGPS; cd00331 428406009391 active site 428406009392 ribulose/triose binding site [chemical binding]; other site 428406009393 phosphate binding site [ion binding]; other site 428406009394 substrate (anthranilate) binding pocket [chemical binding]; other site 428406009395 product (indole) binding pocket [chemical binding]; other site 428406009396 Uncharacterized subgroup of the CYTH-like superfamily having an associated CHAD domain; Region: CYTH-like_Pase_CHAD; cd07756 428406009397 putative active site [active] 428406009398 putative metal binding residues [ion binding]; other site 428406009399 signature motif; other site 428406009400 putative triphosphate binding site [ion binding]; other site 428406009401 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 428406009402 ligand binding site [chemical binding]; other site 428406009403 active site 428406009404 UGI interface [polypeptide binding]; other site 428406009405 catalytic site [active] 428406009406 Predicted membrane protein [Function unknown]; Region: COG1289 428406009407 FUSC-like inner membrane protein yccS; Region: FUSC-like; pfam12805 428406009408 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 428406009409 Predicted protease with the C-terminal PDZ domain [General function prediction only]; Region: COG3975 428406009410 M61 glycyl aminopeptidase; Region: Peptidase_M61; pfam05299 428406009411 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 428406009412 protein binding site [polypeptide binding]; other site 428406009413 Yhdh putative quinone oxidoreductases; Region: MDR_yhdh; cd08288 428406009414 putative quinone oxidoreductase, YhdH/YhfP family; Region: oxido_YhdH; TIGR02823 428406009415 NADP binding site [chemical binding]; other site 428406009416 dimer interface [polypeptide binding]; other site 428406009417 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 428406009418 DsbA family, DsbC and DsbG subfamily; V-shaped homodimeric proteins containing a redox active CXXC motif imbedded in a TRX fold. They function as protein disulfide isomerases and chaperones in the bacterial periplasm to correct non-native disulfide bonds...; Region: DsbA_DsbC_DsbG; cd03020 428406009419 dimerization domain [polypeptide binding]; other site 428406009420 dimer interface [polypeptide binding]; other site 428406009421 catalytic residues [active] 428406009422 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608 428406009423 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 428406009424 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 428406009425 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 428406009426 N-acetyl-D-glucosamine binding site [chemical binding]; other site 428406009427 catalytic residue [active] 428406009428 Flagellar protein FliT; Region: FliT; pfam05400 428406009429 GTP-binding protein YchF; Reviewed; Region: PRK09601 428406009430 YchF GTPase; Region: YchF; cd01900 428406009431 G1 box; other site 428406009432 GTP/Mg2+ binding site [chemical binding]; other site 428406009433 Switch I region; other site 428406009434 G2 box; other site 428406009435 Switch II region; other site 428406009436 G3 box; other site 428406009437 G4 box; other site 428406009438 G5 box; other site 428406009439 TGS_YchF_C: This subfamily represents TGS domain-containing YchF GTP-binding protein, a universally conserved GTPase whose function is unknown. The N-terminal domain of the YchF protein belongs to the Obg-like family of GTPases, and some members of the...; Region: TGS_YchF_C; cd04867 428406009440 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 428406009441 active site 428406009442 catalytic residues [active] 428406009443 DNA binding site [nucleotide binding] 428406009444 Int/Topo IB signature motif; other site 428406009445 Rieske non-heme iron oxygenase (RO) family, Phthalate 4,5-dioxygenase (PhDO)-like subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; composed of the oxygenase alpha subunits of PhDO and similar proteins including 3-chlorobenzoate 3; Region: Rieske_RO_Alpha_PhDO_like; cd03479 428406009446 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 428406009447 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 428406009448 hydrophobic ligand binding site; other site 428406009449 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 428406009450 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 428406009451 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 428406009452 nicotinate-nucleotide pyrophosphorylase; Provisional; Region: PRK06978 428406009453 Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase), also called nicotinate-nucleotide pyrophosphorylase, is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid (QA) with...; Region: QPRTase; cd01572 428406009454 dimerization interface [polypeptide binding]; other site 428406009455 active site 428406009456 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 428406009457 MarR family; Region: MarR_2; cl17246 428406009458 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 428406009459 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 428406009460 trimer interface [polypeptide binding]; other site 428406009461 eyelet of channel; other site 428406009462 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cl17432 428406009463 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406009464 D-galactonate transporter; Region: 2A0114; TIGR00893 428406009465 putative substrate translocation pore; other site 428406009466 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 428406009467 Phthalate dioxygenase reductase (PDR) is an FMN-dependent reductase that mediates electron transfer from NADH to FMN to an iron sulfur cluster. PDR has an an N-terminal ferrredoxin reductase (FNR)-like NAD(H) binding domain and a C-terminal iron-sulfur; Region: PDR_like; cd06185 428406009468 FMN-binding pocket [chemical binding]; other site 428406009469 flavin binding motif; other site 428406009470 phosphate binding motif [ion binding]; other site 428406009471 beta-alpha-beta structure motif; other site 428406009472 NAD binding pocket [chemical binding]; other site 428406009473 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 428406009474 catalytic loop [active] 428406009475 iron binding site [ion binding]; other site 428406009476 Hemerythrin; Region: Hemerythrin; cd12107 428406009477 Fe binding site [ion binding]; other site 428406009478 Superinfection exclusion protein B; Region: SieB; pfam14163 428406009479 TOPRIM_OLD: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in bacterial and archaeal nucleases of the OLD (overcome lysogenization defect) family. The bacteriophage P2 OLD protein, which has DNase as well as...; Region: TOPRIM_OLD; cd01026 428406009480 putative active site [active] 428406009481 putative metal-binding site [ion binding]; other site 428406009482 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 428406009483 Part of AAA domain; Region: AAA_19; pfam13245 428406009484 Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]; Region: COG4251 428406009485 GAF domain; Region: GAF; pfam01590 428406009486 Phytochrome region; Region: PHY; pfam00360 428406009487 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 428406009488 dimer interface [polypeptide binding]; other site 428406009489 phosphorylation site [posttranslational modification] 428406009490 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406009491 ATP binding site [chemical binding]; other site 428406009492 Mg2+ binding site [ion binding]; other site 428406009493 G-X-G motif; other site 428406009494 Response regulator receiver domain; Region: Response_reg; pfam00072 428406009495 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406009496 active site 428406009497 phosphorylation site [posttranslational modification] 428406009498 intermolecular recognition site; other site 428406009499 dimerization interface [polypeptide binding]; other site 428406009500 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 428406009501 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406009502 active site 428406009503 phosphorylation site [posttranslational modification] 428406009504 intermolecular recognition site; other site 428406009505 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 428406009506 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 428406009507 putative active site [active] 428406009508 heme pocket [chemical binding]; other site 428406009509 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 428406009510 dimer interface [polypeptide binding]; other site 428406009511 phosphorylation site [posttranslational modification] 428406009512 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406009513 ATP binding site [chemical binding]; other site 428406009514 Mg2+ binding site [ion binding]; other site 428406009515 G-X-G motif; other site 428406009516 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 428406009517 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406009518 active site 428406009519 phosphorylation site [posttranslational modification] 428406009520 intermolecular recognition site; other site 428406009521 dimerization interface [polypeptide binding]; other site 428406009522 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 428406009523 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 428406009524 tRNA; other site 428406009525 putative tRNA binding site [nucleotide binding]; other site 428406009526 putative NADP binding site [chemical binding]; other site 428406009527 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 428406009528 peptide chain release factor 1; Validated; Region: prfA; PRK00591 428406009529 This domain is found in peptide chain release factors; Region: PCRF; smart00937 428406009530 RF-1 domain; Region: RF-1; pfam00472 428406009531 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 428406009532 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 428406009533 Glutaredoxin (GRX) family, PKC-interacting cousin of TRX (PICOT)-like subfamily; composed of PICOT and GRX-PICOT-like proteins. The non-PICOT members of this family contain only the GRX-like domain, whereas PICOT contains an N-terminal TRX-like domain...; Region: GRX_PICOT_like; cd03028 428406009534 putative GSH binding site [chemical binding]; other site 428406009535 catalytic residues [active] 428406009536 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Provisional; Region: PRK06029 428406009537 Flavoprotein; Region: Flavoprotein; pfam02441 428406009538 glucan biosynthesis protein G; Provisional; Region: mdoG; PRK13274 428406009539 glucan biosynthesis protein D; Provisional; Region: mdoD; PRK13273 428406009540 Glycosyltransferases, probably involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG1215 428406009541 Glucan_BSP_ModH catalyzes the elongation of beta-1,2 polyglucose chains of glucan; Region: Glucan_BSP_ModH; cd04191 428406009542 Ligand binding site; other site 428406009543 DXD motif; other site 428406009544 YbaK-like. The YbaK family of deacylase domains includes the INS amino acid-editing domain of the bacterial class II prolyl tRNA synthetase (ProRS), and it's trans-acting homologs, YbaK, ProX, and PrdX. The primary function of INS is to hydrolyze...; Region: YbaK_like; cd04332 428406009545 putative deacylase active site [active] 428406009546 Zinc finger domain containing protein (CDGSH-type) [Function unknown]; Region: COG3369 428406009547 Iron-binding zinc finger CDGSH type; Region: zf-CDGSH; pfam09360 428406009548 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 428406009549 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 428406009550 Walker A/P-loop; other site 428406009551 ATP binding site [chemical binding]; other site 428406009552 Q-loop/lid; other site 428406009553 ABC transporter signature motif; other site 428406009554 Walker B; other site 428406009555 D-loop; other site 428406009556 H-loop/switch region; other site 428406009557 ABC transporter; Region: ABC_tran_2; pfam12848 428406009558 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 428406009559 Prokaryotic Cytochrome C oxidase subunit IV; Region: COX4_pro; cl01204 428406009560 Ubiquinol oxidase subunit III subfamily. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously...; Region: Ubiquinol_oxidase_III; cd02863 428406009561 Subunit I/III interface [polypeptide binding]; other site 428406009562 Subunit III/IV interface [polypeptide binding]; other site 428406009563 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 428406009564 Ubiquinol oxidase subunit I. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously pumps protons...; Region: Ubiquinol_Oxidase_I; cd01662 428406009565 D-pathway; other site 428406009566 Putative ubiquinol binding site [chemical binding]; other site 428406009567 Low-spin heme (heme b) binding site [chemical binding]; other site 428406009568 Putative water exit pathway; other site 428406009569 Binuclear center (heme o3/CuB) [ion binding]; other site 428406009570 K-pathway; other site 428406009571 Putative proton exit pathway; other site 428406009572 cytochrome o ubiquinol oxidase subunit II; Region: CyoA; TIGR01433 428406009573 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 428406009574 COX Aromatic Rich Motif; Region: COX_ARM; pfam06481 428406009575 Mn2+ and Fe2+ transporters of the NRAMP family [Inorganic ion transport and metabolism]; Region: MntH; COG1914 428406009576 Natural resistance-associated macrophage protein; Region: Nramp; pfam01566 428406009577 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 428406009578 putative transposase OrfB; Reviewed; Region: PHA02517 428406009579 HTH-like domain; Region: HTH_21; pfam13276 428406009580 Integrase core domain; Region: rve; pfam00665 428406009581 Integrase core domain; Region: rve_3; cl15866 428406009582 LabA_like proteins; Region: LabA_like; cd06167 428406009583 putative metal binding site [ion binding]; other site 428406009584 Uncharacterized conserved protein [Function unknown]; Region: COG1432 428406009585 Uncharacterized ACR, COG2135; Region: DUF159; pfam02586 428406009586 conjugal transfer protein TrbJ; Provisional; Region: PRK13874; cl02193 428406009587 integrase; Provisional; Region: int; PHA02601 428406009588 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 428406009589 active site 428406009590 DNA binding site [nucleotide binding] 428406009591 Int/Topo IB signature motif; other site 428406009592 ClpXP protease specificity-enhancing factor; Provisional; Region: PRK11798 428406009593 stringent starvation protein A; Provisional; Region: sspA; PRK09481 428406009594 GST_N family, Stringent starvation protein A (SspA) subfamily; SspA is a RNA polymerase (RNAP)-associated protein required for the lytic development of phage P1 and for stationary phase-induced acid tolerance of E. coli. It is implicated in survival...; Region: GST_N_SspA; cd03059 428406009595 C-terminal domain interface [polypeptide binding]; other site 428406009596 putative GSH binding site (G-site) [chemical binding]; other site 428406009597 dimer interface [polypeptide binding]; other site 428406009598 C-terminal, alpha helical domain of Stringent starvation protein A; Region: GST_C_SspA; cd03186 428406009599 dimer interface [polypeptide binding]; other site 428406009600 N-terminal domain interface [polypeptide binding]; other site 428406009601 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 428406009602 Cytochrome c; Region: Cytochrom_C; cl11414 428406009603 Cytochrome b subunit of the bc complex [Energy production and conversion]; Region: QcrB; COG1290 428406009604 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cd00284 428406009605 Qi binding site; other site 428406009606 intrachain domain interface; other site 428406009607 interchain domain interface [polypeptide binding]; other site 428406009608 heme bH binding site [chemical binding]; other site 428406009609 heme bL binding site [chemical binding]; other site 428406009610 Qo binding site; other site 428406009611 interchain domain interface [polypeptide binding]; other site 428406009612 intrachain domain interface; other site 428406009613 Qi binding site; other site 428406009614 Cytochrome b(C-terminal)/b6/petD; Region: Cytochrom_B_C; pfam00032 428406009615 Qo binding site; other site 428406009616 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 428406009617 Iron-sulfur protein (ISP) component of the bc(1) complex family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The bc(1) complex is a multisubunit enzyme found in many different organisms including...; Region: Rieske_cytochrome_bc1; cd03470 428406009618 [2Fe-2S] cluster binding site [ion binding]; other site 428406009619 large-conductance mechanosensitive channel; Provisional; Region: mscL; PRK13952 428406009620 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 428406009621 Uncharacterized conserved protein [Function unknown]; Region: COG0327 428406009622 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl15371 428406009623 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 428406009624 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 428406009625 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 428406009626 protein binding site [polypeptide binding]; other site 428406009627 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 428406009628 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 428406009629 trimer interface [polypeptide binding]; other site 428406009630 eyelet of channel; other site 428406009631 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 428406009632 transcriptional regulatory protein TctD; Provisional; Region: PRK15479 428406009633 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406009634 active site 428406009635 phosphorylation site [posttranslational modification] 428406009636 intermolecular recognition site; other site 428406009637 dimerization interface [polypeptide binding]; other site 428406009638 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 428406009639 DNA binding site [nucleotide binding] 428406009640 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 428406009641 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 428406009642 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 428406009643 dimer interface [polypeptide binding]; other site 428406009644 phosphorylation site [posttranslational modification] 428406009645 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406009646 ATP binding site [chemical binding]; other site 428406009647 Mg2+ binding site [ion binding]; other site 428406009648 G-X-G motif; other site 428406009649 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 428406009650 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 428406009651 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 428406009652 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406009653 dimer interface [polypeptide binding]; other site 428406009654 conserved gate region; other site 428406009655 ABC-ATPase subunit interface; other site 428406009656 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406009657 dimer interface [polypeptide binding]; other site 428406009658 conserved gate region; other site 428406009659 putative PBP binding loops; other site 428406009660 ABC-ATPase subunit interface; other site 428406009661 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 428406009662 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 428406009663 Walker A/P-loop; other site 428406009664 ATP binding site [chemical binding]; other site 428406009665 Q-loop/lid; other site 428406009666 ABC transporter signature motif; other site 428406009667 Walker B; other site 428406009668 D-loop; other site 428406009669 H-loop/switch region; other site 428406009670 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 428406009671 sec-independent translocase; Provisional; Region: tatB; PRK01919 428406009672 twin arginine translocase protein A; Provisional; Region: tatA; PRK02958 428406009673 Predicted membrane protein [Function unknown]; Region: COG3671 428406009674 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in Escherichia coli phosphoribosyl-ATP pyrophosphohydrolase (HisIE or PRATP-PH) and its homologs; Region: NTP-PPase_HisIE_like; cd11534 428406009675 metal binding site [ion binding]; metal-binding site 428406009676 phosphoribosyl-AMP cyclohydrolase; Reviewed; Region: hisI; PRK00051 428406009677 The cyclase subunit of imidazoleglycerol phosphate synthase (HisF). Imidazole glycerol phosphate synthase (IGPS) catalyzes the fifth step of histidine biosynthesis, the formation of the imidazole ring. IGPS converts N1-(5'-phosphoribulosyl)...; Region: HisF; cd04731 428406009678 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 428406009679 substrate binding site [chemical binding]; other site 428406009680 glutamase interaction surface [polypeptide binding]; other site 428406009681 HisA. Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase catalyzes the fourth step in histidine biosynthesis, an isomerisation of the aminoaldose moiety of ProFAR to the aminoketose of PRFAR (N-(5'-phospho-D-1...; Region: HisA; cd04732 428406009682 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 428406009683 catalytic residues [active] 428406009684 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13146 428406009685 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 428406009686 putative active site [active] 428406009687 oxyanion strand; other site 428406009688 catalytic triad [active] 428406009689 MarC family integral membrane protein; Region: MarC; cl00919 428406009690 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 428406009691 putative active site pocket [active] 428406009692 4-fold oligomerization interface [polypeptide binding]; other site 428406009693 metal binding residues [ion binding]; metal-binding site 428406009694 3-fold/trimer interface [polypeptide binding]; other site 428406009695 histidinol-phosphate aminotransferase; Provisional; Region: PRK04870 428406009696 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 428406009697 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406009698 homodimer interface [polypeptide binding]; other site 428406009699 catalytic residue [active] 428406009700 Histidinol dehydrogenase [Amino acid transport and metabolism]; Region: HisD; COG0141 428406009701 Histidinol dehydrogenase, HisD, E.C 1.1.1.23. Histidinol dehydrogenase catalyzes the last two steps in the L-histidine biosynthesis pathway, which is conserved in bacteria, archaea, fungi, and plants. These last two steps are (i) the NAD-dependent...; Region: Histidinol_dh; cd06572 428406009702 NAD binding site [chemical binding]; other site 428406009703 dimerization interface [polypeptide binding]; other site 428406009704 product binding site; other site 428406009705 substrate binding site [chemical binding]; other site 428406009706 zinc binding site [ion binding]; other site 428406009707 catalytic residues [active] 428406009708 ATP phosphoribosyltransferase catalytic subunit; Reviewed; Region: hisG; PRK01686 428406009709 ATP phosphoribosyltransferase [Amino acid transport and metabolism]; Region: HisG; COG0040 428406009710 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 428406009711 UDP-N-acetylglucosamine enolpyruvyl transferase catalyzes enolpyruvyl transfer as part of the first step in the biosynthesis of peptidoglycan, a component of the bacterial cell wall. The reaction is phosphoenolpyruvate + UDP-N-acetyl-D-glucosamine =...; Region: UdpNAET; cd01555 428406009712 hinge; other site 428406009713 active site 428406009714 Predicted transcriptional regulator, BolA superfamily [Transcription]; Region: COG5007 428406009715 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 428406009716 ABC-2 type transporter; Region: ABC2_membrane; cl17235 428406009717 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 428406009718 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 428406009719 Walker A/P-loop; other site 428406009720 ATP binding site [chemical binding]; other site 428406009721 Q-loop/lid; other site 428406009722 ABC transporter signature motif; other site 428406009723 Walker B; other site 428406009724 D-loop; other site 428406009725 H-loop/switch region; other site 428406009726 Sulphate Transporter and Anti-Sigma factor antagonist) domain of anti-anti-sigma factors, key regulators of anti-sigma factors by phosphorylation; Region: STAS_anti-anti-sigma_factors; cd07043 428406009727 anti sigma factor interaction site; other site 428406009728 regulatory phosphorylation site [posttranslational modification]; other site 428406009729 ABC-type transport system involved in resistance to organic solvents, auxiliary component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2D; COG2854 428406009730 Surface lipoprotein [Cell envelope biogenesis, outer membrane]; Region: VacJ; COG2853 428406009731 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 428406009732 mce related protein; Region: MCE; pfam02470 428406009733 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 428406009734 Permease; Region: Permease; pfam02405 428406009735 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 428406009736 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 428406009737 Walker A/P-loop; other site 428406009738 ATP binding site [chemical binding]; other site 428406009739 Q-loop/lid; other site 428406009740 ABC transporter signature motif; other site 428406009741 Walker B; other site 428406009742 D-loop; other site 428406009743 H-loop/switch region; other site 428406009744 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 428406009745 glutamate synthase subunit beta; Reviewed; Region: gltD; PRK12810 428406009746 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 428406009747 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 428406009748 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 428406009749 Glutamine amidotransferases class-II (Gn-AT), glutamate synthase (GltS)-type. GltS is a homodimer that synthesizes L-glutamate from 2-oxoglutarate and L-glutamine, an important step in ammonia assimilation in bacteria, cyanobacteria and plants. The...; Region: GltS; cd00713 428406009750 active site 428406009751 dimer interface [polypeptide binding]; other site 428406009752 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 428406009753 Glutamate synthase (GltS) FMN-binding domain. GltS is a complex iron-sulfur flavoprotein that catalyzes the reductive synthesis of L-glutamate from 2-oxoglutarate and L-glutamine via intramolecular channelling of ammonia, a reaction in the plant, yeast...; Region: GltS_FMN; cd02808 428406009754 active site 428406009755 FMN binding site [chemical binding]; other site 428406009756 substrate binding site [chemical binding]; other site 428406009757 3Fe-4S cluster binding site [ion binding]; other site 428406009758 gltb_C. This domain is found at the C-terminus of the large subunit (gltB) of glutamate synthase (GltS). GltS encodes a complex iron-sulfur flavoprotein that catalyzes the synthesis of L-glutamate from L-glutamine and 2-oxoglutarate. It requires the...; Region: gltB_C; cd00982 428406009759 domain interface; other site 428406009760 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG1943 428406009761 Outer membrane protein W [Cell envelope biogenesis, outer membrane]; Region: OmpW; COG3047 428406009762 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 428406009763 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 428406009764 Zn2+ binding site [ion binding]; other site 428406009765 Mg2+ binding site [ion binding]; other site 428406009766 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 428406009767 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 428406009768 active site 428406009769 dimer interface [polypeptide binding]; other site 428406009770 metal binding site [ion binding]; metal-binding site 428406009771 shikimate kinase; Reviewed; Region: aroK; PRK00131 428406009772 Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants. Chorismic acid is a important intermediate in the synthesis...; Region: SK; cd00464 428406009773 ADP binding site [chemical binding]; other site 428406009774 magnesium binding site [ion binding]; other site 428406009775 putative shikimate binding site; other site 428406009776 Type II secretory pathway, component HofQ [Intracellular trafficking and secretion]; Region: HofQ; COG4796 428406009777 AMIN domain; Region: AMIN; pfam11741 428406009778 Secretin and TonB N terminus short domain; Region: STN; smart00965 428406009779 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 428406009780 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 428406009781 Tfp pilus assembly protein PilP [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilP; COG3168 428406009782 Pilus assembly protein, PilP; Region: PilP; pfam04351 428406009783 Tfp pilus assembly protein PilO [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilO; COG3167 428406009784 Tfp pilus assembly protein PilN [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilN; COG3166 428406009785 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 428406009786 Cell division protein FtsA; Region: FtsA; cl17206 428406009787 Competence protein A; Region: Competence_A; pfam11104 428406009788 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 428406009789 Transglycosylase; Region: Transgly; pfam00912 428406009790 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 428406009791 frataxin-like protein; Provisional; Region: cyaY; PRK00446 428406009792 putative iron binding site [ion binding]; other site 428406009793 diaminopimelate decarboxylase; Region: lysA; TIGR01048 428406009794 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 428406009795 active site 428406009796 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 428406009797 substrate binding site [chemical binding]; other site 428406009798 catalytic residues [active] 428406009799 dimer interface [polypeptide binding]; other site 428406009800 putative sulfite oxidase subunit YedZ; Reviewed; Region: PRK05419 428406009801 TMAO/DMSO reductase; Reviewed; Region: PRK05363 428406009802 YedY_like molybdopterin cofactor (Moco) binding domain, a subgroup of the sulfite oxidase (SO) family of molybdopterin binding domains. Escherichia coli YedY has been propsed to form a heterodimer, consisting of a soluble catalytic subunit termed YedY; Region: YedY_like_Moco; cd02107 428406009803 Moco binding site; other site 428406009804 metal coordination site [ion binding]; other site 428406009805 Predicted transmembrane transcriptional regulator (anti-sigma factor) [Transcription]; Region: COG5662 428406009806 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 428406009807 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 428406009808 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 428406009809 DNA binding residues [nucleotide binding] 428406009810 Secreted repeat of unknown function; Region: Lipoprotein_15; pfam03640 428406009811 Secreted repeat of unknown function; Region: Lipoprotein_15; pfam03640 428406009812 cytochrome c-type biogenesis protein CcsB; Region: cytochr_II_ccsB; TIGR03144 428406009813 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 428406009814 ResB-like family; Region: ResB; pfam05140 428406009815 Cytochrome c553 [Energy production and conversion]; Region: COG2863 428406009816 Cytochrome c; Region: Cytochrom_C; cl11414 428406009817 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 428406009818 G1 box; other site 428406009819 GTP/Mg2+ binding site [chemical binding]; other site 428406009820 Switch I region; other site 428406009821 G2 box; other site 428406009822 G3 box; other site 428406009823 Switch II region; other site 428406009824 G4 box; other site 428406009825 G5 box; other site 428406009826 Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the...; Region: ALAD_PBGS_aspartate_rich; cd04823 428406009827 dimer interface [polypeptide binding]; other site 428406009828 active site 428406009829 aspartate-rich active site metal binding site; other site 428406009830 allosteric magnesium binding site [ion binding]; other site 428406009831 Schiff base residues; other site 428406009832 thiol:disulfide interchange protein precursor; Provisional; Region: dipZ; PRK00293 428406009833 Disulphide bond corrector protein DsbC; Region: DsbC; pfam11412 428406009834 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 428406009835 DsbD gamma family; DsbD gamma is the C-terminal periplasmic domain of the bacterial protein DsbD. It contains a CXXC motif in a TRX fold and shuttles the reducing potential from the membrane domain (DsbD beta) to the N-terminal periplasmic domain (DsbD...; Region: DsbDgamma; cd02953 428406009836 DsbD alpha interface [polypeptide binding]; other site 428406009837 catalytic residues [active] 428406009838 Uncharacterized protein involved in tolerance to divalent cations [Inorganic ion transport and metabolism]; Region: CutA; COG1324 428406009839 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 428406009840 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 428406009841 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 428406009842 alphaNTD homodimer interface [polypeptide binding]; other site 428406009843 alphaNTD - beta interaction site [polypeptide binding]; other site 428406009844 alphaNTD - beta' interaction site [polypeptide binding]; other site 428406009845 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 428406009846 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 428406009847 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 428406009848 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cd00165 428406009849 RNA binding surface [nucleotide binding]; other site 428406009850 30S ribosomal protein S11; Validated; Region: PRK05309 428406009851 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 428406009852 30S ribosomal protein S13; Region: bact_S13; TIGR03631 428406009853 Ribosomal protein L36; Region: Ribosomal_L36; pfam00444 428406009854 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the...; Region: S1_IF1; cd04451 428406009855 rRNA binding site [nucleotide binding]; other site 428406009856 predicted 30S ribosome binding site; other site 428406009857 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 428406009858 SecY translocase; Region: SecY; pfam00344 428406009859 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 428406009860 Ribosomal protein L30, which is found in eukaryotes and prokaryotes but not in archaea, is one of the smallest ribosomal proteins with a molecular mass of about 7kDa. L30 binds the 23SrRNA as well as the 5S rRNA and is one of five ribosomal proteins that...; Region: Ribosomal_L30; cd01658 428406009861 23S rRNA binding site [nucleotide binding]; other site 428406009862 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 428406009863 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 428406009864 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 428406009865 Ribosomal L18/L5e: L18 (L5e) is a ribosomal protein found in the central protuberance (CP) of the large subunit. L18 binds 5S rRNA and induces a conformational change that stimulates the binding of L5 to 5S rRNA. Association of 5S rRNA with 23S rRNA...; Region: Ribosomal_L18_L5e; cd00432 428406009866 5S rRNA interface [nucleotide binding]; other site 428406009867 L27 interface [polypeptide binding]; other site 428406009868 23S rRNA interface [nucleotide binding]; other site 428406009869 L5 interface [polypeptide binding]; other site 428406009870 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 428406009871 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 428406009872 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 428406009873 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 428406009874 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 428406009875 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 428406009876 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 428406009877 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 428406009878 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 428406009879 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 428406009880 RNA binding site [nucleotide binding]; other site 428406009881 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 428406009882 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 428406009883 Ribosomal L29 protein/HIP. L29 is a protein of the large ribosomal Subunit. A homolog, called heparin/heparan sulfate interacting protein (HIP), has also been identified in mammals. L29 is located on the surface of the large ribosomal subunit, where it...; Region: Ribosomal_L29_HIP; cd00427 428406009884 23S rRNA interface [nucleotide binding]; other site 428406009885 putative translocon interaction site; other site 428406009886 signal recognition particle (SRP54) interaction site; other site 428406009887 L23 interface [polypeptide binding]; other site 428406009888 trigger factor interaction site; other site 428406009889 Ribosomal_L16_L10e: L16 is an essential protein in the large ribosomal subunit of bacteria, mitochondria, and chloroplasts. Large subunits that lack L16 are defective in peptidyl transferase activity, peptidyl-tRNA hydrolysis activity, association with...; Region: Ribosomal_L16_L10e; cd01433 428406009890 23S rRNA interface [nucleotide binding]; other site 428406009891 5S rRNA interface [nucleotide binding]; other site 428406009892 putative antibiotic binding site [chemical binding]; other site 428406009893 L25 interface [polypeptide binding]; other site 428406009894 L27 interface [polypeptide binding]; other site 428406009895 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 428406009896 K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH...; Region: 30S_S3_KH; cd02412 428406009897 G-X-X-G motif; other site 428406009898 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 428406009899 Ribosomal protein L22/L17e. L22 (L17 in eukaryotes) is a core protein of the large ribosomal subunit. It is the only ribosomal protein that interacts with all six domains of 23S rRNA, and is one of the proteins important for directing the proper...; Region: Ribosomal_L22; cd00336 428406009900 putative translocon binding site; other site 428406009901 protein-rRNA interface [nucleotide binding]; other site 428406009902 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 428406009903 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 428406009904 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 428406009905 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 428406009906 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 428406009907 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 428406009908 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 428406009909 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 428406009910 elongation factor Tu; Reviewed; Region: PRK00049 428406009911 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 428406009912 G1 box; other site 428406009913 GEF interaction site [polypeptide binding]; other site 428406009914 GTP/Mg2+ binding site [chemical binding]; other site 428406009915 Switch I region; other site 428406009916 G2 box; other site 428406009917 G3 box; other site 428406009918 Switch II region; other site 428406009919 G4 box; other site 428406009920 G5 box; other site 428406009921 EFTU_II: Elongation factor Tu domain II. Elongation factors Tu (EF-Tu) are three-domain GTPases with an essential function in the elongation phase of mRNA translation. The GTPase center of EF-Tu is in the N-terminal domain (domain I), also known as the...; Region: EFTU_II; cd03697 428406009922 Domain III of elongation factor (EF) Tu. Ef-Tu consists of three structural domains, designated I, II and III. Domain III adopts a beta barrel structure. Domain III is involved in binding to both charged tRNA and binding to elongation factor Ts (EF-Ts); Region: EFTU_III; cd03707 428406009923 Antibiotic Binding Site [chemical binding]; other site 428406009924 elongation factor G; Reviewed; Region: PRK00007 428406009925 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 428406009926 G1 box; other site 428406009927 putative GEF interaction site [polypeptide binding]; other site 428406009928 GTP/Mg2+ binding site [chemical binding]; other site 428406009929 Switch I region; other site 428406009930 G2 box; other site 428406009931 G3 box; other site 428406009932 Switch II region; other site 428406009933 G4 box; other site 428406009934 G5 box; other site 428406009935 EFG_mtEFG_II: this subfamily represents the domain II of elongation factor G (EF-G) in bacteria and, the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2)_like proteins found in eukaryotes. During the process of peptide synthesis...; Region: EFG_mtEFG_II; cd04088 428406009936 EFG_mtEFG1_IV: domains similar to domain IV of the bacterial translational elongation factor (EF) EF-G. Included in this group is a domain of mitochondrial Elongation factor G1 (mtEFG1) proteins homologous to domain IV of EF-G. Eukaryotic cells harbor 2...; Region: EFG_mtEFG1_IV; cd01434 428406009937 EFG_mtEFG_C: domains similar to the C-terminal domain of the bacterial translational elongation factor (EF) EF-G. Included in this group is the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2) proteins. Eukaryotic cells harbor 2...; Region: EFG_mtEFG_C; cd03713 428406009938 30S ribosomal protein S7; Validated; Region: PRK05302 428406009939 S12-like family, 30S ribosomal protein S12 subfamily; S12 is located at the interface of the large and small ribosomal subunits of prokaryotes, chloroplasts and mitochondria, where it plays an important role in both tRNA and ribosomal subunit...; Region: Ribosomal_S12; cd03368 428406009940 S17 interaction site [polypeptide binding]; other site 428406009941 S8 interaction site; other site 428406009942 16S rRNA interaction site [nucleotide binding]; other site 428406009943 streptomycin interaction site [chemical binding]; other site 428406009944 23S rRNA interaction site [nucleotide binding]; other site 428406009945 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 428406009946 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406009947 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 428406009948 LysR family transcriptional regulator; Provisional; Region: PRK14997 428406009949 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406009950 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 428406009951 putative effector binding pocket; other site 428406009952 dimerization interface [polypeptide binding]; other site 428406009953 ATP-dependent DNA helicase RecQ; Region: recQ; TIGR01389 428406009954 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 428406009955 ATP binding site [chemical binding]; other site 428406009956 putative Mg++ binding site [ion binding]; other site 428406009957 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 428406009958 nucleotide binding region [chemical binding]; other site 428406009959 ATP-binding site [chemical binding]; other site 428406009960 This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure; Region: RQC; smart00956 428406009961 HRDC domain; Region: HRDC; pfam00570 428406009962 Methyltransferase domain; Region: Methyltransf_23; pfam13489 428406009963 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 428406009964 S-adenosylmethionine binding site [chemical binding]; other site 428406009965 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4676 428406009966 Uncharacterized protein conserved in bacteria (DUF2135); Region: DUF2135; pfam09906 428406009967 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4676 428406009968 Uncharacterized protein conserved in bacteria (DUF2135); Region: DUF2135; pfam09906 428406009969 Predicted secreted protein [Function unknown]; Region: COG5445 428406009970 Predicted secreted protein (DUF2300); Region: DUF2300; pfam10062 428406009971 Predicted secreted protein [Function unknown]; Region: COG5445 428406009972 Predicted secreted protein (DUF2300); Region: DUF2300; pfam10062 428406009973 Large extracellular alpha-helical protein [General function prediction only]; Region: COG2373 428406009974 MG2 domain; Region: A2M_N; pfam01835 428406009975 Alpha-2-macroglobulin family; Region: A2M; pfam00207 428406009976 This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2-macroglobulin (alpha (2)-M) and pregnancy zone protein (PZP) and, the C3 C4 and C5 components of vertebrate...; Region: ISOPREN_C2_like; cl08267 428406009977 Protein of unknown function (DUF1175); Region: DUF1175; cl14898 428406009978 Uncharacterized protein conserved in bacteria (DUF2138); Region: DUF2138; pfam09909 428406009979 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 428406009980 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 428406009981 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 428406009982 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 428406009983 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 428406009984 RNA polymerase Rpb1, domain 5; Region: RNA_pol_Rpb1_5; pfam04998 428406009985 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 428406009986 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 428406009987 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 428406009988 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 428406009989 DNA binding site [nucleotide binding] 428406009990 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 428406009991 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 428406009992 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl17585 428406009993 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 428406009994 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cd00653 428406009995 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 428406009996 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cd00653 428406009997 RPB3 interaction site [polypeptide binding]; other site 428406009998 RPB1 interaction site [polypeptide binding]; other site 428406009999 RPB11 interaction site [polypeptide binding]; other site 428406010000 RPB10 interaction site [polypeptide binding]; other site 428406010001 Ribosomal protein L7/L12. Ribosomal protein L7/L12 refers to the large ribosomal subunit proteins L7 and L12, which are identical except that L7 is acetylated at the N terminus. It is a component of the L7/L12 stalk, which is located at the surface of...; Region: Ribosomal_L7_L12; cd00387 428406010002 core dimer interface [polypeptide binding]; other site 428406010003 peripheral dimer interface [polypeptide binding]; other site 428406010004 L10 interface [polypeptide binding]; other site 428406010005 L11 interface [polypeptide binding]; other site 428406010006 putative EF-Tu interaction site [polypeptide binding]; other site 428406010007 putative EF-G interaction site [polypeptide binding]; other site 428406010008 Ribosomal protein L10 family, L10 subfamily; composed of bacterial 50S ribosomal protein and eukaryotic mitochondrial 39S ribosomal protein, L10. L10 occupies the L7/L12 stalk of the ribosome. The N-terminal domain (NTD) of L10 interacts with L11 protein...; Region: Ribosomal_L10; cd05797 428406010009 23S rRNA interface [nucleotide binding]; other site 428406010010 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 428406010011 Ribosomal protein L1. The L1 protein, located near the E-site of the ribosome, forms part of the L1 stalk along with 23S rRNA. In bacteria and archaea, L1 functions both as a ribosomal protein that binds rRNA, and as a translation repressor that binds...; Region: Ribosomal_L1; cd00403 428406010012 mRNA/rRNA interface [nucleotide binding]; other site 428406010013 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 428406010014 Ribosomal protein L11. Ribosomal protein L11, together with proteins L10 and L7/L12, and 23S rRNA, form the L7/L12 stalk on the surface of the large subunit of the ribosome. The homologous eukaryotic cytoplasmic protein is also called 60S ribosomal...; Region: Ribosomal_L11; cd00349 428406010015 23S rRNA interface [nucleotide binding]; other site 428406010016 L7/L12 interface [polypeptide binding]; other site 428406010017 putative thiostrepton binding site; other site 428406010018 L25 interface [polypeptide binding]; other site 428406010019 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 428406010020 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 428406010021 putative homodimer interface [polypeptide binding]; other site 428406010022 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 428406010023 heterodimer interface [polypeptide binding]; other site 428406010024 homodimer interface [polypeptide binding]; other site 428406010025 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK05740 428406010026 elongation factor Tu; Reviewed; Region: PRK00049 428406010027 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 428406010028 G1 box; other site 428406010029 GEF interaction site [polypeptide binding]; other site 428406010030 GTP/Mg2+ binding site [chemical binding]; other site 428406010031 Switch I region; other site 428406010032 G2 box; other site 428406010033 G3 box; other site 428406010034 Switch II region; other site 428406010035 G4 box; other site 428406010036 G5 box; other site 428406010037 EFTU_II: Elongation factor Tu domain II. Elongation factors Tu (EF-Tu) are three-domain GTPases with an essential function in the elongation phase of mRNA translation. The GTPase center of EF-Tu is in the N-terminal domain (domain I), also known as the...; Region: EFTU_II; cd03697 428406010038 Domain III of elongation factor (EF) Tu. Ef-Tu consists of three structural domains, designated I, II and III. Domain III adopts a beta barrel structure. Domain III is involved in binding to both charged tRNA and binding to elongation factor Ts (EF-Ts); Region: EFTU_III; cd03707 428406010039 Antibiotic Binding Site [chemical binding]; other site 428406010040 Transposase C of IS166 homeodomain; Region: LZ_Tnp_IS66; pfam13007 428406010041 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3436 428406010042 putative Helix-turn-helix domain of transposase IS66; Region: HTH_Tnp_IS66; pfam13005 428406010043 Transposase IS66 family; Region: DDE_Tnp_IS66; pfam03050 428406010044 IS66 C-terminal element; Region: DDE_Tnp_IS66_C; pfam13817 428406010045 IS66 Orf2 like protein; Region: TnpB_IS66; pfam05717 428406010046 Transposase; Region: HTH_Tnp_1; cl17663 428406010047 CHAD domain; Region: CHAD; pfam05235 428406010048 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 428406010049 DeoR-like helix-turn-helix domain; Region: HTH_DeoR; pfam08220 428406010050 DeoR C terminal sensor domain; Region: DeoRC; pfam00455 428406010051 glycerol-3-phosphate dehydrogenase; Reviewed; Region: glpD; PRK12266 428406010052 ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]; Region: MalK; COG3839 428406010053 ATP-binding cassette domain of the carbohydrate and solute transporters-like; Region: ABC_Carb_Solutes_like; cd03259 428406010054 Walker A/P-loop; other site 428406010055 ATP binding site [chemical binding]; other site 428406010056 Q-loop/lid; other site 428406010057 ABC transporter signature motif; other site 428406010058 Walker B; other site 428406010059 D-loop; other site 428406010060 H-loop/switch region; other site 428406010061 TOBE domain; Region: TOBE_2; pfam08402 428406010062 ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]; Region: MalK; COG3839 428406010063 ATP-binding cassette domain of the carbohydrate and solute transporters-like; Region: ABC_Carb_Solutes_like; cd03259 428406010064 Walker A/P-loop; other site 428406010065 ATP binding site [chemical binding]; other site 428406010066 Q-loop/lid; other site 428406010067 ABC transporter signature motif; other site 428406010068 Walker B; other site 428406010069 D-loop; other site 428406010070 H-loop/switch region; other site 428406010071 TOBE domain; Region: TOBE_2; pfam08402 428406010072 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 428406010073 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406010074 dimer interface [polypeptide binding]; other site 428406010075 conserved gate region; other site 428406010076 putative PBP binding loops; other site 428406010077 ABC-ATPase subunit interface; other site 428406010078 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 428406010079 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406010080 dimer interface [polypeptide binding]; other site 428406010081 conserved gate region; other site 428406010082 putative PBP binding loops; other site 428406010083 ABC-ATPase subunit interface; other site 428406010084 Predicted small integral membrane protein (DUF2160); Region: DUF2160; pfam09928 428406010085 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 428406010086 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 428406010087 Glycerol kinase [Energy production and conversion]; Region: GlpK; COG0554 428406010088 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 428406010089 N- and C-terminal domain interface [polypeptide binding]; other site 428406010090 active site 428406010091 MgATP binding site [chemical binding]; other site 428406010092 catalytic site [active] 428406010093 metal binding site [ion binding]; metal-binding site 428406010094 glycerol binding site [chemical binding]; other site 428406010095 homotetramer interface [polypeptide binding]; other site 428406010096 homodimer interface [polypeptide binding]; other site 428406010097 FBP binding site [chemical binding]; other site 428406010098 protein IIAGlc interface [polypeptide binding]; other site 428406010099 Protein of unknown function (DUF1415); Region: DUF1415; pfam07209 428406010100 glucan biosynthesis protein D; Provisional; Region: mdoD; PRK13273 428406010101 AGE domain; N-acyl-D-glucosamine 2-epimerase domain; Responsible for intermediate epimerization during biosynthesis of N-acetylneuraminic acid. Catalytic mechanism is believed to be via nucleotide elimination and readdition and is ATP modulated. AGE is...; Region: AGE; cl00183 428406010102 dimerization interface [polypeptide binding]; other site 428406010103 putative active cleft [active] 428406010104 citrate-proton symporter; Provisional; Region: PRK15075 428406010105 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406010106 putative substrate translocation pore; other site 428406010107 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 428406010108 Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins; Region: PBP1_STKc_like; cd06326 428406010109 putative ligand binding site [chemical binding]; other site 428406010110 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 428406010111 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 428406010112 Helix-turn-helix domain; Region: HTH_18; pfam12833 428406010113 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 428406010114 Predicted alpha/beta hydrolase [General function prediction only]; Region: COG4757 428406010115 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cd00312 428406010116 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 428406010117 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 428406010118 non-specific DNA binding site [nucleotide binding]; other site 428406010119 salt bridge; other site 428406010120 sequence-specific DNA binding site [nucleotide binding]; other site 428406010121 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3295 428406010122 PepSY-associated TM helix; Region: PepSY_TM_1; pfam13172 428406010123 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 428406010124 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 428406010125 RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate...; Region: SIS_RpiR; cd05013 428406010126 putative active site [active] 428406010127 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 428406010128 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 428406010129 trimer interface [polypeptide binding]; other site 428406010130 eyelet of channel; other site 428406010131 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 428406010132 Mechanosensitive ion channel; Region: MS_channel; pfam00924 428406010133 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406010134 Major Facilitator Superfamily; Region: MFS_1; pfam07690 428406010135 putative substrate translocation pore; other site 428406010136 glutathione s-transferase; Provisional; Region: PTZ00057 428406010137 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 428406010138 C-terminal, alpha helical domain of Class Sigma-like Glutathione S-transferases; Region: GST_C_Sigma_like; cd03192 428406010139 N-terminal domain interface [polypeptide binding]; other site 428406010140 dimer interface [polypeptide binding]; other site 428406010141 substrate binding pocket (H-site) [chemical binding]; other site 428406010142 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 428406010143 cation diffusion facilitator family transporter; Region: CDF; TIGR01297 428406010144 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 428406010145 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406010146 active site 428406010147 phosphorylation site [posttranslational modification] 428406010148 intermolecular recognition site; other site 428406010149 dimerization interface [polypeptide binding]; other site 428406010150 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 428406010151 DNA binding residues [nucleotide binding] 428406010152 dimerization interface [polypeptide binding]; other site 428406010153 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 428406010154 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 428406010155 substrate binding pocket [chemical binding]; other site 428406010156 membrane-bound complex binding site; other site 428406010157 hinge residues; other site 428406010158 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 428406010159 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 428406010160 substrate binding pocket [chemical binding]; other site 428406010161 membrane-bound complex binding site; other site 428406010162 hinge residues; other site 428406010163 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 428406010164 PAS domain; Region: PAS_9; pfam13426 428406010165 putative active site [active] 428406010166 heme pocket [chemical binding]; other site 428406010167 PAS domain; Region: PAS_9; pfam13426 428406010168 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 428406010169 putative active site [active] 428406010170 heme pocket [chemical binding]; other site 428406010171 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 428406010172 dimer interface [polypeptide binding]; other site 428406010173 phosphorylation site [posttranslational modification] 428406010174 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406010175 ATP binding site [chemical binding]; other site 428406010176 Mg2+ binding site [ion binding]; other site 428406010177 G-X-G motif; other site 428406010178 Response regulator receiver domain; Region: Response_reg; pfam00072 428406010179 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406010180 active site 428406010181 phosphorylation site [posttranslational modification] 428406010182 intermolecular recognition site; other site 428406010183 dimerization interface [polypeptide binding]; other site 428406010184 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 428406010185 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_3; pfam13738 428406010186 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 428406010187 short chain dehydrogenase; Provisional; Region: PRK05650 428406010188 NAD(P) binding site [chemical binding]; other site 428406010189 active site 428406010190 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 428406010191 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 428406010192 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 428406010193 Predicted metal-dependent hydrolase; Region: Metal_hydrol; pfam10118 428406010194 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG3687 428406010195 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily; Region: HTH_MerR-like_sg2; cd04778 428406010196 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 428406010197 DNA binding residues [nucleotide binding] 428406010198 putative dimer interface [polypeptide binding]; other site 428406010199 Cytochrome c5 [Energy production and conversion]; Region: CycB; COG3245 428406010200 Cytochrome c5 [Energy production and conversion]; Region: CycB; COG3245 428406010201 Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase [Amino acid transport and metabolism]; Region: HisC; COG0079 428406010202 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 428406010203 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406010204 homodimer interface [polypeptide binding]; other site 428406010205 catalytic residue [active] 428406010206 formate dehydrogenase region TAT target; Region: formate_TAT; TIGR02811 428406010207 High potential iron-sulfur protein; Region: HIPIP; pfam01355 428406010208 DNA-binding transcriptional activator KdpE; Provisional; Region: PRK10529 428406010209 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406010210 active site 428406010211 phosphorylation site [posttranslational modification] 428406010212 intermolecular recognition site; other site 428406010213 dimerization interface [polypeptide binding]; other site 428406010214 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 428406010215 DNA binding site [nucleotide binding] 428406010216 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3181 428406010217 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 428406010218 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 428406010219 trimer interface [polypeptide binding]; other site 428406010220 eyelet of channel; other site 428406010221 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 428406010222 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; Region: Ald_Xan_dh_C; smart01008 428406010223 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 428406010224 Aerobic-type carbon monoxide dehydrogenase, middle subunit CoxM/CutM homologs [Energy production and conversion]; Region: CoxM; COG1319 428406010225 CO dehydrogenase flavoprotein C-terminal domain; Region: CO_deh_flav_C; pfam03450 428406010226 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 428406010227 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 428406010228 catalytic loop [active] 428406010229 iron binding site [ion binding]; other site 428406010230 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 428406010231 glutamate carboxypeptidase; Reviewed; Region: PRK06133 428406010232 M20 Peptidase Glutamate carboxypeptidase, a periplasmic enzyme; Region: M20_CPDG2; cd03885 428406010233 metal binding site [ion binding]; metal-binding site 428406010234 dimer interface [polypeptide binding]; other site 428406010235 Domain of unknown function (DUF1835); Region: DUF1835; pfam08874 428406010236 Protein of unknown function; Region: DUF3658; pfam12395 428406010237 glutathione-regulated potassium-efflux system protein KefC; Provisional; Region: PRK03562 428406010238 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 428406010239 TrkA-N domain; Region: TrkA_N; pfam02254 428406010240 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 428406010241 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 428406010242 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 428406010243 Coenzyme A binding pocket [chemical binding]; other site 428406010244 Cupin domain; Region: Cupin_2; cl17218 428406010245 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 428406010246 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 428406010247 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 428406010248 putative DNA binding site [nucleotide binding]; other site 428406010249 putative Zn2+ binding site [ion binding]; other site 428406010250 AsnC family; Region: AsnC_trans_reg; pfam01037 428406010251 4-hydroxyphenylpyruvate dioxygenase and related hemolysins [Amino acid transport and metabolism / General function prediction only]; Region: COG3185 428406010252 N-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate Synthase (HmaS); Region: HPPD_N_like; cd08342 428406010253 dimer interface [polypeptide binding]; other site 428406010254 C-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HppD) and hydroxymandelate Synthase (HmaS); Region: HPPD_C_like; cd07250 428406010255 active site 428406010256 Fe binding site [ion binding]; other site 428406010257 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cd00051 428406010258 EF-hand domain pair; Region: EF_hand_5; pfam13499 428406010259 Ca2+ binding site [ion binding]; other site 428406010260 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cl17302 428406010261 EF-hand domain pair; Region: EF_hand_5; pfam13499 428406010262 Ca2+ binding site [ion binding]; other site 428406010263 Type IV pilus biogenesis; Region: Pilus_PilP; pfam11356 428406010264 type II secretion system protein G; Region: typeII_sec_gspG; TIGR01710 428406010265 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 428406010266 type II secretion system protein H; Region: typeII_sec_gspH; TIGR01708 428406010267 Type II transport protein GspH; Region: GspH; pfam12019 428406010268 Type II secretion system (T2SS), protein I; Region: T2SI; pfam02501 428406010269 Type II secretion system (T2SS), protein J; Region: T2SJ; pfam11612 428406010270 Type II secretion system (T2SS), protein K; Region: T2SK; pfam03934 428406010271 Type II secretion system (T2SS), protein L; Region: T2SL; pfam05134 428406010272 GspL periplasmic domain; Region: GspL_C; pfam12693 428406010273 Type II secretory pathway, component PulM [Intracellular trafficking and secretion]; Region: PulM; COG3149 428406010274 Type II secretion system (T2SS), protein N; Region: T2SN; pfam01203 428406010275 type II secretion system protein D; Region: type_II_gspD; TIGR02517 428406010276 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 428406010277 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 428406010278 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 428406010279 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 428406010280 type II secretion system protein E; Region: type_II_gspE; TIGR02533 428406010281 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 428406010282 Walker A motif; other site 428406010283 ATP binding site [chemical binding]; other site 428406010284 Walker B motif; other site 428406010285 type II secretion system protein F; Region: GspF; TIGR02120 428406010286 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 428406010287 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 428406010288 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 428406010289 Helix-turn-helix domain; Region: HTH_38; pfam13936 428406010290 Integrase core domain; Region: rve; pfam00665 428406010291 Integrase core domain; Region: rve_3; cl15866 428406010292 Predicted flavin-nucleotide-binding protein [General function prediction only]; Region: COG3467 428406010293 indolepyruvate ferredoxin oxidoreductase; Validated; Region: PRK09193 428406010294 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 428406010295 dimer interface [polypeptide binding]; other site 428406010296 PYR/PP interface [polypeptide binding]; other site 428406010297 TPP binding site [chemical binding]; other site 428406010298 substrate binding site [chemical binding]; other site 428406010299 Thiamine pyrophosphate (TPP) family, IOR-alpha subfamily, TPP-binding module; composed of proteins similar to indolepyruvate ferredoxin oxidoreductase (IOR) alpha subunit. IOR catalyzes the oxidative decarboxylation of arylpyruvates, such as...; Region: TPP_IOR_alpha; cd02008 428406010300 TPP-binding site; other site 428406010301 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit [Energy production and conversion]; Region: PorG; COG1014 428406010302 exonuclease I; Provisional; Region: sbcB; PRK11779 428406010303 N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins; Region: ExoI_N; cd06138 428406010304 active site 428406010305 catalytic site [active] 428406010306 substrate binding site [chemical binding]; other site 428406010307 Exonuclease C-terminal; Region: Exonuc_X-T_C; pfam08411 428406010308 D-Lactate and related Dehydrogenases, NAD-binding and catalytic domains; Region: LDH_like_2; cd12183 428406010309 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 428406010310 putative ligand binding site [chemical binding]; other site 428406010311 putative NAD binding site [chemical binding]; other site 428406010312 catalytic site [active] 428406010313 Predicted HD phosphohydrolase [General function prediction only]; Region: COG4341; cl17564 428406010314 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 428406010315 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 428406010316 ligand binding site [chemical binding]; other site 428406010317 flexible hinge region; other site 428406010318 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 428406010319 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 428406010320 dinuclear metal binding motif [ion binding]; other site 428406010321 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 428406010322 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 428406010323 trimer interface [polypeptide binding]; other site 428406010324 eyelet of channel; other site 428406010325 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 428406010326 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406010327 active site 428406010328 phosphorylation site [posttranslational modification] 428406010329 intermolecular recognition site; other site 428406010330 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 428406010331 DNA binding residues [nucleotide binding] 428406010332 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 428406010333 dimerization interface [polypeptide binding]; other site 428406010334 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 428406010335 dimer interface [polypeptide binding]; other site 428406010336 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 428406010337 putative CheW interface [polypeptide binding]; other site 428406010338 Uncharacterized conserved protein [Function unknown]; Region: COG3868 428406010339 C-terminal Putative NodB-like catalytic domain of PelA-like uncharacterized hypothetical proteins found in bacteria; Region: CE4_PelA_like_C; cd10922 428406010340 putative active site [active] 428406010341 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 428406010342 classical (c) SDRs; Region: SDR_c; cd05233 428406010343 NAD(P) binding site [chemical binding]; other site 428406010344 active site 428406010345 MarR family; Region: MarR_2; cl17246 428406010346 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 428406010347 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 428406010348 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406010349 active site 428406010350 phosphorylation site [posttranslational modification] 428406010351 intermolecular recognition site; other site 428406010352 dimerization interface [polypeptide binding]; other site 428406010353 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 428406010354 DNA binding residues [nucleotide binding] 428406010355 dimerization interface [polypeptide binding]; other site 428406010356 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 428406010357 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 428406010358 transcriptional repressor BetI; Region: betaine_BetI; TIGR03384 428406010359 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406010360 Major Facilitator Superfamily; Region: MFS_1; pfam07690 428406010361 putative substrate translocation pore; other site 428406010362 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406010363 PAP2_like proteins, BcrC_like subfamily. Several members of this family have been annotated as bacitracin transport permeases, as it was suspected that they form the permease component of an ABC transporter system. It was shown, however, that BcrC from...; Region: PAP2_BcrC_like; cd03385 428406010364 active site 428406010365 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 428406010366 PAS domain; Region: PAS_9; pfam13426 428406010367 putative active site [active] 428406010368 heme pocket [chemical binding]; other site 428406010369 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 428406010370 Histidine kinase; Region: HisKA_3; pfam07730 428406010371 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 428406010372 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 428406010373 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 428406010374 GroEL_like type I chaperonin. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings, each composed of 7-9 subunits. The symmetry of type I is seven-fold and they are found...; Region: GroEL; cd03344 428406010375 ring oligomerisation interface [polypeptide binding]; other site 428406010376 ATP/Mg binding site [chemical binding]; other site 428406010377 stacking interactions; other site 428406010378 hinge regions; other site 428406010379 Chaperonin 10 Kd subunit (cpn10 or GroES); Cpn10 cooperates with chaperonin 60 (cpn60 or GroEL), an ATPase, to assist the folding and assembly of proteins and is found in eubacterial cytosol, as well as in the matrix of mitochondria and chloroplasts. It...; Region: cpn10; cd00320 428406010380 oligomerisation interface [polypeptide binding]; other site 428406010381 mobile loop; other site 428406010382 roof hairpin; other site 428406010383 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 428406010384 Alpha-crystallin domain (ACD) of alpha-crystallin-type small(s) heat shock proteins (Hsps). sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is the Alpha-crystallin domain (ACD). sHsps are generally...; Region: ACD_sHsps-like; cd06464 428406010385 putative dimer interface [polypeptide binding]; other site 428406010386 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 428406010387 Alpha-crystallin domain (ACD) of alpha-crystallin-type small(s) heat shock proteins (Hsps). sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is the Alpha-crystallin domain (ACD). sHsps are generally...; Region: ACD_sHsps-like; cd06464 428406010388 putative dimer interface [polypeptide binding]; other site 428406010389 A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various...; Region: Peptidase_C39G; cd02423 428406010390 putative active site [active] 428406010391 Esterase/lipase [Lipid metabolism]; Region: Aes; COG0657 428406010392 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cd00312 428406010393 EthD domain; Region: EthD; cl17553 428406010394 Dehydratase small subunit; Region: Dehydratase_SU; cl02055 428406010395 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 428406010396 MarR family; Region: MarR; pfam01047 428406010397 peroxiredoxin, Ohr subfamily; Region: organ_hyd_perox; TIGR03561 428406010398 putative chaperone; Provisional; Region: PRK11678 428406010399 Escherichia coli YegD, a putative chaperone protein, and related proteins; Region: YegD_like; cd10231 428406010400 nucleotide binding site [chemical binding]; other site 428406010401 putative NEF/HSP70 interaction site [polypeptide binding]; other site 428406010402 SBD interface [polypeptide binding]; other site 428406010403 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a...; Region: TlpA_like_family; cd02966 428406010404 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 428406010405 catalytic residues [active] 428406010406 Putative MetA-pathway of phenol degradation; Region: Phenol_MetA_deg; cl01768 428406010407 Protein of unknown function (DUF2946); Region: DUF2946; pfam11162 428406010408 Domain of unknown function (DUF4209); Region: DUF4209; pfam13910 428406010409 Clavaminic acid synthetase (CAS) -like; CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG oxygenases...; Region: CAS_like; cl00184 428406010410 active site 428406010411 iron coordination sites [ion binding]; other site 428406010412 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4694 428406010413 DNA primase domain-containing protein; Region: PHA02415 428406010414 TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG...; Region: TOPRIM_primases; cd01029 428406010415 active site 428406010416 metal binding site [ion binding]; metal-binding site 428406010417 interdomain interaction site; other site 428406010418 Protein of unknown function (DUF1484); Region: DUF1484; pfam07363 428406010419 Ogr/Delta-like zinc finger; Region: Ogr_Delta; pfam04606 428406010420 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 428406010421 Predicted transcriptional regulator [Transcription]; Region: AlpA; COG3311 428406010422 integrase; Provisional; Region: PRK09692 428406010423 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall...; Region: INT_P4; cd00801 428406010424 active site 428406010425 Int/Topo IB signature motif; other site 428406010426 Thermus thermophilus SoxB and related proteins, N-terminal metallophosphatase domain; Region: MPP_SoxB_N; cd07411 428406010427 active site 428406010428 metal binding site [ion binding]; metal-binding site 428406010429 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases [Nucleotide transport and metabolism]; Region: UshA; COG0737 428406010430 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 428406010431 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a...; Region: TlpA_like_family; cd02966 428406010432 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 428406010433 catalytic residues [active] 428406010434 Cytochrome c; Region: Cytochrom_C; cl11414 428406010435 Uncharacterized conserved protein [Function unknown]; Region: COG1416 428406010436 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 428406010437 Predicted secreted protein [Function unknown]; Region: COG5501 428406010438 Sulfur oxidation protein SoxY; Region: SoxY; pfam13501 428406010439 Cytochrome c551/c552 [Energy production and conversion]; Region: COG4654 428406010440 O-acetylserine/cysteine export protein; Provisional; Region: PRK11453 428406010441 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 428406010442 Flavocytochrome c sulphide dehydrogenase, flavin-binding; Region: FCSD-flav_bind; pfam09242 428406010443 Cytochrome c; Region: Cytochrom_C; cl11414 428406010444 Predicted periplasmic or secreted lipoprotein [General function prediction only]; Region: OsmY; COG2823 428406010445 BON domain; Region: BON; pfam04972 428406010446 bacterial OsmY and nodulation domain; Region: BON; smart00749 428406010447 hypothetical protein; Provisional; Region: PRK14673 428406010448 Predicted methyltransferases [General function prediction only]; Region: COG0313 428406010449 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 428406010450 putative SAM binding site [chemical binding]; other site 428406010451 putative homodimer interface [polypeptide binding]; other site 428406010452 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 428406010453 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 428406010454 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 428406010455 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 428406010456 active site 428406010457 substrate binding site [chemical binding]; other site 428406010458 catalytic site [active] 428406010459 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 428406010460 ArsC family; Region: ArsC; pfam03960 428406010461 Transposase, Mutator family; Region: Transposase_mut; pfam00872 428406010462 MULE transposase domain; Region: MULE; pfam10551 428406010463 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK08651 428406010464 M20 Zn-peptidases include exopeptidases; Region: M20_like; cd02697 428406010465 putative metal binding site [ion binding]; other site 428406010466 ureidoglycolate hydrolase; Provisional; Region: PRK03606 428406010467 Ureidoglycolate hydrolase [Nucleotide transport and metabolism]; Region: DAL3; COG3194 428406010468 allantoicase; Provisional; Region: PRK13257 428406010469 Allantoicase repeat; Region: Allantoicase; pfam03561 428406010470 Allantoicase repeat; Region: Allantoicase; pfam03561 428406010471 C4-dicarboxylate transporter DctA; Reviewed; Region: PRK13027 428406010472 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 428406010473 Transcriptional regulators [Transcription]; Region: GntR; COG1802 428406010474 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 428406010475 DNA-binding site [nucleotide binding]; DNA binding site 428406010476 This entry represents the C-terminal ligand binding domain of many members of the GntR family; Region: FCD; smart00895 428406010477 Uncharacterized conserved protein [Function unknown]; Region: COG1739 428406010478 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 428406010479 Domain of unknown function (DUF1949); Region: DUF1949; pfam09186 428406010480 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406010481 transcriptional activator TtdR; Provisional; Region: PRK09801 428406010482 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 428406010483 putative effector binding pocket; other site 428406010484 dimerization interface [polypeptide binding]; other site 428406010485 glyoxylate carboligase; Provisional; Region: PRK11269 428406010486 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 428406010487 PYR/PP interface [polypeptide binding]; other site 428406010488 dimer interface [polypeptide binding]; other site 428406010489 TPP binding site [chemical binding]; other site 428406010490 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 428406010491 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cl01629 428406010492 TPP-binding site [chemical binding]; other site 428406010493 Hydroxypyruvate isomerase [Carbohydrate transport and metabolism]; Region: Hfi; COG3622 428406010494 tartronate semialdehyde reductase; Provisional; Region: PRK15059 428406010495 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 428406010496 Putative glycerate kinase [Carbohydrate transport and metabolism]; Region: GckA; COG2379 428406010497 Domain of unknown function (DUF4147); Region: DUF4147; pfam13660 428406010498 MOFRL family; Region: MOFRL; pfam05161 428406010499 pyruvate kinase; Provisional; Region: PRK06247 428406010500 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl17342 428406010501 domain interfaces; other site 428406010502 active site 428406010503 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 428406010504 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 428406010505 FeS/SAM binding site; other site 428406010506 HemN C-terminal domain; Region: HemN_C; pfam06969 428406010507 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 428406010508 Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins; Region: PBP1_STKc_like; cd06326 428406010509 putative ligand binding site [chemical binding]; other site 428406010510 ATP-dependent DNA helicase Rep; Region: rep; TIGR01074 428406010511 Part of AAA domain; Region: AAA_19; pfam13245 428406010512 Family description; Region: UvrD_C_2; pfam13538 428406010513 glycine cleavage system aminomethyltransferase T; Reviewed; Region: gcvT; PRK00389 428406010514 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 428406010515 Glycine cleavage H-protein. Glycine cleavage H-proteins are part of the glycine cleavage system (GCS) found in bacteria, archea and the mitochondria of eukaryotes. GCS is a multienzyme complex consisting of 4 different components (P-, H-, T- and...; Region: GCS_H; cd06848 428406010516 lipoyl attachment site [posttranslational modification]; other site 428406010517 glycine dehydrogenase; Provisional; Region: PRK05367 428406010518 Glycine cleavage system P-protein, alpha- and beta-subunits. This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2.1; Region: GDC-P; cd00613 428406010519 tetramer interface [polypeptide binding]; other site 428406010520 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406010521 catalytic residue [active] 428406010522 Glycine cleavage system P-protein, alpha- and beta-subunits. This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2.1; Region: GDC-P; cd00613 428406010523 tetramer interface [polypeptide binding]; other site 428406010524 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406010525 catalytic residue [active] 428406010526 Alginate lyase; Region: Alginate_lyase; pfam05426 428406010527 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 428406010528 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 428406010529 Serine dehydratase alpha chain; Region: SDH_alpha; pfam03313 428406010530 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]; Region: Tra8; COG2826 428406010531 Helix-turn-helix domain; Region: HTH_38; pfam13936 428406010532 Integrase core domain; Region: rve; pfam00665 428406010533 Integrase core domain; Region: rve_3; cl15866 428406010534 Predicted membrane protein [Function unknown]; Region: COG1297 428406010535 putative oligopeptide transporter, OPT family; Region: TIGR00733 428406010536 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 428406010537 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 428406010538 Coenzyme A binding pocket [chemical binding]; other site 428406010539 gamma-glutamyl:cysteine ligase; Provisional; Region: PRK13516 428406010540 carboxylate-amine ligase, YbdK family; Region: gshA_cyan_rel; TIGR02050 428406010541 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 428406010542 Type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine); Region: PBP1_ABC_LIVBP_like; cd06342 428406010543 dimerization interface [polypeptide binding]; other site 428406010544 ligand binding site [chemical binding]; other site 428406010545 trifunctional transcriptional regulator/proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed; Region: putA; PRK11809 428406010546 Predicted transcriptional regulator [Transcription]; Region: COG3905 428406010547 Proline dehydrogenase [Amino acid transport and metabolism]; Region: PutA; COG0506 428406010548 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 428406010549 Glutamate binding site [chemical binding]; other site 428406010550 NAD binding site [chemical binding]; other site 428406010551 catalytic residues [active] 428406010552 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 428406010553 Transposase, Mutator family; Region: Transposase_mut; pfam00872 428406010554 MULE transposase domain; Region: MULE; pfam10551 428406010555 primosome assembly protein PriA; Validated; Region: PRK05580 428406010556 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 428406010557 ATP binding site [chemical binding]; other site 428406010558 putative Mg++ binding site [ion binding]; other site 428406010559 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cl17351 428406010560 methylcobalamin:coenzyme M methyltransferase; Validated; Region: PRK06252 428406010561 Uroporphyrinogen decarboxylase (URO-D) is a dimeric cytosolic enzyme that decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, without requiring any prosthetic groups or cofactors. This reaction...; Region: URO-D; cd00717 428406010562 substrate binding site [chemical binding]; other site 428406010563 active site 428406010564 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 428406010565 Cache domain; Region: Cache_1; pfam02743 428406010566 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 428406010567 dimerization interface [polypeptide binding]; other site 428406010568 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 428406010569 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 428406010570 dimer interface [polypeptide binding]; other site 428406010571 putative CheW interface [polypeptide binding]; other site 428406010572 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 428406010573 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; pfam04116 428406010574 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406010575 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406010576 LysR substrate binding domain; Region: LysR_substrate; pfam03466 428406010577 dimerization interface [polypeptide binding]; other site 428406010578 glutathionine S-transferase; Provisional; Region: PRK10542 428406010579 GST_N family, Class Beta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens; Region: GST_N_Beta; cd03057 428406010580 C-terminal domain interface [polypeptide binding]; other site 428406010581 GSH binding site (G-site) [chemical binding]; other site 428406010582 dimer interface [polypeptide binding]; other site 428406010583 C-terminal, alpha helical domain of Class Beta Glutathione S-transferases; Region: GST_C_Beta; cd03188 428406010584 N-terminal domain interface [polypeptide binding]; other site 428406010585 dimer interface [polypeptide binding]; other site 428406010586 substrate binding pocket (H-site) [chemical binding]; other site 428406010587 PBP superfamily domain; Region: PBP_like_2; cl17296 428406010588 Protein of unknown function (DUF3562); Region: DUF3562; pfam12085 428406010589 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cd00312 428406010590 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 428406010591 Predicted CoA-binding protein [General function prediction only]; Region: COG1832 428406010592 Protein of unknown function (DUF3298); Region: DUF3298; pfam11738 428406010593 FecR protein; Region: FecR; pfam04773 428406010594 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 428406010595 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 428406010596 gamma subunit interface [polypeptide binding]; other site 428406010597 epsilon subunit interface [polypeptide binding]; other site 428406010598 LBP interface [polypeptide binding]; other site 428406010599 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 428406010600 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 428406010601 F1 ATP synthase beta subunit, nucleotide-binding domain. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a...; Region: F1-ATPase_beta; cd01133 428406010602 alpha subunit interaction interface [polypeptide binding]; other site 428406010603 Walker A motif; other site 428406010604 ATP binding site [chemical binding]; other site 428406010605 Walker B motif; other site 428406010606 inhibitor binding site; inhibition site 428406010607 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 428406010608 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 428406010609 core domain interface [polypeptide binding]; other site 428406010610 delta subunit interface [polypeptide binding]; other site 428406010611 epsilon subunit interface [polypeptide binding]; other site 428406010612 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 428406010613 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 428406010614 F1 ATP synthase alpha, central domain. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to...; Region: F1_ATPase_alpha; cd01132 428406010615 beta subunit interaction interface [polypeptide binding]; other site 428406010616 Walker A motif; other site 428406010617 ATP binding site [chemical binding]; other site 428406010618 Walker B motif; other site 428406010619 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 428406010620 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 428406010621 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 428406010622 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 428406010623 F0F1 ATP synthase subunit B; Validated; Region: PRK05759 428406010624 F0F1 ATP synthase subunit C; Validated; Region: PRK06876 428406010625 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 428406010626 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 428406010627 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 428406010628 ParB-like nuclease domain; Region: ParB; smart00470 428406010629 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 428406010630 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 428406010631 P-loop; other site 428406010632 Magnesium ion binding site [ion binding]; other site 428406010633 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 428406010634 Magnesium ion binding site [ion binding]; other site 428406010635 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 428406010636 Putative methyltransferase; Region: Methyltransf_16; pfam10294 428406010637 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 428406010638 S-adenosylmethionine binding site [chemical binding]; other site 428406010639 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 428406010640 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 428406010641 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 428406010642 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 428406010643 Type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids; Region: PBP1_ABC-type_HAAT_like; cd06333 428406010644 putative ligand binding site [chemical binding]; other site 428406010645 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 428406010646 Lin1944 and related proteins, classical (c) SDRs; Region: Lin1944_like_SDR_c; cd11731 428406010647 putative NAD(P) binding site [chemical binding]; other site 428406010648 homodimer interface [polypeptide binding]; other site 428406010649 Protein of unknown function (DUF3820); Region: DUF3820; pfam12843 428406010650 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406010651 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406010652 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 428406010653 dimerization interface [polypeptide binding]; other site 428406010654 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 428406010655 atypical (a) SDRs, subgroup 3; Region: SDR_a3; cd05229 428406010656 putative NAD(P) binding site [chemical binding]; other site 428406010657 putative active site [active] 428406010658 phosphonate degradation operons associated HDIG domain protein; Region: Phn-HD; TIGR03276 428406010659 Cupin domain; Region: Cupin_2; cl17218 428406010660 hypothetical protein; Provisional; Region: PRK10621 428406010661 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 428406010662 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 428406010663 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 428406010664 TM-ABC transporter signature motif; other site 428406010665 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 428406010666 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 428406010667 TM-ABC transporter signature motif; other site 428406010668 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 428406010669 Periplasmic solute-binding domain of active transport proteins that belong to the type I periplasmic binding fold protein family; Region: PBP1_SBP_like_1; cd06327 428406010670 putative ligand binding site [chemical binding]; other site 428406010671 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 428406010672 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 428406010673 Walker A/P-loop; other site 428406010674 ATP binding site [chemical binding]; other site 428406010675 Q-loop/lid; other site 428406010676 ABC transporter signature motif; other site 428406010677 Walker B; other site 428406010678 D-loop; other site 428406010679 H-loop/switch region; other site 428406010680 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 428406010681 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 428406010682 Walker A/P-loop; other site 428406010683 ATP binding site [chemical binding]; other site 428406010684 Q-loop/lid; other site 428406010685 ABC transporter signature motif; other site 428406010686 Walker B; other site 428406010687 D-loop; other site 428406010688 H-loop/switch region; other site 428406010689 choline dehydrogenase; Validated; Region: PRK02106 428406010690 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 428406010691 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 428406010692 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 428406010693 Cu(I)-responsive transcriptional regulator; Region: CueR; TIGR02044 428406010694 Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators; Region: HTH_CueR; cd01108 428406010695 DNA binding residues [nucleotide binding] 428406010696 dimer interface [polypeptide binding]; other site 428406010697 copper binding site [ion binding]; other site 428406010698 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 428406010699 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 428406010700 metal-binding site [ion binding] 428406010701 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 428406010702 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 428406010703 motif II; other site 428406010704 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 428406010705 metal-binding site [ion binding] 428406010706 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 428406010707 Outer membrane protein W [Cell envelope biogenesis, outer membrane]; Region: OmpW; COG3047 428406010708 ornithine cyclodeaminase; Validated; Region: PRK07340 428406010709 ornithine cyclodeaminase; Validated; Region: PRK06823; cl17400 428406010710 Predicted membrane protein [Function unknown]; Region: COG3714 428406010711 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 428406010712 Winged helix-turn-helix DNA-binding; Region: HTH_24; pfam13412 428406010713 AsnC family; Region: AsnC_trans_reg; pfam01037 428406010714 Prokaryotic phenylalanine-4-hydroxylase (pro_PheOH); a member of the biopterin-dependent aromatic amino acid hydroxylase family of non-heme, iron(II)-dependent enzymes that also includes the eukaryotic proteins, phenylalanine-4-hydroxylase (eu_PheOH); Region: pro_PheOH; cd03348 428406010715 cofactor binding site; other site 428406010716 metal binding site [ion binding]; metal-binding site 428406010717 PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by...; Region: PCD_DCoH_subfamily_b; cd00914 428406010718 aromatic arch; other site 428406010719 DCoH dimer interaction site [polypeptide binding]; other site 428406010720 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 428406010721 DCoH tetramer interaction site [polypeptide binding]; other site 428406010722 substrate binding site [chemical binding]; other site 428406010723 Protein of unknown function (DUF3717); Region: DUF3717; pfam12512 428406010724 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 428406010725 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406010726 active site 428406010727 phosphorylation site [posttranslational modification] 428406010728 intermolecular recognition site; other site 428406010729 dimerization interface [polypeptide binding]; other site 428406010730 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 428406010731 DNA binding site [nucleotide binding] 428406010732 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 428406010733 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 428406010734 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 428406010735 dimer interface [polypeptide binding]; other site 428406010736 phosphorylation site [posttranslational modification] 428406010737 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406010738 ATP binding site [chemical binding]; other site 428406010739 Mg2+ binding site [ion binding]; other site 428406010740 G-X-G motif; other site 428406010741 Proteins containing SET domain [General function prediction only]; Region: COG2940 428406010742 SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain; Region: SET; smart00317 428406010743 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 428406010744 IHF dimer interface [polypeptide binding]; other site 428406010745 IHF - DNA interface [nucleotide binding]; other site 428406010746 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4322 428406010747 aldolase II superfamily protein; Provisional; Region: PRK07044 428406010748 intersubunit interface [polypeptide binding]; other site 428406010749 active site 428406010750 Zn2+ binding site [ion binding]; other site 428406010751 2-dehydropantoate 2-reductase; Reviewed; Region: PRK06522 428406010752 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 428406010753 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 428406010754 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 428406010755 Sel1 repeat; Region: Sel1; cl02723 428406010756 Sel1-like repeats; Region: SEL1; smart00671 428406010757 Sel1-like repeats; Region: SEL1; smart00671 428406010758 bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase periplasmic precursor protein; Reviewed; Region: cpdB; PRK09420 428406010759 Escherichia coli CpdB and related proteins, N-terminal metallophosphatase domain; Region: MPP_CpdB_N; cd07410 428406010760 active site 428406010761 metal binding site [ion binding]; metal-binding site 428406010762 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 428406010763 septum formation inhibitor; Reviewed; Region: PRK01973 428406010764 Septum formation inhibitor MinC, N-terminal domain; Region: MinC_N; pfam05209 428406010765 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 428406010766 Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]; Region: MinD; COG2894 428406010767 Bacterial cell division requires the formation of a septum at mid-cell. The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a pivotal...; Region: MinD; cd02036 428406010768 Switch I; other site 428406010769 Switch II; other site 428406010770 cell division topological specificity factor MinE; Provisional; Region: PRK13989 428406010771 Helix-turn-helix domain; Region: HTH_17; pfam12728 428406010772 Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the glyoxylate...; Region: citrate_synt_like_2; cd06102 428406010773 dimer interface [polypeptide binding]; other site 428406010774 active site 428406010775 coenzyme A binding site [chemical binding]; other site 428406010776 citrylCoA binding site [chemical binding]; other site 428406010777 Citrate synthase; Region: Citrate_synt; pfam00285 428406010778 oxalacetate/citrate binding site [chemical binding]; other site 428406010779 catalytic triad [active] 428406010780 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 428406010781 CoA-transferase family III; Region: CoA_transf_3; pfam02515 428406010782 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 428406010783 polyphosphate kinase 2, PA0141 family; Region: PPK2_P_aer; TIGR03707 428406010784 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 428406010785 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 428406010786 Acylphosphatase; Region: Acylphosphatase; pfam00708 428406010787 ABC-type anion transport system, duplicated permease component [Inorganic ion transport and metabolism]; Region: COG4986 428406010788 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406010789 dimer interface [polypeptide binding]; other site 428406010790 conserved gate region; other site 428406010791 putative PBP binding loops; other site 428406010792 ABC-ATPase subunit interface; other site 428406010793 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406010794 dimer interface [polypeptide binding]; other site 428406010795 conserved gate region; other site 428406010796 putative PBP binding loops; other site 428406010797 ABC-ATPase subunit interface; other site 428406010798 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 428406010799 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 428406010800 Walker A/P-loop; other site 428406010801 ATP binding site [chemical binding]; other site 428406010802 Q-loop/lid; other site 428406010803 ABC transporter signature motif; other site 428406010804 Walker B; other site 428406010805 D-loop; other site 428406010806 H-loop/switch region; other site 428406010807 Uncharacterized conserved protein [Function unknown]; Region: COG4754 428406010808 poly(beta-D-mannuronate) lyase; Provisional; Region: algL; PRK00325 428406010809 active site 428406010810 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 428406010811 Chromate resistance exported protein; Region: Chrome_Resist; pfam09828 428406010812 chromate transporter, chromate ion transporter (CHR) family; Region: 2A51; TIGR00937 428406010813 Chromate transport protein ChrA [Inorganic ion transport and metabolism]; Region: ChrA; COG2059 428406010814 Chromate transporter; Region: Chromate_transp; pfam02417 428406010815 Protein of unknown function (DUF1311); Region: DUF1311; pfam07007 428406010816 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 428406010817 dimerization interface [polypeptide binding]; other site 428406010818 putative DNA binding site [nucleotide binding]; other site 428406010819 putative Zn2+ binding site [ion binding]; other site 428406010820 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 428406010821 Low molecular weight phosphatase family; Region: LMWPc; cd00115 428406010822 active site 428406010823 Glycerol uptake facilitator and related permeases (Major Intrinsic Protein Family) [Carbohydrate transport and metabolism]; Region: GlpF; COG0580 428406010824 amphipathic channel; other site 428406010825 Asn-Pro-Ala signature motifs; other site 428406010826 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 428406010827 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 428406010828 Protein of unknown function (DUF3828); Region: DUF3828; pfam12883 428406010829 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 428406010830 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 428406010831 Ligand Binding Site [chemical binding]; other site 428406010832 conserved hypothetical protein, proteobacterial; Region: gcw_chp; TIGR02001 428406010833 potassium-transporting ATPase subunit A; Provisional; Region: PRK05482 428406010834 potassium-transporting ATPase subunit B; Provisional; Region: PRK01122 428406010835 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 428406010836 potassium-transporting ATPase subunit C; Reviewed; Region: PRK00315 428406010837 Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]; Region: KdpD; COG2205 428406010838 Osmosensitive K+ channel His kinase sensor domain; Region: KdpD; pfam02702 428406010839 USP domain is located between the N-terminal sensor domain and C-terminal catalytic domain of this Osmosensitive K+ channel histidine kinase family. The family of KdpD sensor kinase proteins regulates the kdpFABC operon responsible for potassium...; Region: USP_OKCHK; cd01987 428406010840 Ligand Binding Site [chemical binding]; other site 428406010841 GAF domain; Region: GAF_3; pfam13492 428406010842 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 428406010843 dimer interface [polypeptide binding]; other site 428406010844 phosphorylation site [posttranslational modification] 428406010845 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406010846 ATP binding site [chemical binding]; other site 428406010847 Mg2+ binding site [ion binding]; other site 428406010848 G-X-G motif; other site 428406010849 ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]; Region: NlpA; COG1464 428406010850 NLPA lipoprotein; Region: Lipoprotein_9; pfam03180 428406010851 Response regulator receiver domain; Region: Response_reg; pfam00072 428406010852 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406010853 active site 428406010854 phosphorylation site [posttranslational modification] 428406010855 intermolecular recognition site; other site 428406010856 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 428406010857 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 428406010858 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406010859 active site 428406010860 phosphorylation site [posttranslational modification] 428406010861 intermolecular recognition site; other site 428406010862 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 428406010863 DNA binding residues [nucleotide binding] 428406010864 dimerization interface [polypeptide binding]; other site 428406010865 Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-terminal...; Region: MIP; cl00200 428406010866 amphipathic channel; other site 428406010867 Asn-Pro-Ala signature motifs; other site 428406010868 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 428406010869 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 428406010870 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 428406010871 salt bridge; other site 428406010872 non-specific DNA binding site [nucleotide binding]; other site 428406010873 sequence-specific DNA binding site [nucleotide binding]; other site 428406010874 Isochorismatase family; Region: Isochorismatase; pfam00857 428406010875 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cd00431 428406010876 catalytic triad [active] 428406010877 conserved cis-peptide bond; other site 428406010878 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 428406010879 CoenzymeA binding site [chemical binding]; other site 428406010880 subunit interaction site [polypeptide binding]; other site 428406010881 PHB binding site; other site 428406010882 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 428406010883 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 428406010884 trimer interface [polypeptide binding]; other site 428406010885 eyelet of channel; other site 428406010886 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 428406010887 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cl17432 428406010888 transcriptional regulatory protein TctD; Provisional; Region: PRK15479 428406010889 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406010890 active site 428406010891 phosphorylation site [posttranslational modification] 428406010892 intermolecular recognition site; other site 428406010893 dimerization interface [polypeptide binding]; other site 428406010894 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 428406010895 DNA binding site [nucleotide binding] 428406010896 Two-component sensor kinase N-terminal; Region: 2CSK_N; pfam08521 428406010897 sensor protein QseC; Provisional; Region: PRK10337 428406010898 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cl00080 428406010899 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406010900 ATP binding site [chemical binding]; other site 428406010901 Mg2+ binding site [ion binding]; other site 428406010902 G-X-G motif; other site 428406010903 Domain of unknown function (DUF4142); Region: DUF4142; pfam13628 428406010904 Protein of unknown function (DUF2795); Region: DUF2795; pfam11387 428406010905 Transcriptional regulator; Region: Rrf2; cl17282 428406010906 Rrf2 family protein; Region: rrf2_super; TIGR00738 428406010907 bifunctional nitric oxide dioxygenase/dihydropteridine reductase 2; Provisional; Region: PRK13289 428406010908 Globins are heme proteins, which bind and transport oxygen. This family summarizes a diverse set of homologous protein domains, including: (1) tetrameric vertebrate hemoglobins, which are the major protein component of erythrocytes and transport oxygen...; Region: globin; cd01040 428406010909 heme-binding site [chemical binding]; other site 428406010910 FAD_NAD(P)H binding domain of flavohemoglobin. Flavohemoglobins have a globin domain containing a B-type heme fused with a ferredoxin reductase-like FAD/NAD-binding domain. Flavohemoglobins detoxify nitric oxide (NO) via an NO dioxygenase reaction. The...; Region: flavohem_like_fad_nad_binding; cd06184 428406010911 FAD binding pocket [chemical binding]; other site 428406010912 FAD binding motif [chemical binding]; other site 428406010913 phosphate binding motif [ion binding]; other site 428406010914 beta-alpha-beta structure motif; other site 428406010915 NAD binding pocket [chemical binding]; other site 428406010916 Heme binding pocket [chemical binding]; other site 428406010917 NnrS protein; Region: NnrS; pfam05940 428406010918 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 428406010919 DNA-binding site [nucleotide binding]; DNA binding site 428406010920 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 428406010921 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 428406010922 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406010923 homodimer interface [polypeptide binding]; other site 428406010924 catalytic residue [active] 428406010925 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 428406010926 Uncharacterized conserved protein [Function unknown]; Region: COG2128 428406010927 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406010928 Major Facilitator Superfamily; Region: MFS_1; pfam07690 428406010929 putative substrate translocation pore; other site 428406010930 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406010931 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406010932 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 428406010933 dimerization interface [polypeptide binding]; other site 428406010934 N-acetyl-gamma-glutamyl-phosphate reductase; Provisional; Region: PRK11863 428406010935 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 428406010936 hypothetical protein; Provisional; Region: PRK11171 428406010937 Cupin domain; Region: Cupin_2; pfam07883 428406010938 Cupin domain; Region: Cupin_2; pfam07883 428406010939 Transcriptional regulators RcnR and FrmR, and related domains; this domain family was previously known as part of DUF156; Region: RcnR-FrmR-like_DUF156; cd10153 428406010940 putative metal binding site [ion binding]; other site 428406010941 putative homodimer interface [polypeptide binding]; other site 428406010942 putative homotetramer interface [polypeptide binding]; other site 428406010943 putative homodimer-homodimer interface [polypeptide binding]; other site 428406010944 putative allosteric switch controlling residues; other site 428406010945 putative DMT superfamily transporter inner membrane protein; Provisional; Region: PRK11272 428406010946 EamA-like transporter family; Region: EamA; pfam00892 428406010947 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 428406010948 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 428406010949 dimer interface [polypeptide binding]; other site 428406010950 phosphorylation site [posttranslational modification] 428406010951 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406010952 ATP binding site [chemical binding]; other site 428406010953 Mg2+ binding site [ion binding]; other site 428406010954 G-X-G motif; other site 428406010955 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 428406010956 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406010957 active site 428406010958 phosphorylation site [posttranslational modification] 428406010959 intermolecular recognition site; other site 428406010960 dimerization interface [polypeptide binding]; other site 428406010961 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 428406010962 DNA binding site [nucleotide binding] 428406010963 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 428406010964 Ligand Binding Site [chemical binding]; other site 428406010965 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 428406010966 active site 428406010967 Domain of unknown function (DUF4285); Region: DUF4285; pfam14113 428406010968 PAAR motif; Region: PAAR_motif; pfam05488 428406010969 Glyoxalase-like domain; Region: Glyoxalase_3; pfam13468 428406010970 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406010971 aminoethylphosphonate catabolism associated LysR family transcriptional regulator; Region: phn_lysR; TIGR03339 428406010972 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 428406010973 dimerization interface [polypeptide binding]; other site 428406010974 choline dehydrogenase; Validated; Region: PRK02106 428406010975 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 428406010976 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 428406010977 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 428406010978 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 428406010979 substrate binding pocket [chemical binding]; other site 428406010980 membrane-bound complex binding site; other site 428406010981 hinge residues; other site 428406010982 glutamate and aspartate transporter subunit; Provisional; Region: PRK10797 428406010983 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 428406010984 substrate binding pocket [chemical binding]; other site 428406010985 membrane-bound complex binding site; other site 428406010986 hinge residues; other site 428406010987 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 428406010988 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 428406010989 active site 428406010990 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 428406010991 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase...; Region: NPD_like; cd04730 428406010992 FMN binding site [chemical binding]; other site 428406010993 substrate binding site [chemical binding]; other site 428406010994 putative catalytic residue [active] 428406010995 thiamine biosynthesis protein ThiC; Provisional; Region: PRK09284 428406010996 ThiC-associated domain; Region: ThiC-associated; pfam13667 428406010997 Thiamine biosynthesis protein ThiC [Coenzyme metabolism]; Region: ThiC; COG0422 428406010998 tRNA (uracil-5-)-methyltransferase Gid; Reviewed; Region: PRK05335 428406010999 glycine oxidase ThiO; Region: thiamin_ThiO; TIGR02352 428406011000 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 428406011001 thiS-thiF/thiG interaction site; other site 428406011002 Thiazole synthase (ThiG) is the tetrameric enzyme that is involved in the formation of the thiazole moiety of thiamin pyrophosphate, an essential ubiquitous cofactor that plays an important role in carbohydrate and amino acid metabolism. ThiG catalyzes...; Region: ThiG; cd04728 428406011003 ThiS interaction site; other site 428406011004 putative active site [active] 428406011005 tetramer interface [polypeptide binding]; other site 428406011006 Thiamine monophosphate synthase (TMP synthase)/TenI. TMP synthase catalyzes an important step in the thiamine biosynthesis pathway, the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5-; Region: TMP_TenI; cd00564 428406011007 thiamine phosphate binding site [chemical binding]; other site 428406011008 active site 428406011009 pyrophosphate binding site [ion binding]; other site 428406011010 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_8; cd07246 428406011011 putative dimer interface [polypeptide binding]; other site 428406011012 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 428406011013 4-amino-5-hydroxymethyl-2-methyl-pyrimidine phosphate kinase (HMPP-kinase) catalyzes two consecutive phosphorylation steps in the thiamine phosphate biosynthesis pathway, leading to the synthesis of vitamin B1. The first step is the phosphorylation of...; Region: HMPP_kinase; cd01169 428406011014 dimer interface [polypeptide binding]; other site 428406011015 substrate binding site [chemical binding]; other site 428406011016 ATP binding site [chemical binding]; other site 428406011017 Alkaline phosphatase homologues; Region: alkPPc; smart00098 428406011018 Alkaline phosphatase homologues; alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH; Region: alkPPc; cd00016 428406011019 active site 428406011020 dimer interface [polypeptide binding]; other site 428406011021 Alkaline phosphatase homologues; Region: alkPPc; smart00098 428406011022 Alkaline phosphatase homologues; alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH; Region: alkPPc; cd00016 428406011023 active site 428406011024 dimer interface [polypeptide binding]; other site 428406011025 Predicted ATPase [General function prediction only]; Region: COG3910 428406011026 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 428406011027 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 428406011028 Walker A/P-loop; other site 428406011029 Walker A/P-loop; other site 428406011030 ATP binding site [chemical binding]; other site 428406011031 ATP binding site [chemical binding]; other site 428406011032 Q-loop/lid; other site 428406011033 ABC transporter signature motif; other site 428406011034 Walker B; other site 428406011035 D-loop; other site 428406011036 H-loop/switch region; other site 428406011037 S-adenosyl-L-homocysteine hydrolase; Provisional; Region: PRK05476 428406011038 S-Adenosylhomocysteine Hydrolase, NAD-binding and catalytic domains; Region: SAHH; cd00401 428406011039 homotetramer interface [polypeptide binding]; other site 428406011040 ligand binding site [chemical binding]; other site 428406011041 catalytic site [active] 428406011042 NAD binding site [chemical binding]; other site 428406011043 Membrane protein of unknown function; Region: DUF360; cl00850 428406011044 Methylenetetrahydrofolate reductase (MTHFR). 5,10-Methylenetetrahydrofolate is reduced to 5-methyltetrahydrofolate by methylenetetrahydrofolate reductase, a cytoplasmic, NAD(P)-dependent enzyme. 5-methyltetrahydrofolate is utilized by methionine synthase...; Region: MTHFR; cd00537 428406011045 FAD binding site [chemical binding]; other site 428406011046 TfoX N-terminal domain; Region: TfoX_N; pfam04993 428406011047 PPOX class probable FMN-dependent enzyme, DR_2398 family; Region: PPOX_FMN_DR2398; TIGR04025 428406011048 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212 428406011049 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 428406011050 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 428406011051 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 428406011052 N-acetyl-D-glucosamine binding site [chemical binding]; other site 428406011053 catalytic residue [active] 428406011054 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs; Region: NDUFA9_like_SDR_a; cd05271 428406011055 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 428406011056 putative NAD(P) binding site [chemical binding]; other site 428406011057 active site 428406011058 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 428406011059 GST_N family, unknown subfamily 1; composed of uncharacterized proteins, predominantly from bacteria, with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with...; Region: GST_N_1; cd03043 428406011060 putative C-terminal domain interface [polypeptide binding]; other site 428406011061 putative GSH binding site (G-site) [chemical binding]; other site 428406011062 putative dimer interface [polypeptide binding]; other site 428406011063 C-terminal, alpha helical domain of an unknown subfamily 3 of Glutathione S-transferases; Region: GST_C_3; cd03194 428406011064 putative N-terminal domain interface [polypeptide binding]; other site 428406011065 putative dimer interface [polypeptide binding]; other site 428406011066 putative substrate binding pocket (H-site) [chemical binding]; other site 428406011067 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 428406011068 multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed; Region: cca; PRK10885 428406011069 active site 428406011070 NTP binding site [chemical binding]; other site 428406011071 metal binding triad [ion binding]; metal-binding site 428406011072 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 428406011073 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 428406011074 Zn2+ binding site [ion binding]; other site 428406011075 Mg2+ binding site [ion binding]; other site 428406011076 glutamate and aspartate transporter subunit; Provisional; Region: PRK10797 428406011077 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 428406011078 substrate binding pocket [chemical binding]; other site 428406011079 membrane-bound complex binding site; other site 428406011080 hinge residues; other site 428406011081 Uncharacterized conserved protein [Function unknown]; Region: COG3246 428406011082 hypothetical protein; Provisional; Region: PRK07483 428406011083 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 428406011084 inhibitor-cofactor binding pocket; inhibition site 428406011085 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406011086 catalytic residue [active] 428406011087 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 428406011088 RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate...; Region: SIS_RpiR; cd05013 428406011089 putative active site [active] 428406011090 Response regulator receiver domain; Region: Response_reg; pfam00072 428406011091 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406011092 active site 428406011093 phosphorylation site [posttranslational modification] 428406011094 intermolecular recognition site; other site 428406011095 dimerization interface [polypeptide binding]; other site 428406011096 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 428406011097 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 428406011098 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 428406011099 dimerization interface [polypeptide binding]; other site 428406011100 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 428406011101 dimer interface [polypeptide binding]; other site 428406011102 phosphorylation site [posttranslational modification] 428406011103 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406011104 ATP binding site [chemical binding]; other site 428406011105 Mg2+ binding site [ion binding]; other site 428406011106 G-X-G motif; other site 428406011107 Domain of unknown function (DUF4390); Region: DUF4390; pfam14334 428406011108 16S rRNA methyltransferase B; Provisional; Region: PRK10901 428406011109 RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the...; Region: NusB_Sun; cl00223 428406011110 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 428406011111 S-adenosylmethionine binding site [chemical binding]; other site 428406011112 M48 family peptidase; Provisional; Region: PRK03001 428406011113 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 428406011114 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 428406011115 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 428406011116 putative active site [active] 428406011117 substrate binding site [chemical binding]; other site 428406011118 putative cosubstrate binding site; other site 428406011119 catalytic site [active] 428406011120 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 428406011121 substrate binding site [chemical binding]; other site 428406011122 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 428406011123 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 428406011124 Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of the N-terminal formyl group in a growing polypeptide chain following translation initiation during protein synthesis in prokaryotes. These enzymes utilize Fe(II)...; Region: Pep_deformylase; cd00487 428406011125 active site 428406011126 catalytic residues [active] 428406011127 metal binding site [ion binding]; metal-binding site 428406011128 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 428406011129 Uncharacterized protein containing LysM domain [Function unknown]; Region: XkdP; COG1652 428406011130 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 428406011131 DNA protecting protein DprA; Region: dprA; TIGR00732 428406011132 TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains. Group I TRX is a small ancient protein that alter the redox...; Region: TRX_family; cd02947 428406011133 catalytic residues [active] 428406011134 DNA topoisomerase III; Validated; Region: PRK08173 428406011135 TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving...; Region: TOPRIM_TopoIA_TopoIII; cd03362 428406011136 active site 428406011137 putative interdomain interaction site [polypeptide binding]; other site 428406011138 putative metal-binding site [ion binding]; other site 428406011139 putative nucleotide binding site [chemical binding]; other site 428406011140 DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA...; Region: TOP1Ac; cd00186 428406011141 domain I; other site 428406011142 DNA binding groove [nucleotide binding] 428406011143 phosphate binding site [ion binding]; other site 428406011144 domain II; other site 428406011145 domain III; other site 428406011146 nucleotide binding site [chemical binding]; other site 428406011147 catalytic site [active] 428406011148 domain IV; other site 428406011149 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 428406011150 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 428406011151 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406011152 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406011153 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 428406011154 putative effector binding pocket; other site 428406011155 dimerization interface [polypeptide binding]; other site 428406011156 acyl-CoA synthetase; Validated; Region: PRK06178 428406011157 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 428406011158 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 428406011159 acyl-activating enzyme (AAE) consensus motif; other site 428406011160 acyl-activating enzyme (AAE) consensus motif; other site 428406011161 AMP binding site [chemical binding]; other site 428406011162 active site 428406011163 CoA binding site [chemical binding]; other site 428406011164 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 428406011165 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 428406011166 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 428406011167 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 428406011168 Cell shape-determining protein [Cell envelope biogenesis, outer membrane]; Region: MreD; COG2891 428406011169 rod shape-determining protein MreC; Provisional; Region: PRK13922 428406011170 rod shape-determining protein MreC; Region: MreC; pfam04085 428406011171 rod shape-determining protein MreB; Provisional; Region: PRK13927 428406011172 MreB and similar proteins; Region: MreB_like; cd10225 428406011173 nucleotide binding site [chemical binding]; other site 428406011174 Mg binding site [ion binding]; other site 428406011175 putative protofilament interaction site [polypeptide binding]; other site 428406011176 RodZ interaction site [polypeptide binding]; other site 428406011177 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 428406011178 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 428406011179 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 428406011180 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 428406011181 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 428406011182 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 428406011183 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 428406011184 GatB domain; Region: GatB_Yqey; smart00845 428406011185 Protein of unknown function, DUF484; Region: DUF484; cl17449 428406011186 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 428406011187 XerD and XerC integrases, DNA breaking-rejoining enzymes, N- and C-terminal domains. XerD-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination...; Region: INT_XerDC; cd00798 428406011188 active site 428406011189 Int/Topo IB signature motif; other site 428406011190 Predicted SAM-dependent methyltransferases [General function prediction only]; Region: COG1092 428406011191 Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase; Region: PUA; smart00359 428406011192 Middle domain of the SAM-dependent methyltransferase RlmI and related proteins; Region: RlmI_M_like; cd11572 428406011193 putative RNA binding site [nucleotide binding]; other site 428406011194 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 428406011195 S-adenosylmethionine binding site [chemical binding]; other site 428406011196 Predicted membrane-bound metal-dependent hydrolase (DUF457); Region: DUF457; pfam04307 428406011197 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 428406011198 FAD binding domain; Region: FAD_binding_4; pfam01565 428406011199 Berberine and berberine like; Region: BBE; pfam08031 428406011200 3-carboxymuconate cyclase [Carbohydrate transport and metabolism]; Region: COG2706 428406011201 Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]; Region: Fur; COG0735 428406011202 metal binding site 2 [ion binding]; metal-binding site 428406011203 putative DNA binding helix; other site 428406011204 metal binding site 1 [ion binding]; metal-binding site 428406011205 structural Zn2+ binding site [ion binding]; other site 428406011206 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 428406011207 The function of this protein family is unkown. The amino acid sequence of YjiA protein in E. coli contains several conserved motifs that characterizes it as a P-loop GTPase. YijA gene is among the genes significantly induced in response to DNA-damage...; Region: CobW_like; cd03112 428406011208 P-loop, Walker A motif; other site 428406011209 Base recognition motif; other site 428406011210 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; pfam07683 428406011211 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 428406011212 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 428406011213 CobW/HypB/UreG, nucleotide-binding domain; Region: cobW; pfam02492 428406011214 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; smart00833 428406011215 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 428406011216 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_2; cd08498 428406011217 Protease HslV and the ATPase/chaperone HslU are part of an ATP-dependent proteolytic system that is the prokaryotic homolog of the proteasome. HslV is a dimer of hexamers (a dodecamer) that forms a central proteolytic chamber with active sites on the...; Region: protease_HslV; cd01913 428406011218 active site 428406011219 HslU subunit interaction site [polypeptide binding]; other site 428406011220 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 428406011221 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406011222 Walker A motif; other site 428406011223 ATP binding site [chemical binding]; other site 428406011224 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406011225 Walker B motif; other site 428406011226 arginine finger; other site 428406011227 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 428406011228 CsbD-like; Region: CsbD; cl17424 428406011229 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]; Region: COG4567 428406011230 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406011231 active site 428406011232 phosphorylation site [posttranslational modification] 428406011233 intermolecular recognition site; other site 428406011234 dimerization interface [polypeptide binding]; other site 428406011235 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 428406011236 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 428406011237 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406011238 ATP binding site [chemical binding]; other site 428406011239 Mg2+ binding site [ion binding]; other site 428406011240 G-X-G motif; other site 428406011241 Copper(I)-binding protein [Inorganic ion transport and metabolism]; Region: COG2847 428406011242 Putative zinc-finger; Region: zf-HC2; pfam13490 428406011243 RNA polymerase sigma factor; Provisional; Region: PRK12520 428406011244 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 428406011245 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 428406011246 DNA binding residues [nucleotide binding] 428406011247 AAK_NAGK-C: N-Acetyl-L-glutamate kinase - cyclic (NAGK-C) catalyzes the phosphorylation of the gamma-COOH group of N-acetyl-L-glutamate (NAG) by ATP in the second step of arginine biosynthesis found in some bacteria and photosynthetic organisms using the...; Region: AAK_NAGK-C; cd04250 428406011248 feedback inhibition sensing region; other site 428406011249 homohexameric interface [polypeptide binding]; other site 428406011250 nucleotide binding site [chemical binding]; other site 428406011251 N-acetyl-L-glutamate binding site [chemical binding]; other site 428406011252 pyrimidine 5'-nucleotidase; Region: Pyr-5-nucltdase; TIGR01993 428406011253 HAD-hyrolase-like; Region: Hydrolase_like; pfam13242 428406011254 division inhibitor protein; Provisional; Region: slmA; PRK09480 428406011255 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 428406011256 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 428406011257 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 428406011258 DNA-binding site [nucleotide binding]; DNA binding site 428406011259 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 428406011260 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406011261 homodimer interface [polypeptide binding]; other site 428406011262 catalytic residue [active] 428406011263 4-aminobutyrate aminotransferase; Provisional; Region: PRK06777 428406011264 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 428406011265 inhibitor-cofactor binding pocket; inhibition site 428406011266 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406011267 catalytic residue [active] 428406011268 succinic semialdehyde dehydrogenase; Region: PLN02278 428406011269 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 428406011270 tetramerization interface [polypeptide binding]; other site 428406011271 NAD(P) binding site [chemical binding]; other site 428406011272 catalytic residues [active] 428406011273 homoserine O-acetyltransferase; Provisional; Region: metX; PRK00175 428406011274 homoserine O-acetyltransferase; Region: homoserO_Ac_trn; TIGR01392 428406011275 Methyltransferase domain; Region: Methyltransf_23; pfam13489 428406011276 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 428406011277 S-adenosylmethionine binding site [chemical binding]; other site 428406011278 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 428406011279 Sel1 repeat; Region: Sel1; cl02723 428406011280 Sel1-like repeats; Region: SEL1; smart00671 428406011281 Sel1-like repeats; Region: SEL1; smart00671 428406011282 Sel1-like repeats; Region: SEL1; smart00671 428406011283 Protein of unknown function (DUF466); Region: DUF466; pfam04328 428406011284 carbon starvation protein A; Provisional; Region: PRK15015 428406011285 Carbon starvation protein CstA; Region: CstA; pfam02554 428406011286 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 428406011287 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4564 428406011288 Cache domain; Region: Cache_2; pfam08269 428406011289 Histidine kinase; Region: HisKA_3; pfam07730 428406011290 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406011291 ATP binding site [chemical binding]; other site 428406011292 Mg2+ binding site [ion binding]; other site 428406011293 G-X-G motif; other site 428406011294 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 428406011295 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406011296 active site 428406011297 phosphorylation site [posttranslational modification] 428406011298 intermolecular recognition site; other site 428406011299 dimerization interface [polypeptide binding]; other site 428406011300 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 428406011301 DNA binding residues [nucleotide binding] 428406011302 dimerization interface [polypeptide binding]; other site 428406011303 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 428406011304 Escherichia coli Gne (a nucleoside-diphosphate-sugar 4-epimerase)-like, extended (e) SDRs; Region: Gne_like_SDR_e; cd05238 428406011305 putative NAD(P) binding site [chemical binding]; other site 428406011306 active site 428406011307 putative substrate binding site [chemical binding]; other site 428406011308 Transcriptional regulators [Transcription]; Region: FadR; COG2186 428406011309 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 428406011310 DNA-binding site [nucleotide binding]; DNA binding site 428406011311 FCD domain; Region: FCD; pfam07729 428406011312 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 428406011313 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 428406011314 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3395 428406011315 putative aldolase; Validated; Region: PRK08130 428406011316 intersubunit interface [polypeptide binding]; other site 428406011317 active site 428406011318 Zn2+ binding site [ion binding]; other site 428406011319 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406011320 D-galactonate transporter; Region: 2A0114; TIGR00893 428406011321 putative substrate translocation pore; other site 428406011322 Hydroxypyruvate isomerase [Carbohydrate transport and metabolism]; Region: Hfi; COG3622 428406011323 Protein of unknown function (DUF3617); Region: DUF3617; pfam12276 428406011324 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 428406011325 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406011326 active site 428406011327 phosphorylation site [posttranslational modification] 428406011328 intermolecular recognition site; other site 428406011329 dimerization interface [polypeptide binding]; other site 428406011330 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 428406011331 DNA binding site [nucleotide binding] 428406011332 Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and...; Region: PEPCK_GTP; cd00819 428406011333 active site 428406011334 substrate-binding site [chemical binding]; other site 428406011335 metal-binding site [ion binding] 428406011336 GTP binding site [chemical binding]; other site 428406011337 Putative D-3-Phosphoglycerate Dehydrogenases; Region: PGDH_like_1; cd12169 428406011338 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 428406011339 dimerization interface [polypeptide binding]; other site 428406011340 NAD binding site [chemical binding]; other site 428406011341 ligand binding site [chemical binding]; other site 428406011342 catalytic site [active] 428406011343 The Class III extradiol dioxygenase, 4,5-DOPA Dioxygenase, catalyzes the incorporation of both atoms of molecular oxygen into 4,5-dihydroxy-phenylalanine; Region: 45_DOPA_Dioxygenase; cd07363 428406011344 Catalytic LigB subunit of aromatic ring-opening dioxygenase; Region: LigB; pfam02900 428406011345 putative active site [active] 428406011346 metal binding site [ion binding]; metal-binding site 428406011347 Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component, and related enzymes [Energy production and conversion]; Region: Lpd; COG1249 428406011348 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 428406011349 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 428406011350 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 428406011351 Patatin-like phospholipase; Region: Patatin; pfam01734 428406011352 active site 428406011353 nucleophile elbow; other site 428406011354 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 428406011355 DNA-binding transcriptional repressor AcrR; Provisional; Region: PRK10668 428406011356 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 428406011357 MAATS-type transcriptional repressor, C-terminal region; Region: TetR_C_2; pfam08361 428406011358 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 428406011359 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 428406011360 HlyD family secretion protein; Region: HlyD_3; pfam13437 428406011361 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 428406011362 Protein export membrane protein; Region: SecD_SecF; cl14618 428406011363 copper/silver efflux system outer membrane protein CusC; Provisional; Region: PRK09837 428406011364 Topoisomerase IB [DNA replication, recombination, and repair]; Region: COG3569 428406011365 DNA topoisomerase IB, C-terminal catalytic domain. Topoisomerase I promotes the relaxation of both positive and negative DNA superhelical tension by introducing a transient single-stranded break in duplex DNA. This function is vital for the processes of...; Region: Topo_IB_C; cd00659 428406011366 active site 428406011367 DNA binding site [nucleotide binding] 428406011368 Int/Topo IB signature motif; other site 428406011369 catalytic residues [active] 428406011370 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 428406011371 Predicted protein tyrosine phosphatase [General function prediction only]; Region: COG4551 428406011372 active site 428406011373 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cl00447 428406011374 nudix motif; other site 428406011375 Putative regulator of cell autolysis [Signal transduction mechanisms]; Region: LytS; COG3275 428406011376 TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG...; Region: TOPRIM_primases; cd01029 428406011377 active site 428406011378 metal binding site [ion binding]; metal-binding site 428406011379 interdomain interaction site; other site 428406011380 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 428406011381 Walker A motif; other site 428406011382 ATP binding site [chemical binding]; other site 428406011383 AAA domain; Region: AAA_25; pfam13481 428406011384 Walker B motif; other site 428406011385 Helix-turn-helix domain; Region: HTH_36; pfam13730 428406011386 Helix-turn-helix domain; Region: HTH_39; pfam14090 428406011387 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl17523 428406011388 integrase; Provisional; Region: PRK09692 428406011389 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall...; Region: INT_P4; cd00801 428406011390 active site 428406011391 Int/Topo IB signature motif; other site 428406011392 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 428406011393 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 428406011394 trmE is a tRNA modification GTPase; Region: trmE; cd04164 428406011395 G1 box; other site 428406011396 GTP/Mg2+ binding site [chemical binding]; other site 428406011397 Switch I region; other site 428406011398 G2 box; other site 428406011399 Switch II region; other site 428406011400 G3 box; other site 428406011401 G4 box; other site 428406011402 G5 box; other site 428406011403 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 428406011404 membrane protein insertase; Provisional; Region: PRK01318 428406011405 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 428406011406 hypothetical protein; Validated; Region: PRK00041 428406011407 Ribonuclease P; Region: Ribonuclease_P; cl00457 428406011408 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 428406011409 homogentisate 1,2-dioxygenase; Provisional; Region: PRK05341 428406011410 fumarylacetoacetase; Region: PLN02856 428406011411 Domain of unknown function (DUF1969); Region: DUF1969; pfam09298 428406011412 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 428406011413 Transcriptional regulator [Transcription]; Region: PaiB; COG2808 428406011414 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 428406011415 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 428406011416 Walker A/P-loop; other site 428406011417 ATP binding site [chemical binding]; other site 428406011418 Q-loop/lid; other site 428406011419 ABC transporter signature motif; other site 428406011420 Walker B; other site 428406011421 D-loop; other site 428406011422 H-loop/switch region; other site 428406011423 ABC nitrate/sulfonate/bicarbonate family transporter, ATPase subunit; Region: ABC_transp; pfam09821 428406011424 ABC-type anion transport system, duplicated permease component [Inorganic ion transport and metabolism]; Region: COG4986 428406011425 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406011426 dimer interface [polypeptide binding]; other site 428406011427 conserved gate region; other site 428406011428 putative PBP binding loops; other site 428406011429 ABC-ATPase subunit interface; other site 428406011430 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406011431 dimer interface [polypeptide binding]; other site 428406011432 conserved gate region; other site 428406011433 putative PBP binding loops; other site 428406011434 ABC-ATPase subunit interface; other site 428406011435 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 428406011436 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 428406011437 active site 428406011438 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406011439 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406011440 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 428406011441 putative effector binding pocket; other site 428406011442 dimerization interface [polypeptide binding]; other site 428406011443 DNA-binding transcriptional regulator MetR; Provisional; Region: PRK15421 428406011444 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 428406011445 putative DNA binding site [nucleotide binding]; other site 428406011446 putative Zn2+ binding site [ion binding]; other site 428406011447 The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold; Region: PBP2_MetR; cd08441 428406011448 putative dimerization interface [polypeptide binding]; other site 428406011449 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional; Region: PRK05222 428406011450 CIMS - Cobalamine-independent methonine synthase, or MetE, N-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme...; Region: CIMS_N_terminal_like; cd03312 428406011451 THF binding site; other site 428406011452 CIMS - Cobalamine-independent methonine synthase, or MetE, C-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme...; Region: CIMS_C_terminal_like; cd03311 428406011453 substrate binding site [chemical binding]; other site 428406011454 THF binding site; other site 428406011455 zinc-binding site [ion binding]; other site 428406011456 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 428406011457 Protein export membrane protein; Region: SecD_SecF; cl14618 428406011458 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 428406011459 HlyD family secretion protein; Region: HlyD_3; pfam13437 428406011460 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 428406011461 Protein of unknown function (DUF3309); Region: DUF3309; pfam11752 428406011462 Rossmann-like domain; Region: Rossmann-like; pfam10727 428406011463 Domain of unknown function (DUF2520); Region: DUF2520; pfam10728 428406011464 Cyanate permease [Inorganic ion transport and metabolism]; Region: CynX; COG2807 428406011465 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406011466 Methyladenine glycosylase; Region: Adenine_glyco; pfam03352 428406011467 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 428406011468 Mycobacterium tuberculosis CorA-like subfamily; Region: MtCorA-like; cd12830 428406011469 oligomer interface [polypeptide binding]; other site 428406011470 metal binding site [ion binding]; metal-binding site 428406011471 metal binding site [ion binding]; metal-binding site 428406011472 putative Cl binding site [ion binding]; other site 428406011473 basic sphincter; other site 428406011474 hydrophobic gate; other site 428406011475 periplasmic entrance; other site 428406011476 Transcriptional regulators [Transcription]; Region: MarR; COG1846 428406011477 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 428406011478 putative DNA binding site [nucleotide binding]; other site 428406011479 putative Zn2+ binding site [ion binding]; other site 428406011480 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 428406011481 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406011482 putative substrate translocation pore; other site 428406011483 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 428406011484 Aconitase B swivel domain. Aconitate hydratase B is involved in energy metabolism as part of the TCA cycle. It catalyses the formation of cis-aconitate from citrate. This is the aconitase swivel domain, which undergoes swivelling conformational change in...; Region: AcnB_Swivel; cd01576 428406011485 substrate binding site [chemical binding]; other site 428406011486 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 428406011487 substrate binding site [chemical binding]; other site 428406011488 ligand binding site [chemical binding]; other site 428406011489 Antibiotic biosynthesis monooxygenase; Region: ABM; pfam03992 428406011490 aromatic amino acid exporter; Provisional; Region: PRK11689 428406011491 transcriptional activator NhaR; Provisional; Region: nhaR; PRK11062 428406011492 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406011493 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 428406011494 dimerization interface [polypeptide binding]; other site 428406011495 NADH dehydrogenase subunit L; Provisional; Region: PRK08168 428406011496 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 428406011497 Uncharacterized protein conserved in bacteria (DUF2309); Region: DUF2309; pfam10070 428406011498 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3002 428406011499 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 428406011500 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 428406011501 S-adenosylmethionine binding site [chemical binding]; other site 428406011502 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 428406011503 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 428406011504 phenylacetate-CoA oxygenase/reductase, PaaK subunit; Region: PA_CoA_Oxy5; TIGR02160 428406011505 NAD(P) binding domain of ferredoxin reductase like phenylacetic acid (PA) degradation oxidoreductase. PA oxidoreductases of E. coli hydroxylate PA-CoA in the second step of PA degradation. Members of this group typically fuse a ferredoxin reductase-like...; Region: PA_degradation_oxidoreductase_like; cd06214 428406011506 FAD binding pocket [chemical binding]; other site 428406011507 FAD binding motif [chemical binding]; other site 428406011508 phosphate binding motif [ion binding]; other site 428406011509 beta-alpha-beta structure motif; other site 428406011510 NAD(p) ribose binding residues [chemical binding]; other site 428406011511 NAD binding pocket [chemical binding]; other site 428406011512 NAD(P)-pyrophosphate-nicotinamide binding residues [chemical binding]; other site 428406011513 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 428406011514 catalytic loop [active] 428406011515 iron binding site [ion binding]; other site 428406011516 phenylacetate-CoA oxygenase, PaaJ subunit; Region: PA_CoA_Oxy4; TIGR02159 428406011517 Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]; Region: PaaD; COG2151 428406011518 Phenylacetic acid catabolic protein; Region: PaaA_PaaC; pfam05138 428406011519 phenylacetate-CoA oxygenase subunit PaaB; Provisional; Region: paaB; PRK13781 428406011520 phenylacetate-CoA oxygenase subunit PaaA; Provisional; Region: paaA; PRK13778 428406011521 phenylacetate-CoA oxygenase, PaaG subunit; Region: PA_CoA_Oxy1; TIGR02156 428406011522 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 428406011523 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406011524 putative substrate translocation pore; other site 428406011525 Escherichia coli PhnB and similar proteins; the E. coli phnB gene is found next to an operon involved in the cleavage of carbon-phosphorus bonds in unactivated alkylphosphonates; Region: PhnB_like; cd06588 428406011526 dimer interface [polypeptide binding]; other site 428406011527 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 428406011528 Ketosteroid isomerase homolog [Function unknown]; Region: COG4319 428406011529 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 428406011530 WHG domain; Region: WHG; pfam13305 428406011531 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 428406011532 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 428406011533 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406011534 active site 428406011535 phosphorylation site [posttranslational modification] 428406011536 intermolecular recognition site; other site 428406011537 dimerization interface [polypeptide binding]; other site 428406011538 TniQ; Region: TniQ; pfam06527 428406011539 Predicted transcriptional regulator [Transcription]; Region: COG2944 428406011540 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 428406011541 salt bridge; other site 428406011542 non-specific DNA binding site [nucleotide binding]; other site 428406011543 sequence-specific DNA binding site [nucleotide binding]; other site 428406011544 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 428406011545 AAA domain; Region: AAA_22; pfam13401 428406011546 Walker A motif; other site 428406011547 ATP binding site [chemical binding]; other site 428406011548 TnsA endonuclease N terminal; Region: Tn7_Tnp_TnsA_N; pfam08722 428406011549 Integrase core domain; Region: rve; pfam00665 428406011550 DNA polymerase III subunits gamma and tau; Provisional; Region: PRK14965 428406011551 Plasmid stability protein [General function prediction only]; Region: StbC; COG4691 428406011552 Uncharacterized ACR, COG2135; Region: DUF159; pfam02586 428406011553 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 428406011554 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 428406011555 Repeat of Unknown Function (DUF347); Region: DUF347; pfam03988 428406011556 Major Facilitator Superfamily; Region: MFS_1; pfam07690 428406011557 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406011558 putative substrate translocation pore; other site 428406011559 uncharacterized peroxidase-related enzyme; Region: peroxid_rel; TIGR01926 428406011560 alkylhydroperoxidase AhpD family core domain; Region: ahpD_dom; TIGR00778 428406011561 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 428406011562 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 428406011563 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 428406011564 DNA binding residues [nucleotide binding] 428406011565 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 428406011566 Cytochrome c biogenesis protein [Posttranslational modification, protein turnover, chaperones]; Region: CcdA; COG0785 428406011567 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 428406011568 TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains. Group I TRX is a small ancient protein that alter the redox...; Region: TRX_family; cd02947 428406011569 catalytic residues [active] 428406011570 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406011571 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406011572 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 428406011573 putative effector binding pocket; other site 428406011574 dimerization interface [polypeptide binding]; other site 428406011575 DinB superfamily; Region: DinB_2; pfam12867 428406011576 CopC domain; Region: CopC; pfam04234 428406011577 YHS domain; Region: YHS; pfam04945 428406011578 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 428406011579 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 428406011580 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 428406011581 motif II; other site 428406011582 disulfide isomerase/thiol-disulfide oxidase; Provisional; Region: dsbG; PRK11657 428406011583 Disulfide bond isomerase protein N-terminus; Region: DsbC_N; pfam10411 428406011584 DsbA family, DsbC and DsbG subfamily; V-shaped homodimeric proteins containing a redox active CXXC motif imbedded in a TRX fold. They function as protein disulfide isomerases and chaperones in the bacterial periplasm to correct non-native disulfide bonds...; Region: DsbA_DsbC_DsbG; cd03020 428406011585 dimerization domain [polypeptide binding]; other site 428406011586 dimer interface [polypeptide binding]; other site 428406011587 catalytic residues [active] 428406011588 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 428406011589 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 428406011590 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 428406011591 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the GGDEF (DiGuanylate-Cyclase (DGC)) domain. The GGDEF domain has been suggested to be homologous to the adenylyl cyclase catalytic domain and...; Region: CBS_pair_GGDEF_assoc; cd04598 428406011592 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 428406011593 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 428406011594 metal binding site [ion binding]; metal-binding site 428406011595 active site 428406011596 I-site; other site 428406011597 Phosphoesterase family; Region: Phosphoesterase; pfam04185 428406011598 Phosphoesterase family; Region: Phosphoesterase; pfam04185 428406011599 Chromate transport protein ChrA [Inorganic ion transport and metabolism]; Region: ChrA; COG2059 428406011600 chromate transporter, chromate ion transporter (CHR) family; Region: 2A51; TIGR00937 428406011601 Chromate transporter; Region: Chromate_transp; pfam02417 428406011602 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cd00491 428406011603 active site 1 [active] 428406011604 dimer interface [polypeptide binding]; other site 428406011605 hexamer interface [polypeptide binding]; other site 428406011606 active site 2 [active] 428406011607 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic acid aldolase,; Validated; Region: PRK08195 428406011608 4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_HOA; cd07943 428406011609 active site 428406011610 catalytic residues [active] 428406011611 metal binding site [ion binding]; metal-binding site 428406011612 DmpG-like communication domain; Region: DmpG_comm; pfam07836 428406011613 acetaldehyde dehydrogenase; Validated; Region: PRK08300 428406011614 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 428406011615 Prokaryotic acetaldehyde dehydrogenase, dimerisation; Region: AcetDehyd-dimer; pfam09290 428406011616 4-oxalocrotonate decarboxylase; Region: catechol_dmpH; TIGR03218 428406011617 2-oxopent-4-enoate hydratase; Region: catechol_dmpE; TIGR03220 428406011618 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase; Region: biphenyl_bphD; TIGR03343 428406011619 2-hydroxymuconic semialdehyde dehydrogenase; Region: OH_muco_semi_DH; TIGR03216 428406011620 Human aldehyde dehydrogenase family 8 member A1-like; Region: ALDH_F8_HMSADH; cd07093 428406011621 NAD binding site [chemical binding]; other site 428406011622 catalytic residues [active] 428406011623 Domain of unknown function (DUF336); Region: DUF336; pfam03928 428406011624 catechol 2,3 dioxygenase; Region: catechol_2_3; TIGR03211 428406011625 N-terminal domain of catechol 2,3-dioxygenase; Region: 2_3_CTD_N; cd07265 428406011626 tetramer interface [polypeptide binding]; other site 428406011627 C-terminal domain of catechol 2,3-dioxygenase; Region: 2_3_CTD_C; cd07243 428406011628 tetramer interface [polypeptide binding]; other site 428406011629 active site 428406011630 Fe binding site [ion binding]; other site 428406011631 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 428406011632 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 428406011633 catalytic loop [active] 428406011634 iron binding site [ion binding]; other site 428406011635 Phenol 2-monooxygenase (phenol hydroxylase) is a flavoprotein monooxygenase, able to use molecular oxygen as a substrate in the microbial degredation of phenol. This protein is encoded by a single gene and uses a tightly bound FAD cofactor in the NAD(P)H...; Region: phenol_2-monooxygenase_like; cd06211 428406011636 FAD binding pocket [chemical binding]; other site 428406011637 FAD binding motif [chemical binding]; other site 428406011638 phosphate binding motif [ion binding]; other site 428406011639 beta-alpha-beta structure motif; other site 428406011640 NAD binding pocket [chemical binding]; other site 428406011641 Phenol hydroxylase conserved region; Region: Phenol_monoox; pfam04663 428406011642 Aromatic and Alkene Monooxygenase Hydroxylase, subunit A, ferritin-like diiron-binding domain; Region: AAMH_A; cd01057 428406011643 dimerization interface [polypeptide binding]; other site 428406011644 putative path to active site cavity [active] 428406011645 diiron center [ion binding]; other site 428406011646 MmoB/DmpM family; Region: MmoB_DmpM; pfam02406 428406011647 Aromatic and Alkene Monooxygenase Hydroxylase, subunit B, ferritin-like diiron-binding domain; Region: AAMH_B; cd01058 428406011648 dimerization interface [polypeptide binding]; other site 428406011649 Phenol hydroxylase subunit; Region: Phenol_hyd_sub; pfam06099 428406011650 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 428406011651 dinuclear metal binding motif [ion binding]; other site 428406011652 Toluene-4-monooxygenase system protein B (TmoB); Region: TmoB; pfam06234 428406011653 Toluene-4-monooxygenase effector protein complex (T4mo), Rieske ferredoxin subunit; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. T4mo is a four-protein complex that catalyzes the NADH- and O2-dependent...; Region: Rieske_T4moC; cd03474 428406011654 [2Fe-2S] cluster binding site [ion binding]; other site 428406011655 MmoB/DmpM family; Region: MmoB_DmpM; pfam02406 428406011656 Aromatic and Alkene Monooxygenase Hydroxylase, subunit B, ferritin-like diiron-binding domain; Region: AAMH_B; cd01058 428406011657 dimerization interface [polypeptide binding]; other site 428406011658 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 428406011659 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 428406011660 catalytic loop [active] 428406011661 iron binding site [ion binding]; other site 428406011662 Toluene-4-monoxygenase electron transfer component of Pseudomonas mendocina hydroxylates toluene and forms p-cresol as part of a three component toluene-4-monoxygenase system. Electron transfer is from NADH to an NADH:ferredoxin oxidoreductase (TmoF in P; Region: T4MO_e_transfer_like; cd06190 428406011663 FAD binding pocket [chemical binding]; other site 428406011664 FAD binding motif [chemical binding]; other site 428406011665 phosphate binding motif [ion binding]; other site 428406011666 beta-alpha-beta structure motif; other site 428406011667 NAD binding pocket [chemical binding]; other site 428406011668 Activator of aromatic catabolism; Region: XylR_N; pfam06505 428406011669 V4R domain; Region: V4R; pfam02830 428406011670 Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]; Region: PspF; COG1221 428406011671 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406011672 Walker A motif; other site 428406011673 ATP binding site [chemical binding]; other site 428406011674 Walker B motif; other site 428406011675 arginine finger; other site 428406011676 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 428406011677 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; pfam03349 428406011678 Activator of aromatic catabolism; Region: XylR_N; pfam06505 428406011679 V4R domain; Region: V4R; pfam02830 428406011680 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 428406011681 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406011682 Walker A motif; other site 428406011683 ATP binding site [chemical binding]; other site 428406011684 Walker B motif; other site 428406011685 arginine finger; other site 428406011686 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 428406011687 Transcriptional regulators [Transcription]; Region: FadR; COG2186 428406011688 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 428406011689 DNA-binding site [nucleotide binding]; DNA binding site 428406011690 FCD domain; Region: FCD; pfam07729 428406011691 Uncharacterized anaerobic dehydrogenase [General function prediction only]; Region: COG3383 428406011692 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 428406011693 catalytic loop [active] 428406011694 iron binding site [ion binding]; other site 428406011695 Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is...; Region: MopB_Formate-Dh-H; cd02753 428406011696 [4Fe-4S] binding site [ion binding]; other site 428406011697 molybdopterin cofactor binding site; other site 428406011698 This CD includes formate dehydrogenases (Fdh) H and N; nitrate reductases, Nap and Nas; and other related proteins. Formate dehydrogenase H is a component of the anaerobic formate hydrogen lyase complex and catalyzes the reversible oxidation of formate...; Region: MopB_CT_Fdh-Nap-like; cd00508 428406011699 molybdopterin cofactor binding site; other site 428406011700 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 428406011701 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; pfam10589 428406011702 acetyl-CoA synthetase; Provisional; Region: PRK04319 428406011703 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 428406011704 Uncharacterized subfamily of Acetyl-CoA synthetase like family (ACS); Region: MACS_like_4; cd05969 428406011705 active site 428406011706 acyl-activating enzyme (AAE) consensus motif; other site 428406011707 putative CoA binding site [chemical binding]; other site 428406011708 AMP binding site [chemical binding]; other site 428406011709 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 428406011710 Thiamine pyrophosphate (TPP) family, E1 of PDC_ADC_BCADC subfamily, TPP-binding module; composed of proteins similar to the E1 components of the human pyruvate dehydrogenase complex (PDC), the acetoin dehydrogenase complex (ADC) and the branched chain...; Region: TPP_E1_PDC_ADC_BCADC; cd02000 428406011711 tetramer interface [polypeptide binding]; other site 428406011712 TPP-binding site [chemical binding]; other site 428406011713 heterodimer interface [polypeptide binding]; other site 428406011714 phosphorylation loop region [posttranslational modification] 428406011715 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 428406011716 Pyrimidine (PYR) binding domain of the beta subunits of the E1 components of human pyruvate dehydrogenase complex (E1- PDHc) and related proteins; Region: TPP_PYR_E1-PDHc-beta_like; cd07036 428406011717 alpha subunit interface [polypeptide binding]; other site 428406011718 TPP binding site [chemical binding]; other site 428406011719 heterodimer interface [polypeptide binding]; other site 428406011720 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 428406011721 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed; Region: PRK11856 428406011722 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 428406011723 E3 interaction surface; other site 428406011724 lipoyl attachment site [posttranslational modification]; other site 428406011725 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 428406011726 Acyl carrier protein [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcpP; COG0236 428406011727 RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal...; Region: RaiA; cl00250 428406011728 30S subunit binding site; other site 428406011729 PAS domain S-box; Region: sensory_box; TIGR00229 428406011730 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 428406011731 putative active site [active] 428406011732 heme pocket [chemical binding]; other site 428406011733 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG4585 428406011734 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406011735 ATP binding site [chemical binding]; other site 428406011736 Mg2+ binding site [ion binding]; other site 428406011737 G-X-G motif; other site 428406011738 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 428406011739 GroEL_like type I chaperonin. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings, each composed of 7-9 subunits. The symmetry of type I is seven-fold and they are found...; Region: GroEL; cd03344 428406011740 ring oligomerisation interface [polypeptide binding]; other site 428406011741 ATP/Mg binding site [chemical binding]; other site 428406011742 stacking interactions; other site 428406011743 hinge regions; other site 428406011744 nicotinate phosphoribosyltransferase; Validated; Region: PRK09243 428406011745 Nicotinate phosphoribosyltransferase (NAPRTase), subgroup A. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting, reaction...; Region: NAPRTase_A; cd01570 428406011746 active site 428406011747 iron-sulfur cluster repair di-iron protein; Provisional; Region: PRK10992 428406011748 Domain of Unknown function (DUF542); Region: ScdA_N; pfam04405 428406011749 Hemerythrin-like domain; Region: Hr-like; cd12108 428406011750 Fe binding site [ion binding]; other site 428406011751 anaerobic nitric oxide reductase transcription regulator; Provisional; Region: PRK05022 428406011752 GAF domain; Region: GAF; cl17456 428406011753 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406011754 Walker A motif; other site 428406011755 ATP binding site [chemical binding]; other site 428406011756 Walker B motif; other site 428406011757 arginine finger; other site 428406011758 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK08270 428406011759 ATP cone domain; Region: ATP-cone; pfam03477 428406011760 Class III ribonucleotide reductase; Region: RNR_III; cd01675 428406011761 effector binding site; other site 428406011762 active site 428406011763 Zn binding site [ion binding]; other site 428406011764 Anaerobic ribonucleoside-triphosphate reductase; Region: NRDD; pfam13597 428406011765 anaerobic ribonucleoside-triphosphate reductase activating protein; Region: NrdG2; TIGR02495 428406011766 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 428406011767 FeS/SAM binding site; other site 428406011768 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 428406011769 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 428406011770 ligand binding site [chemical binding]; other site 428406011771 flexible hinge region; other site 428406011772 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 428406011773 putative switch regulator; other site 428406011774 non-specific DNA interactions [nucleotide binding]; other site 428406011775 DNA binding site [nucleotide binding] 428406011776 sequence specific DNA binding site [nucleotide binding]; other site 428406011777 putative cAMP binding site [chemical binding]; other site 428406011778 Uncharacterized conserved protein [Function unknown]; Region: COG4273 428406011779 SCP-2 sterol transfer family; Region: SCP2; cl01225 428406011780 putative protease; Provisional; Region: PRK15447 428406011781 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 428406011782 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 428406011783 Peptidase family U32; Region: Peptidase_U32; pfam01136 428406011784 Nitrate/nitrite transporter [Inorganic ion transport and metabolism]; Region: NarK; COG2223 428406011785 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406011786 putative substrate translocation pore; other site 428406011787 nitrate/nitrite transport protein NarU; Provisional; Region: PRK15034 428406011788 Uncharacterized conserved protein [Function unknown]; Region: COG1284 428406011789 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 428406011790 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 428406011791 Nitrate reductase alpha subunit [Energy production and conversion]; Region: NarG; COG5013 428406011792 Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to...; Region: MopB_Nitrate-R-NarG-like; cd02750 428406011793 [4Fe-4S] binding site [ion binding]; other site 428406011794 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 428406011795 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 428406011796 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 428406011797 Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to...; Region: MopB_CT_Nitrate-R-NarG-like; cd02776 428406011798 molybdopterin cofactor binding site; other site 428406011799 Nitrate reductase beta subunit [Energy production and conversion]; Region: NarY; COG1140 428406011800 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 428406011801 Nitrate reductase delta subunit [Energy production and conversion]; Region: NarJ; COG2180 428406011802 Nitrate reductase gamma subunit; Region: Nitrate_red_gam; pfam02665 428406011803 Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes. In E. coli, the synthesis of Moco involves genes from several loci: moa; Region: MobB; cd03116 428406011804 Walker A motif; other site 428406011805 Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]; Region: NarQ; COG3850 428406011806 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 428406011807 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 428406011808 dimerization interface [polypeptide binding]; other site 428406011809 GAF domain; Region: GAF; pfam01590 428406011810 Histidine kinase; Region: HisKA_3; pfam07730 428406011811 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406011812 ATP binding site [chemical binding]; other site 428406011813 Mg2+ binding site [ion binding]; other site 428406011814 G-X-G motif; other site 428406011815 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 428406011816 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406011817 active site 428406011818 phosphorylation site [posttranslational modification] 428406011819 intermolecular recognition site; other site 428406011820 dimerization interface [polypeptide binding]; other site 428406011821 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 428406011822 DNA binding residues [nucleotide binding] 428406011823 dimerization interface [polypeptide binding]; other site 428406011824 Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis]; Region: HemK; COG2890 428406011825 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 428406011826 S-adenosylmethionine binding site [chemical binding]; other site 428406011827 uncharacterized flavoprotein, PP_4765 family; Region: flavo_PP4765; TIGR03862 428406011828 Methyltransferase domain; Region: Methyltransf_32; pfam13679 428406011829 Methyltransferase domain; Region: Methyltransf_31; pfam13847 428406011830 PAS domain; Region: PAS_9; pfam13426 428406011831 PAS domain; Region: PAS_9; pfam13426 428406011832 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 428406011833 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 428406011834 metal binding site [ion binding]; metal-binding site 428406011835 active site 428406011836 I-site; other site 428406011837 Peptidase family M1; Region: Peptidase_M1; pfam01433 428406011838 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 428406011839 Zn binding site [ion binding]; other site 428406011840 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 428406011841 Nitrogen regulatory protein P-II; Region: P-II; smart00938 428406011842 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 428406011843 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 428406011844 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 428406011845 HlyD family secretion protein; Region: HlyD_3; pfam13437 428406011846 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 428406011847 sensor protein QseC; Provisional; Region: PRK10337 428406011848 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 428406011849 dimer interface [polypeptide binding]; other site 428406011850 phosphorylation site [posttranslational modification] 428406011851 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406011852 ATP binding site [chemical binding]; other site 428406011853 Mg2+ binding site [ion binding]; other site 428406011854 G-X-G motif; other site 428406011855 DNA-binding transcriptional regulator BasR; Provisional; Region: PRK10643 428406011856 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406011857 active site 428406011858 phosphorylation site [posttranslational modification] 428406011859 intermolecular recognition site; other site 428406011860 dimerization interface [polypeptide binding]; other site 428406011861 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 428406011862 DNA binding site [nucleotide binding] 428406011863 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 428406011864 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 428406011865 metal binding site [ion binding]; metal-binding site 428406011866 active site 428406011867 I-site; other site 428406011868 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 428406011869 Mechanosensitive ion channel; Region: MS_channel; pfam00924 428406011870 Putative NodB-like catalytic domain of uncharacterized proteins found in bacteria; Region: CE4_COG5298; cd10923 428406011871 Uncharacterized protein conserved in bacteria (DUF2334); Region: DUF2334; pfam10096 428406011872 NodB motif; other site 428406011873 putative active site [active] 428406011874 putative catalytic site [active] 428406011875 putative Zn binding site [ion binding]; other site 428406011876 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 428406011877 Bacterial members of the UDP-N-Acetylglucosamine (GlcNAc) 2-Epimerase family are known to catalyze the reversible interconversion of UDP-GlcNAc and UDP-N-acetylmannosamine (UDP-ManNAc). The enzyme serves to produce an activated form of ManNAc residues; Region: GT1_UDP-GlcNAc_2-Epimerase; cd03786 428406011878 active site 428406011879 homodimer interface [polypeptide binding]; other site 428406011880 Bacteriophage N adsorption protein A C-term; Region: NfrA_C; pfam13283 428406011881 bacteriophage N4 adsorption protein B; Provisional; Region: nfrB; PRK15489 428406011882 active site 428406011883 Glycosyl transferase family group 2; Region: Glyco_trans_2_3; pfam13632 428406011884 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 428406011885 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 428406011886 ligand binding domain of Tar- and Tsr-related chemoreceptors; Region: Tar_Tsr_LBD; cd00181 428406011887 dimer interface [polypeptide binding]; other site 428406011888 ligand binding site [chemical binding]; other site 428406011889 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 428406011890 dimerization interface [polypeptide binding]; other site 428406011891 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 428406011892 dimer interface [polypeptide binding]; other site 428406011893 putative CheW interface [polypeptide binding]; other site 428406011894 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 428406011895 Hydroxy(phenyl)pyruvate Reductase, D-isomer-specific 2-hydroxyacid-related dehydrogenase; Region: HPPR; cd12156 428406011896 putative ligand binding site [chemical binding]; other site 428406011897 NAD binding site [chemical binding]; other site 428406011898 catalytic site [active] 428406011899 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 428406011900 Periplasmic solute-binding domain of active transport proteins; Region: PBP1_SBP_like_3; cd06329 428406011901 putative ligand binding site [chemical binding]; other site 428406011902 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 428406011903 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 428406011904 benzoate transport; Region: 2A0115; TIGR00895 428406011905 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406011906 Protein of unknown function (DUF2917); Region: DUF2917; pfam11142 428406011907 hypothetical protein; Provisional; Region: PRK08262 428406011908 M20 Peptidase, carboxypeptidase yscS; Region: M20_yscS; cd05674 428406011909 metal binding site [ion binding]; metal-binding site 428406011910 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 428406011911 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 428406011912 DNA-binding site [nucleotide binding]; DNA binding site 428406011913 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 428406011914 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406011915 homodimer interface [polypeptide binding]; other site 428406011916 catalytic residue [active] 428406011917 Protein of unknown function (DUF3005); Region: DUF3005; pfam11448 428406011918 enoyl-CoA hydratase; Provisional; Region: PRK06688 428406011919 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 428406011920 substrate binding site [chemical binding]; other site 428406011921 oxyanion hole (OAH) forming residues; other site 428406011922 trimer interface [polypeptide binding]; other site 428406011923 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 428406011924 MarR family; Region: MarR_2; pfam12802 428406011925 Predicted alpha/beta hydrolase [General function prediction only]; Region: COG4757 428406011926 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 428406011927 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 428406011928 dimerization interface [polypeptide binding]; other site 428406011929 putative DNA binding site [nucleotide binding]; other site 428406011930 putative Zn2+ binding site [ion binding]; other site 428406011931 Putative hydrophobic ligand-binding SRPBCC domain of Micromonospora echinospora CalC, human Aha1, and related proteins; Region: SRPBCC_CalC_Aha1-like; cd07814 428406011932 putative hydrophobic ligand binding site [chemical binding]; other site 428406011933 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins; Region: SRPBCC_CalC_Aha1-like_7; cd08900 428406011934 putative hydrophobic ligand binding site [chemical binding]; other site 428406011935 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK07515 428406011936 Ketoacyl-acyl carrier protein synthase III (KASIII) initiates the elongation in type II fatty acid synthase systems. It is found in bacteria and plants. Elongation of fatty acids in the type II systems occurs by Claisen condensation of malonyl-acyl...; Region: KAS_III; cd00830 428406011937 dimer interface [polypeptide binding]; other site 428406011938 active site 428406011939 CoA binding pocket [chemical binding]; other site 428406011940 Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP_PGM_like; cd07067 428406011941 catalytic core [active] 428406011942 short chain dehydrogenase; Provisional; Region: PRK07035 428406011943 classical (c) SDRs; Region: SDR_c; cd05233 428406011944 NAD(P) binding site [chemical binding]; other site 428406011945 active site 428406011946 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 428406011947 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406011948 Major Facilitator Superfamily; Region: MFS_1; pfam07690 428406011949 putative substrate translocation pore; other site 428406011950 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; cl00465 428406011951 Protein of unknown function (DUF1345); Region: DUF1345; pfam07077 428406011952 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 428406011953 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 428406011954 Coenzyme A binding pocket [chemical binding]; other site 428406011955 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 428406011956 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 428406011957 GlpE sulfurtransferase (ST) and homologs are members of the Rhodanese Homology Domain superfamily. Unlike other rhodanese sulfurtransferases, GlpE is a single domain protein but indications are that it functions as a dimer. The active site contains a...; Region: GlpE_ST; cd01444 428406011958 active site residue [active] 428406011959 Flagellar hook-length control protein [Cell motility and secretion]; Region: FliK; COG3144 428406011960 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 428406011961 Flagellar biosynthesis chaperone [Cell motility and secretion / Intracellular trafficking and secretion / Posttranslational modification, protein turnover, chaperones]; Region: FliJ; COG2882 428406011962 flagellar biosynthesis chaperone; Validated; Region: fliJ; PRK05689 428406011963 flagellar protein export ATPase FliI; Region: FliI_clade1; TIGR03496 428406011964 Flagellum-specific ATPase/type III secretory pathway virulence-related protein. This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they...; Region: ATPase_flagellum-secretory_path_III; cd01136 428406011965 Walker A motif/ATP binding site; other site 428406011966 Walker B motif; other site 428406011967 flagellar assembly protein H; Validated; Region: fliH; PRK05687 428406011968 Essential protein Yae1, N terminal; Region: Yae1_N; pfam09811 428406011969 Flagellar assembly protein FliH; Region: FliH; pfam02108 428406011970 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 428406011971 FliG C-terminal domain; Region: FliG_C; pfam01706 428406011972 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 428406011973 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; pfam01514 428406011974 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 428406011975 flagellar hook-basal body protein FliE; Reviewed; Region: fliE; PRK00253 428406011976 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 428406011977 active site 428406011978 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 428406011979 binding surface 428406011980 TPR motif; other site 428406011981 Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis/translation initiation factor 2B, gamma/epsilon subunits (eIF-2Bgamma/eIF-2Bepsilon) [Cell envelope biogenesis, outer membrane / Translation, ribosomal structure...; Region: GCD1; COG1208 428406011982 G1P_cytidylyltransferase catalyzes the production of CDP-D-Glucose; Region: G1P_cytidylyltransferase; cd02524 428406011983 substrate binding site; other site 428406011984 CDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: CDP_GD_SDR_e; cd05252 428406011985 CDP-glucose 4,6-dehydratase; Region: CDP_4_6_dhtase; TIGR02622 428406011986 NAD binding site [chemical binding]; other site 428406011987 homotetramer interface [polypeptide binding]; other site 428406011988 homodimer interface [polypeptide binding]; other site 428406011989 substrate binding site [chemical binding]; other site 428406011990 active site 428406011991 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: dTDP_sugar_isom; pfam00908 428406011992 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 428406011993 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary...; Region: AHBA_syn; cd00616 428406011994 inhibitor-cofactor binding pocket; inhibition site 428406011995 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406011996 catalytic residue [active] 428406011997 Phytanoyl-CoA dioxygenase (PhyH); Region: PhyH; cl17312 428406011998 Methyltransferase domain; Region: Methyltransf_23; pfam13489 428406011999 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 428406012000 S-adenosylmethionine binding site [chemical binding]; other site 428406012001 NNMT/PNMT/TEMT family; Region: NNMT_PNMT_TEMT; pfam01234 428406012002 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 428406012003 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 428406012004 WbqC-like protein family; Region: WbqC; pfam08889 428406012005 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 428406012006 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cd00761 428406012007 active site 428406012008 flagellar hook-basal body protein FliE; Reviewed; Region: fliE; PRK00253 428406012009 peroxiredoxin, Ohr subfamily; Region: organ_hyd_perox; TIGR03561 428406012010 Transcriptional regulators [Transcription]; Region: MarR; COG1846 428406012011 MarR family; Region: MarR; pfam01047 428406012012 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 428406012013 active site 428406012014 TPR repeat; Region: TPR_11; pfam13414 428406012015 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 428406012016 binding surface 428406012017 TPR motif; other site 428406012018 Flagellar protein FliT; Region: FliT; pfam05400 428406012019 Flagellar protein FliS; Region: FliS; cl00654 428406012020 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 428406012021 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 428406012022 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 428406012023 flagellin; Provisional; Region: PRK12802 428406012024 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 428406012025 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 428406012026 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 428406012027 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406012028 active site 428406012029 phosphorylation site [posttranslational modification] 428406012030 intermolecular recognition site; other site 428406012031 dimerization interface [polypeptide binding]; other site 428406012032 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 428406012033 DNA binding residues [nucleotide binding] 428406012034 dimerization interface [polypeptide binding]; other site 428406012035 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 428406012036 PAS domain; Region: PAS_9; pfam13426 428406012037 putative active site [active] 428406012038 heme pocket [chemical binding]; other site 428406012039 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 428406012040 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 428406012041 metal binding site [ion binding]; metal-binding site 428406012042 active site 428406012043 I-site; other site 428406012044 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 428406012045 flagellar basal body-associated protein FliL; Reviewed; Region: fliL; PRK07021 428406012046 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 428406012047 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 428406012048 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 428406012049 Flagellar biogenesis protein [Cell motility and secretion]; Region: FliO; COG3190 428406012050 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK05699 428406012051 flagellar biosynthesis protein FliQ; Validated; Region: fliQ; PRK05700 428406012052 Flagellar biosynthesis pathway, component FliR [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FliR; COG1684 428406012053 Beta-ketoacyl synthase, N-terminal domain; Region: Ketoacyl-synt_2; pfam13723 428406012054 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl17185 428406012055 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 428406012056 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 428406012057 putative acyl-acceptor binding pocket; other site 428406012058 Phosphopantetheine attachment site; Region: PP-binding; cl09936 428406012059 acyl carrier protein; Provisional; Region: PRK05350 428406012060 Predicted membrane protein [Function unknown]; Region: COG4648 428406012061 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 428406012062 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 428406012063 AMP binding site [chemical binding]; other site 428406012064 active site 428406012065 acyl-activating enzyme (AAE) consensus motif; other site 428406012066 CoA binding site [chemical binding]; other site 428406012067 FabA/Z, beta-hydroxyacyl-acyl carrier protein (ACP)-dehydratases: One of several distinct enzyme types of the dissociative, type II, fatty acid synthase system (found in bacteria and plants) required to complete successive cycles of fatty acid elongation; Region: FabA_FabZ; cd00493 428406012068 active site 2 [active] 428406012069 dimer interface [polypeptide binding]; other site 428406012070 active site 1 [active] 428406012071 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 428406012072 DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily; Region: DPM_DPG-synthase_like; cd04179 428406012073 Ligand binding site; other site 428406012074 Putative Catalytic site; other site 428406012075 DXD motif; other site 428406012076 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 428406012077 putative acyl-acceptor binding pocket; other site 428406012078 Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL); Region: PAL-HAL; cd00332 428406012079 active sites [active] 428406012080 tetramer interface [polypeptide binding]; other site 428406012081 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 428406012082 active site 428406012083 Predicted exporter [General function prediction only]; Region: COG4258 428406012084 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK09185 428406012085 Beta-ketoacyl-acyl carrier protein (ACP) synthase (KAS), type I and II. KASs are responsible for the elongation steps in fatty acid biosynthesis. KASIII catalyses the initial condensation and KAS I and II catalyze further elongation steps by Claisen...; Region: KAS_I_II; cd00834 428406012086 dimer interface [polypeptide binding]; other site 428406012087 active site 428406012088 Domain of unknown function, appears to be related to a diverse group of beta-hydroxydecanoyl ACP dehydratases (FabA) and beta-hydroxyacyl ACP dehydratases (FabZ). This group appears to lack the conserved active site histidine of FabA and FabZ; Region: FabA_like; cd01289 428406012089 putative active site 1 [active] 428406012090 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 428406012091 3-oxoacyl-(acyl-carrier-protein) reductase, putative; Region: fabG_rel; TIGR01831 428406012092 NAD(P) binding site [chemical binding]; other site 428406012093 homotetramer interface [polypeptide binding]; other site 428406012094 homodimer interface [polypeptide binding]; other site 428406012095 active site 428406012096 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK09116 428406012097 Beta-ketoacyl-acyl carrier protein (ACP) synthase (KAS), type I and II. KASs are responsible for the elongation steps in fatty acid biosynthesis. KASIII catalyses the initial condensation and KAS I and II catalyze further elongation steps by Claisen...; Region: KAS_I_II; cd00834 428406012098 dimer interface [polypeptide binding]; other site 428406012099 active site 428406012100 Beta-ketoacyl-acyl carrier protein (ACP) synthase (KAS), type I and II. KASs are responsible for the elongation steps in fatty acid biosynthesis. KASIII catalyses the initial condensation and KAS I and II catalyze further elongation steps by Claisen...; Region: KAS_I_II; cd00834 428406012101 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK07967 428406012102 dimer interface [polypeptide binding]; other site 428406012103 active site 428406012104 Methyltransferase domain; Region: Methyltransf_23; pfam13489 428406012105 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 428406012106 S-adenosylmethionine binding site [chemical binding]; other site 428406012107 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 428406012108 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 428406012109 Protein of unknown function (DUF1275); Region: DUF1275; pfam06912 428406012110 flagellar hook-associated protein 3; Region: flagell_flgL; TIGR02550 428406012111 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK06945 428406012112 Rod binding protein [Cell envelope biogenesis, outer membrane / Cell motility and secretion / Posttranslational modification, protein turnover, chaperones]; Region: COG3951 428406012113 flagellar rod assembly protein/muramidase FlgJ; Validated; Region: flgJ; PRK05684 428406012114 Muramidase (flagellum-specific) [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FlgJ; COG1705 428406012115 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 428406012116 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 428406012117 Flagellar basal body L-ring protein [Cell motility and secretion]; Region: FlgH; COG2063 428406012118 Flagellar L-ring protein; Region: FlgH; pfam02107 428406012119 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 428406012120 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 428406012121 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 428406012122 Flagellar basal body rod protein [Cell motility and secretion]; Region: FlgF; COG4787 428406012123 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 428406012124 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 428406012125 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 428406012126 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 428406012127 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 428406012128 flagellar basal body rod modification protein; Reviewed; Region: flgD; PRK06655 428406012129 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 428406012130 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 428406012131 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 428406012132 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 428406012133 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 428406012134 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK05680 428406012135 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK07182 428406012136 SAF-like; Region: SAF_2; pfam13144 428406012137 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 428406012138 Anti-sigma-28 factor, FlgM; Region: FlgM; cl01052 428406012139 FlgN protein; Region: FlgN; pfam05130 428406012140 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 428406012141 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406012142 active site 428406012143 phosphorylation site [posttranslational modification] 428406012144 intermolecular recognition site; other site 428406012145 dimerization interface [polypeptide binding]; other site 428406012146 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 428406012147 DNA binding residues [nucleotide binding] 428406012148 dimerization interface [polypeptide binding]; other site 428406012149 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 428406012150 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 428406012151 trimer interface [polypeptide binding]; other site 428406012152 eyelet of channel; other site 428406012153 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 428406012154 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 428406012155 DNA-binding site [nucleotide binding]; DNA binding site 428406012156 The UbiC transcription regulator-associated (UTRA) domain is a conserved ligand-binding domain; Region: UTRA; smart00866 428406012157 H-NS histone family; Region: Histone_HNS; pfam00816 428406012158 Domain in histone-like proteins of HNS family; Region: HNS; smart00528 428406012159 PAS fold; Region: PAS_4; pfam08448 428406012160 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 428406012161 putative active site [active] 428406012162 heme pocket [chemical binding]; other site 428406012163 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 428406012164 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 428406012165 metal binding site [ion binding]; metal-binding site 428406012166 active site 428406012167 I-site; other site 428406012168 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 428406012169 Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate...; Region: ICL_PEPM; cd00377 428406012170 tetramer interface [polypeptide binding]; other site 428406012171 active site 428406012172 Mg2+/Mn2+ binding site [ion binding]; other site 428406012173 isocitrate lyase; Region: PLN02892 428406012174 GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function; Region: GT_2_like_f; cd04182 428406012175 Ligand binding site; other site 428406012176 metal-binding site 428406012177 peroxiredoxin, Ohr subfamily; Region: organ_hyd_perox; TIGR03561 428406012178 Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]; Region: CoxL; COG1529 428406012179 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 428406012180 Molybdopterin-binding domain of aldehyde dehydrogenase; Region: Ald_Xan_dh_C2; pfam02738 428406012181 Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]; Region: CoxS; COG2080 428406012182 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 428406012183 catalytic loop [active] 428406012184 iron binding site [ion binding]; other site 428406012185 [2Fe-2S] binding domain; Region: Fer2_2; pfam01799 428406012186 2-isopropylmalate synthase; Validated; Region: PRK03739 428406012187 Mycobacterium tuberculosis LeuA3 and related proteins, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_LeuA; cd07942 428406012188 active site 428406012189 catalytic residues [active] 428406012190 metal binding site [ion binding]; metal-binding site 428406012191 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 428406012192 Cysteine-rich 4 helical bundle widely conserved in bacteria; Region: DUF326; cd08026 428406012193 dimerization interface [polypeptide binding]; other site 428406012194 Cd(II)/Pb(II)-responsive transcriptional regulator; Region: CadR-PbrR; TIGR02047 428406012195 Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; Region: HTH_CadR-PbrR; cd04784 428406012196 DNA binding residues [nucleotide binding] 428406012197 dimer interface [polypeptide binding]; other site 428406012198 putative metal binding site [ion binding]; other site 428406012199 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 428406012200 Heavy-metal-associated domain; Region: HMA; pfam00403 428406012201 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 428406012202 Soluble P-type ATPase [General function prediction only]; Region: COG4087 428406012203 Serine hydrolase; Region: Ser_hydrolase; pfam06821 428406012204 Citrate transporter; Region: CitMHS; pfam03600 428406012205 H+/citrate symporter [Energy production and conversion]; Region: CitM; COG2851 428406012206 Protein of unknown function (DUF1446); Region: DUF1446; pfam07287 428406012207 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406012208 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406012209 TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_4; cd08440 428406012210 putative dimerization interface [polypeptide binding]; other site 428406012211 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 428406012212 Ligand Binding Site [chemical binding]; other site 428406012213 SnoaL-like domain; Region: SnoaL_2; pfam12680 428406012214 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 428406012215 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase...; Region: NPD_like; cd04730 428406012216 FMN binding site [chemical binding]; other site 428406012217 substrate binding site [chemical binding]; other site 428406012218 putative catalytic residue [active] 428406012219 Predicted transcriptional regulators [Transcription]; Region: COG1695 428406012220 Transcriptional regulator PadR-like family; Region: PadR; cl17335 428406012221 Virulence activator alpha C-term; Region: Vir_act_alpha_C; pfam10400 428406012222 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 428406012223 Beta-lactamase; Region: Beta-lactamase; pfam00144 428406012224 LysR family transcriptional regulator; Provisional; Region: PRK14997 428406012225 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406012226 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 428406012227 putative effector binding pocket; other site 428406012228 dimerization interface [polypeptide binding]; other site 428406012229 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 428406012230 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase...; Region: NPD_like; cd04730 428406012231 FMN binding site [chemical binding]; other site 428406012232 substrate binding site [chemical binding]; other site 428406012233 putative catalytic residue [active] 428406012234 Protein of unknown function (DUF1470); Region: DUF1470; pfam07336 428406012235 CGNR zinc finger; Region: zf-CGNR; pfam11706 428406012236 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 428406012237 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 428406012238 NAD(P) binding site [chemical binding]; other site 428406012239 active site 428406012240 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406012241 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 428406012242 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_1; cd03137 428406012243 conserved cys residue [active] 428406012244 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 428406012245 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 428406012246 C-terminal, alpha helical domain of an unknown subfamily 5 of Glutathione S-transferases; Region: GST_C_5; cd03196 428406012247 putative N-terminal domain interface [polypeptide binding]; other site 428406012248 putative dimer interface [polypeptide binding]; other site 428406012249 putative substrate binding pocket (H-site) [chemical binding]; other site 428406012250 O-Methyltransferase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3315 428406012251 Leucine carboxyl methyltransferase; Region: LCM; pfam04072 428406012252 Protein of Unknown function (DUF2784); Region: DUF2784; pfam10861 428406012253 Response regulator receiver domain; Region: Response_reg; pfam00072 428406012254 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406012255 active site 428406012256 phosphorylation site [posttranslational modification] 428406012257 intermolecular recognition site; other site 428406012258 dimerization interface [polypeptide binding]; other site 428406012259 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 428406012260 dimerization interface [polypeptide binding]; other site 428406012261 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 428406012262 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cd00088 428406012263 putative binding surface; other site 428406012264 active site 428406012265 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406012266 ATP binding site [chemical binding]; other site 428406012267 Mg2+ binding site [ion binding]; other site 428406012268 G-X-G motif; other site 428406012269 Uncharacterized conserved protein [Function unknown]; Region: COG5649 428406012270 Uncharacterized protein conserved in bacteria (DUF2322); Region: DUF2322; pfam10084 428406012271 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 428406012272 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 428406012273 Bacterial NAD-glutamate dehydrogenase; Region: Bac_GDH; pfam05088 428406012274 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Region: ELFV_dehydrog; smart00839 428406012275 PgaD-like protein; Region: PgaD; pfam13994 428406012276 N-glycosyltransferase; Provisional; Region: PRK11204 428406012277 CESA_like is the cellulose synthase superfamily; Region: CESA_like; cd06423 428406012278 DXD motif; other site 428406012279 poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB; Region: deacetyl_PgaB; TIGR03938 428406012280 N-terminal putative catalytic polysaccharide deacetylase domain of bacterial poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB, and similar proteins; Region: CE4_PgaB_5s; cd10964 428406012281 putative active site [active] 428406012282 putative metal binding site [ion binding]; other site 428406012283 poly-beta-1,6 N-acetyl-D-glucosamine export porin PgaA; Region: PGA_TPR_OMP; TIGR03939 428406012284 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 428406012285 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 428406012286 DNA binding residues [nucleotide binding] 428406012287 dimerization interface [polypeptide binding]; other site 428406012288 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 428406012289 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 428406012290 NAD(P) binding site [chemical binding]; other site 428406012291 active site 428406012292 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 428406012293 KBL_like; this family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to serine palmitoyltransferase (SPT), 5-aminolevulinate synthase (ALAS); Region: KBL_like; cd06454 428406012294 substrate-cofactor binding pocket; other site 428406012295 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406012296 catalytic residue [active] 428406012297 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 428406012298 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 428406012299 non-specific DNA binding site [nucleotide binding]; other site 428406012300 salt bridge; other site 428406012301 sequence-specific DNA binding site [nucleotide binding]; other site 428406012302 Cupin domain; Region: Cupin_2; cl17218 428406012303 DinF and similar proteins, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_DinF_like; cd13136 428406012304 DNA-damage-inducible SOS response protein; Provisional; Region: PRK10367 428406012305 Amino acid transporters [Amino acid transport and metabolism]; Region: PotE; COG0531 428406012306 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406012307 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406012308 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_5; cd08474 428406012309 putative effector binding pocket; other site 428406012310 putative dimerization interface [polypeptide binding]; other site 428406012311 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 428406012312 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 428406012313 active site 428406012314 catalytic tetrad [active] 428406012315 TipAS antibiotic-recognition domain; Region: TipAS; pfam07739 428406012316 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 428406012317 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the GGDEF (DiGuanylate-Cyclase (DGC)) domain. The GGDEF domain has been suggested to be homologous to the adenylyl cyclase catalytic domain and...; Region: CBS_pair_GGDEF_assoc; cd04598 428406012318 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 428406012319 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 428406012320 metal binding site [ion binding]; metal-binding site 428406012321 active site 428406012322 I-site; other site 428406012323 Periplasmic component of the Tol biopolymer transport system [Intracellular trafficking and secretion]; Region: TolB; COG0823 428406012324 F5/8 type C domain; Region: F5_F8_type_C; pfam00754 428406012325 PhoD-like phosphatase; Region: PhoD; pfam09423 428406012326 2-dehydropantoate 2-reductase; Provisional; Region: PRK08229 428406012327 Ketopantoate reductase PanE/ApbA; Region: ApbA; pfam02558 428406012328 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 428406012329 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 428406012330 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 428406012331 ligand binding site [chemical binding]; other site 428406012332 flexible hinge region; other site 428406012333 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 428406012334 chorismate mutase; Provisional; Region: PRK09269 428406012335 Chorismate mutase type II; Region: CM_2; cl00693 428406012336 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 428406012337 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 428406012338 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 428406012339 protein binding site [polypeptide binding]; other site 428406012340 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 428406012341 protein binding site [polypeptide binding]; other site 428406012342 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 428406012343 dimer interface [polypeptide binding]; other site 428406012344 phosphorylation site [posttranslational modification] 428406012345 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406012346 ATP binding site [chemical binding]; other site 428406012347 Mg2+ binding site [ion binding]; other site 428406012348 G-X-G motif; other site 428406012349 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 428406012350 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406012351 active site 428406012352 phosphorylation site [posttranslational modification] 428406012353 intermolecular recognition site; other site 428406012354 dimerization interface [polypeptide binding]; other site 428406012355 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 428406012356 DNA binding site [nucleotide binding] 428406012357 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 428406012358 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 428406012359 RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate...; Region: SIS_RpiR; cd05013 428406012360 putative active site [active] 428406012361 glucokinase; Provisional; Region: glk; PRK00292 428406012362 glucokinase, proteobacterial type; Region: glk; TIGR00749 428406012363 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 428406012364 6PGL: 6-Phosphogluconolactonase (6PGL) subfamily; 6PGL catalyzes the second step of the oxidative phase of the pentose phosphate pathway, the hydrolyzation of 6-phosphoglucono-1,5-lactone (delta form) to 6-phosphogluconate. 6PGL is thought to guard...; Region: 6PGL; cd01400 428406012365 putative active site [active] 428406012366 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 428406012367 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 428406012368 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 428406012369 phosphogluconate dehydratase; Validated; Region: PRK09054 428406012370 6-phosphogluconate dehydratase; Region: edd; TIGR01196 428406012371 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 428406012372 Ligand Binding Site [chemical binding]; other site 428406012373 Protein of unknown function (DUF3293); Region: DUF3293; pfam11697 428406012374 Heme/copper-type cytochrome/quinol oxidases, subunit 2 [Energy production and conversion]; Region: CyoA; COG1622 428406012375 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 428406012376 Cytochrome c; Region: Cytochrom_C; cl11414 428406012377 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 428406012378 Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is...; Region: Heme_Cu_Oxidase_I; cd00919 428406012379 D-pathway; other site 428406012380 Low-spin heme binding site [chemical binding]; other site 428406012381 Putative water exit pathway; other site 428406012382 Binuclear center (active site) [active] 428406012383 K-pathway; other site 428406012384 Putative proton exit pathway; other site 428406012385 Heme-copper oxidase subunit III subfamily. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which couple the reduction of molecular oxygen to water to, proton pumping across the membrane; Region: Heme_Cu_Oxidase_III_2; cd02865 428406012386 Subunit I/III interface [polypeptide binding]; other site 428406012387 Heme-copper oxidase subunit III subfamily. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which couple the reduction of molecular oxygen to water to, proton pumping across the membrane; Region: Heme_Cu_Oxidase_III_1; cd02864 428406012388 Subunit I/III interface [polypeptide binding]; other site 428406012389 Predicted small integral membrane protein [Function unknown]; Region: COG5605 428406012390 hypothetical protein; Provisional; Region: PRK05939 428406012391 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 428406012392 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 428406012393 catalytic residue [active] 428406012394 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 428406012395 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 428406012396 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 428406012397 Walker A/P-loop; other site 428406012398 ATP binding site [chemical binding]; other site 428406012399 Q-loop/lid; other site 428406012400 ABC transporter signature motif; other site 428406012401 Walker B; other site 428406012402 D-loop; other site 428406012403 H-loop/switch region; other site 428406012404 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c; pfam02518 428406012405 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 428406012406 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406012407 active site 428406012408 phosphorylation site [posttranslational modification] 428406012409 intermolecular recognition site; other site 428406012410 dimerization interface [polypeptide binding]; other site 428406012411 This family is most closely related to the GT1 family of glycosyltransferases. The sucrose-phosphate synthases in this family may be unique to plants and photosynthetic bacteria. This enzyme catalyzes the synthesis of sucrose 6-phosphate from fructose...; Region: GT1_Sucrose_synthase; cd03800 428406012412 D-inositol-3-phosphate glycosyltransferase; Region: mycothiol_MshA; TIGR03449 428406012413 putative ADP-binding pocket [chemical binding]; other site 428406012414 short chain dehydrogenase; Provisional; Region: PRK07326 428406012415 classical (c) SDRs; Region: SDR_c; cd05233 428406012416 NAD(P) binding site [chemical binding]; other site 428406012417 active site 428406012418 histidinol-phosphate phosphatase family domain; Region: Histidinol-ppas; TIGR01656 428406012419 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 428406012420 active site 428406012421 motif I; other site 428406012422 motif II; other site 428406012423 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 428406012424 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 428406012425 Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from...; Region: GT1_LPS_heptosyltransferase; cd03789 428406012426 putative active site [active] 428406012427 Predicted carbamoyl transferase, NodU family [Posttranslational modification, protein turnover, chaperones]; Region: COG2192 428406012428 Carbamoyltransferase; Region: CmcH_NodU; pfam02543 428406012429 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 428406012430 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 428406012431 Probable Catalytic site; other site 428406012432 metal-binding site 428406012433 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 428406012434 Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from...; Region: GT1_LPS_heptosyltransferase; cd03789 428406012435 putative active site [active] 428406012436 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 428406012437 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 428406012438 UDP-glucuronate decarboxylase (UGD) and related proteins, extended (e) SDRs; Region: UGD_SDR_e; cd05230 428406012439 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 428406012440 NAD binding site [chemical binding]; other site 428406012441 putative substrate binding site 2 [chemical binding]; other site 428406012442 putative substrate binding site 1 [chemical binding]; other site 428406012443 active site 428406012444 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 428406012445 Subfamily of Glycosyltransferase Family GT2 of unknown function; Region: GT_2_like_c; cd04186 428406012446 Probable Catalytic site; other site 428406012447 metal-binding site 428406012448 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 428406012449 GlcNAc-PI de-N-acetylase; Region: PIG-L; pfam02585 428406012450 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 428406012451 Mn2+ and Fe2+ transporters of the NRAMP family [Inorganic ion transport and metabolism]; Region: MntH; COG1914 428406012452 Natural resistance-associated macrophage protein; Region: Nramp; pfam01566 428406012453 Predicted membrane protein [Function unknown]; Region: COG2323 428406012454 short chain dehydrogenase; Provisional; Region: PRK06701 428406012455 classical (c) SDR, subgroup 1; Region: SDR_c1; cd05355 428406012456 NAD binding site [chemical binding]; other site 428406012457 metal binding site [ion binding]; metal-binding site 428406012458 active site 428406012459 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 428406012460 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 428406012461 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 428406012462 E3 interaction surface; other site 428406012463 lipoyl attachment site [posttranslational modification]; other site 428406012464 HlyD family secretion protein; Region: HlyD_3; pfam13437 428406012465 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 428406012466 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence...; Region: YjgF_YER057c_UK114_like_2; cd06150 428406012467 homotrimer interaction site [polypeptide binding]; other site 428406012468 putative active site [active] 428406012469 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 428406012470 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 428406012471 Uncharacterized conserved protein [Function unknown]; Region: COG5476 428406012472 Protein of unknown function (DUF1485); Region: DUF1485; pfam07364 428406012473 MlrC C-terminus; Region: MlrC_C; pfam07171 428406012474 allantoate amidohydrolase; Reviewed; Region: PRK12893 428406012475 M20 Peptidase beta-alanine synthase, an amidohydrolase; Region: M20_bAS; cd03884 428406012476 active site 428406012477 metal binding site [ion binding]; metal-binding site 428406012478 dimer interface [polypeptide binding]; other site 428406012479 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 428406012480 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 428406012481 Walker A/P-loop; other site 428406012482 ATP binding site [chemical binding]; other site 428406012483 Q-loop/lid; other site 428406012484 ABC transporter signature motif; other site 428406012485 Walker B; other site 428406012486 D-loop; other site 428406012487 H-loop/switch region; other site 428406012488 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 428406012489 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 428406012490 Walker A/P-loop; other site 428406012491 ATP binding site [chemical binding]; other site 428406012492 Q-loop/lid; other site 428406012493 ABC transporter signature motif; other site 428406012494 Walker B; other site 428406012495 D-loop; other site 428406012496 H-loop/switch region; other site 428406012497 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 428406012498 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 428406012499 TM-ABC transporter signature motif; other site 428406012500 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 428406012501 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 428406012502 TM-ABC transporter signature motif; other site 428406012503 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 428406012504 Periplasmic solute-binding domain of active transport proteins that belong to the type I periplasmic binding fold protein family; Region: PBP1_SBP_like_1; cd06327 428406012505 putative ligand binding site [chemical binding]; other site 428406012506 Transcriptional regulators [Transcription]; Region: FadR; COG2186 428406012507 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 428406012508 DNA-binding site [nucleotide binding]; DNA binding site 428406012509 This entry represents the C-terminal ligand binding domain of many members of the GntR family; Region: FCD; smart00895 428406012510 cyanate hydratase; Validated; Region: PRK02866 428406012511 Cyanase C-terminal domain. Cyanase (Cyanate lyase) is responsible for the hydrolysis of cyanate. It catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide. This allows organisms that possess the enzyme to overcome the...; Region: Cyanase_C; cd00559 428406012512 oligomer interface [polypeptide binding]; other site 428406012513 active site 428406012514 Carbohydrate-selective porin [Cell envelope biogenesis, outer membrane]; Region: OprB; COG3659 428406012515 Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily; Region: PBP1_ABC_xylose_binding; cd01538 428406012516 D-xylose transporter subunit XylF; Provisional; Region: xylF; PRK10355 428406012517 putative ligand binding site [chemical binding]; other site 428406012518 xylose transporter ATP-binding subunit; Provisional; Region: PRK13549 428406012519 First domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_I; cd03216 428406012520 Walker A/P-loop; other site 428406012521 ATP binding site [chemical binding]; other site 428406012522 Q-loop/lid; other site 428406012523 ABC transporter signature motif; other site 428406012524 Walker B; other site 428406012525 D-loop; other site 428406012526 H-loop/switch region; other site 428406012527 Second domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_II; cd03215 428406012528 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 428406012529 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 428406012530 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 428406012531 TM-ABC transporter signature motif; other site 428406012532 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 428406012533 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 428406012534 NAD(P) binding site [chemical binding]; other site 428406012535 active site 428406012536 Transcriptional regulators [Transcription]; Region: PurR; COG1609 428406012537 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 428406012538 DNA binding site [nucleotide binding] 428406012539 domain linker motif; other site 428406012540 Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_SalR; cd01545 428406012541 putative dimerization interface [polypeptide binding]; other site 428406012542 putative ligand binding site [chemical binding]; other site 428406012543 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 428406012544 EamA-like transporter family; Region: EamA; pfam00892 428406012545 EamA-like transporter family; Region: EamA; pfam00892 428406012546 Cupin domain; Region: Cupin_2; cl17218 428406012547 Helix-turn-helix domain; Region: HTH_18; pfam12833 428406012548 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 428406012549 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 428406012550 MarR family; Region: MarR; pfam01047 428406012551 Uncharacterized protein, 4-oxalocrotonate tautomerase homolog [General function prediction only]; Region: COG1942 428406012552 active site 1 [active] 428406012553 dimer interface [polypeptide binding]; other site 428406012554 hexamer interface [polypeptide binding]; other site 428406012555 active site 2 [active] 428406012556 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 428406012557 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 428406012558 conserved cys residue [active] 428406012559 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 428406012560 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 428406012561 active site 428406012562 acetyl-CoA acetyltransferase; Validated; Region: PRK08242 428406012563 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 428406012564 dimer interface [polypeptide binding]; other site 428406012565 active site 428406012566 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 428406012567 multifunctional fatty acid oxidation complex subunit alpha; Reviewed; Region: fadJ; PRK11154 428406012568 substrate binding site [chemical binding]; other site 428406012569 oxyanion hole (OAH) forming residues; other site 428406012570 trimer interface [polypeptide binding]; other site 428406012571 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 428406012572 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 428406012573 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 428406012574 Cache domain; Region: Cache_1; pfam02743 428406012575 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 428406012576 PAS domain; Region: PAS_9; pfam13426 428406012577 putative active site [active] 428406012578 heme pocket [chemical binding]; other site 428406012579 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 428406012580 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 428406012581 metal binding site [ion binding]; metal-binding site 428406012582 active site 428406012583 I-site; other site 428406012584 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 428406012585 Domain of unknown function (DUF305); Region: DUF305; cl17794 428406012586 PQQ-dependent catabolism-associated beta-propeller protein; Region: PQQ_ABC_repeats; TIGR03866 428406012587 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 428406012588 40-residue YVTN family beta-propeller repeat; Region: beta_rpt_yvtn; TIGR02276 428406012589 DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]; Region: DnaJ; COG0484 428406012590 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s; Region: DnaJ; cd06257 428406012591 HSP70 interaction site [polypeptide binding]; other site 428406012592 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 428406012593 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 428406012594 HAMP domain; Region: HAMP; pfam00672 428406012595 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 428406012596 PAS domain; Region: PAS_9; pfam13426 428406012597 putative active site [active] 428406012598 heme pocket [chemical binding]; other site 428406012599 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 428406012600 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 428406012601 metal binding site [ion binding]; metal-binding site 428406012602 active site 428406012603 I-site; other site 428406012604 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 428406012605 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406012606 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406012607 The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which involved in the malonate catabolism contains the type 2 periplasmic binding fold; Region: PBP2_MdcR; cd08416 428406012608 putative dimerization interface [polypeptide binding]; other site 428406012609 malonate decarboxylase, alpha subunit; Region: mdcA; TIGR01110 428406012610 Coenzyme A transferase; Region: CoA_trans; cl17247 428406012611 triphosphoribosyl-dephospho-CoA synthase; Validated; Region: PRK01237 428406012612 Malonate decarboxylase delta subunit (MdcD); Region: ACP; cl06082 428406012613 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189 428406012614 malonate decarboxylase, gamma subunit; Region: malonate_gamma; TIGR03134 428406012615 Malonate transporter MadL subunit; Region: MadL; cl04273 428406012616 Malonate/sodium symporter MadM subunit; Region: MadM; cl04274 428406012617 phosphoribosyl-dephospho-CoA transferase; Provisional; Region: PRK01293 428406012618 Phosphoribosyl-dephospho-CoA transferase MdcG; Region: MdcG; pfam10620 428406012619 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 428406012620 malonate decarboxylase, epsilon subunit; Region: malonate_mdcH; TIGR03131 428406012621 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 428406012622 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 428406012623 G1 box; other site 428406012624 putative GEF interaction site [polypeptide binding]; other site 428406012625 GTP/Mg2+ binding site [chemical binding]; other site 428406012626 Switch I region; other site 428406012627 G2 box; other site 428406012628 G3 box; other site 428406012629 Switch II region; other site 428406012630 G4 box; other site 428406012631 G5 box; other site 428406012632 RF3_II: this subfamily represents the domain II of bacterial Release Factor 3 (RF3). Termination of protein synthesis by the ribosome requires two release factor (RF) classes. The class II RF3 is a GTPase that removes class I RFs (RF1 or RF2) from the...; Region: RF3_II; cd03689 428406012633 Ribonuclease BN family enzyme [Replication, recombination, and repair]; Region: Rbn; COG1295 428406012634 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 428406012635 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406012636 active site 428406012637 phosphorylation site [posttranslational modification] 428406012638 intermolecular recognition site; other site 428406012639 dimerization interface [polypeptide binding]; other site 428406012640 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406012641 Walker A motif; other site 428406012642 ATP binding site [chemical binding]; other site 428406012643 Walker B motif; other site 428406012644 arginine finger; other site 428406012645 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 428406012646 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 428406012647 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406012648 Walker A motif; other site 428406012649 ATP binding site [chemical binding]; other site 428406012650 Walker B motif; other site 428406012651 arginine finger; other site 428406012652 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 428406012653 RNA polymerase factor sigma-54; Provisional; Region: PRK12469 428406012654 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 428406012655 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 428406012656 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 428406012657 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can...; Region: GT1_like_2; cd03814 428406012658 Glycosyltransferase Family 4; Region: Glyco_transf_4; pfam13439 428406012659 Predicted deacetylase [General function prediction only]; Region: COG3233 428406012660 Putative catalytic domain of uncharacterized bacterial proteins from the carbohydrate esterase 4 superfamily; Region: CE4_u10; cd11374 428406012661 putative active site [active] 428406012662 putative Zn binding site [ion binding]; other site 428406012663 PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid...; Region: PAP2_like; cd01610 428406012664 active site 428406012665 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 428406012666 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can...; Region: GT1_like_2; cd03814 428406012667 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 428406012668 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 428406012669 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 428406012670 putative active site [active] 428406012671 heme pocket [chemical binding]; other site 428406012672 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 428406012673 putative active site [active] 428406012674 heme pocket [chemical binding]; other site 428406012675 PAS fold; Region: PAS_4; pfam08448 428406012676 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 428406012677 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 428406012678 dimer interface [polypeptide binding]; other site 428406012679 phosphorylation site [posttranslational modification] 428406012680 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406012681 ATP binding site [chemical binding]; other site 428406012682 Mg2+ binding site [ion binding]; other site 428406012683 G-X-G motif; other site 428406012684 Response regulator receiver domain; Region: Response_reg; pfam00072 428406012685 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406012686 active site 428406012687 phosphorylation site [posttranslational modification] 428406012688 intermolecular recognition site; other site 428406012689 dimerization interface [polypeptide binding]; other site 428406012690 Domain of unknown function (DUF4397); Region: DUF4397; pfam14344 428406012691 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 428406012692 DNA binding site [nucleotide binding] 428406012693 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 428406012694 Plasmid encoded RepA protein; Region: RepA_C; pfam04796 428406012695 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 428406012696 DNA-binding site [nucleotide binding]; DNA binding site 428406012697 RNA-binding motif; other site 428406012698 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 428406012699 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 428406012700 P-loop; other site 428406012701 Magnesium ion binding site [ion binding]; other site 428406012702 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 428406012703 ParB-like nuclease domain; Region: ParBc; pfam02195 428406012704 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 428406012705 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 428406012706 active site 428406012707 tetramer interface; other site 428406012708 alpha-ketoglutarate transporter; Provisional; Region: PRK10406 428406012709 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406012710 putative substrate translocation pore; other site 428406012711 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 428406012712 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 428406012713 dimer interface [polypeptide binding]; other site 428406012714 phosphorylation site [posttranslational modification] 428406012715 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406012716 ATP binding site [chemical binding]; other site 428406012717 Mg2+ binding site [ion binding]; other site 428406012718 G-X-G motif; other site 428406012719 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 428406012720 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406012721 active site 428406012722 phosphorylation site [posttranslational modification] 428406012723 intermolecular recognition site; other site 428406012724 dimerization interface [polypeptide binding]; other site 428406012725 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406012726 Walker A motif; other site 428406012727 ATP binding site [chemical binding]; other site 428406012728 Walker B motif; other site 428406012729 arginine finger; other site 428406012730 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 428406012731 Putative membrane peptidase family (DUF2324); Region: DUF2324; cl01810 428406012732 Cache domain; Region: Cache_1; pfam02743 428406012733 FOG: HAMP domain [Signal transduction mechanisms]; Region: ResE; COG2770 428406012734 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 428406012735 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 428406012736 putative active site [active] 428406012737 heme pocket [chemical binding]; other site 428406012738 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 428406012739 putative active site [active] 428406012740 heme pocket [chemical binding]; other site 428406012741 PAS domain; Region: PAS; smart00091 428406012742 PAS fold; Region: PAS_4; pfam08448 428406012743 putative active site [active] 428406012744 heme pocket [chemical binding]; other site 428406012745 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 428406012746 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 428406012747 metal binding site [ion binding]; metal-binding site 428406012748 active site 428406012749 I-site; other site 428406012750 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 428406012751 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 428406012752 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 428406012753 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 428406012754 TM-ABC transporter signature motif; other site 428406012755 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 428406012756 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 428406012757 TM-ABC transporter signature motif; other site 428406012758 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 428406012759 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 428406012760 Walker A/P-loop; other site 428406012761 ATP binding site [chemical binding]; other site 428406012762 Q-loop/lid; other site 428406012763 ABC transporter signature motif; other site 428406012764 Walker B; other site 428406012765 D-loop; other site 428406012766 H-loop/switch region; other site 428406012767 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 428406012768 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 428406012769 Walker A/P-loop; other site 428406012770 ATP binding site [chemical binding]; other site 428406012771 Q-loop/lid; other site 428406012772 ABC transporter signature motif; other site 428406012773 Walker B; other site 428406012774 D-loop; other site 428406012775 H-loop/switch region; other site 428406012776 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406012777 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406012778 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 428406012779 dimerization interface [polypeptide binding]; other site 428406012780 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 428406012781 Quinone oxidoreductase (QOR); Region: QOR2; cd05286 428406012782 NADP binding site [chemical binding]; other site 428406012783 dimer interface [polypeptide binding]; other site 428406012784 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2350 428406012785 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 428406012786 CLC voltage-gated chloride channel. The ClC chloride channels catalyse the selective flow of Cl- ions across cell membranes, thereby regulating electrical excitation in skeletal muscle and the flow of salt and water across epithelial barriers. This...; Region: Voltage_gated_ClC; cd00400 428406012787 Cl- selectivity filter; other site 428406012788 Cl- binding residues [ion binding]; other site 428406012789 pore gating glutamate residue; other site 428406012790 dimer interface [polypeptide binding]; other site 428406012791 Outer membrane receptor for monomeric catechols [Inorganic ion transport and metabolism]; Region: Fiu; COG4774 428406012792 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 428406012793 N-terminal plug; other site 428406012794 ligand-binding site [chemical binding]; other site 428406012795 Fe(II)-dependent oxygenase superfamily protein; Provisional; Region: PRK05467 428406012796 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 428406012797 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 428406012798 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 428406012799 proline iminopeptidase, Neisseria-type subfamily; Region: pro_imino_pep_1; TIGR01249 428406012800 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 428406012801 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 428406012802 substrate binding pocket [chemical binding]; other site 428406012803 membrane-bound complex binding site; other site 428406012804 hinge residues; other site 428406012805 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 428406012806 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 428406012807 dimer interface [polypeptide binding]; other site 428406012808 phosphorylation site [posttranslational modification] 428406012809 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406012810 ATP binding site [chemical binding]; other site 428406012811 Mg2+ binding site [ion binding]; other site 428406012812 G-X-G motif; other site 428406012813 Response regulator receiver domain; Region: Response_reg; pfam00072 428406012814 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406012815 active site 428406012816 phosphorylation site [posttranslational modification] 428406012817 intermolecular recognition site; other site 428406012818 dimerization interface [polypeptide binding]; other site 428406012819 P pilus assembly protein, pilin FimA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimA; COG3539 428406012820 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 428406012821 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 428406012822 Gram-negative pili assembly chaperone, C-terminal domain; Region: Pili_assembly_C; pfam02753 428406012823 P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimD; COG3188 428406012824 PapC N-terminal domain; Region: PapC_N; pfam13954 428406012825 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 428406012826 PapC C-terminal domain; Region: PapC_C; pfam13953 428406012827 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 428406012828 Transposase; Region: HTH_Tnp_1; cl17663 428406012829 putative transposase OrfB; Reviewed; Region: PHA02517 428406012830 HTH-like domain; Region: HTH_21; pfam13276 428406012831 Integrase core domain; Region: rve; pfam00665 428406012832 Integrase core domain; Region: rve_3; pfam13683 428406012833 P pilus assembly protein, pilin FimA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimA; COG3539 428406012834 Beta-lactamase class D [Defense mechanisms]; Region: COG2602 428406012835 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 428406012836 putative DNA binding site [nucleotide binding]; other site 428406012837 dimerization interface [polypeptide binding]; other site 428406012838 Transcriptional regulators [Transcription]; Region: MarR; COG1846 428406012839 putative Zn2+ binding site [ion binding]; other site 428406012840 Major Facilitator Superfamily; Region: MFS_1; pfam07690 428406012841 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cl17904 428406012842 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406012843 Protein of unknown function (DUF3311); Region: DUF3311; pfam11755 428406012844 Na+/proline symporter [Amino acid transport and metabolism / General function prediction only]; Region: PutP; COG0591 428406012845 Na binding site [ion binding]; other site 428406012846 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 428406012847 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 428406012848 Sodium Bile acid symporter family; Region: SBF; cl17470 428406012849 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 428406012850 Low molecular weight phosphatase family; Region: LMWPc; cd00115 428406012851 active site 428406012852 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_20; cd07254 428406012853 putative metal binding site [ion binding]; other site 428406012854 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 428406012855 putative DNA binding site [nucleotide binding]; other site 428406012856 dimerization interface [polypeptide binding]; other site 428406012857 putative Zn2+ binding site [ion binding]; other site 428406012858 recombination associated protein; Reviewed; Region: rdgC; PRK00321 428406012859 Uncharacterized protein conserved in bacteria (DUF2076); Region: DUF2076; pfam09849 428406012860 salicylyl-CoA 5-hydroxylase; Reviewed; Region: PRK08255 428406012861 hypothetical protein; Provisional; Region: PRK07236 428406012862 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 428406012863 Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis. Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing...; Region: OYE_YqiM_FMN; cd02932 428406012864 active site 428406012865 FMN binding site [chemical binding]; other site 428406012866 substrate binding site [chemical binding]; other site 428406012867 homotetramer interface [polypeptide binding]; other site 428406012868 catalytic residue [active] 428406012869 classical (c) SDRs; Region: SDR_c; cd05233 428406012870 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 428406012871 NAD(P) binding site [chemical binding]; other site 428406012872 active site 428406012873 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 428406012874 MarR family; Region: MarR; pfam01047 428406012875 MarR family; Region: MarR_2; cl17246 428406012876 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 428406012877 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 428406012878 substrate binding site [chemical binding]; other site 428406012879 oxyanion hole (OAH) forming residues; other site 428406012880 trimer interface [polypeptide binding]; other site 428406012881 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 428406012882 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 428406012883 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 428406012884 active site 428406012885 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 428406012886 Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases [Lipid metabolism]; Region: Acs; COG0365 428406012887 acyl-activating enzyme (AAE) consensus motif; other site 428406012888 AMP binding site [chemical binding]; other site 428406012889 active site 428406012890 CoA binding site [chemical binding]; other site 428406012891 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 428406012892 active site 428406012893 YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no...; Region: YjgF_YER057c_UK114_family; cd00448 428406012894 homotrimer interaction site [polypeptide binding]; other site 428406012895 putative active site [active] 428406012896 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 428406012897 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 428406012898 dimerization interface [polypeptide binding]; other site 428406012899 putative DNA binding site [nucleotide binding]; other site 428406012900 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 428406012901 putative Zn2+ binding site [ion binding]; other site 428406012902 Uncharacterized homolog of gamma-carboxymuconolactone decarboxylase subunit [Function unknown]; Region: COG0599 428406012903 Prokaryotic protein of unknown function (DUF849); Region: DUF849; pfam05853 428406012904 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 428406012905 classical (c) SDRs; Region: SDR_c; cd05233 428406012906 NAD(P) binding site [chemical binding]; other site 428406012907 active site 428406012908 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406012909 D-galactonate transporter; Region: 2A0114; TIGR00893 428406012910 putative substrate translocation pore; other site 428406012911 alpha-ketoglutarate transporter; Provisional; Region: PRK10406 428406012912 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406012913 putative substrate translocation pore; other site 428406012914 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406012915 putative substrate translocation pore; other site 428406012916 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 428406012917 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 428406012918 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 428406012919 DNA-binding site [nucleotide binding]; DNA binding site 428406012920 UTRA domain; Region: UTRA; pfam07702 428406012921 Predicted transcriptional regulators [Transcription]; Region: COG1733 428406012922 HxlR-like helix-turn-helix; Region: HxlR; pfam01638 428406012923 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 428406012924 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 428406012925 Coenzyme A binding pocket [chemical binding]; other site 428406012926 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_18; cd08357 428406012927 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 428406012928 putative metal binding site [ion binding]; other site 428406012929 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406012930 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406012931 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_2; cd08427 428406012932 putative dimerization interface [polypeptide binding]; other site 428406012933 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 428406012934 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 428406012935 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406012936 Major Facilitator Superfamily; Region: MFS_1; pfam07690 428406012937 putative substrate translocation pore; other site 428406012938 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 428406012939 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 428406012940 MoxR-like ATPases [General function prediction only]; Region: COG0714 428406012941 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406012942 Walker A motif; other site 428406012943 ATP binding site [chemical binding]; other site 428406012944 Walker B motif; other site 428406012945 arginine finger; other site 428406012946 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 428406012947 Protein of unknown function DUF58; Region: DUF58; pfam01882 428406012948 Domain of unknown function (DUF3488); Region: DUF3488; pfam11992 428406012949 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 428406012950 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 428406012951 probable AcnD-accessory protein PrpF; Region: prpF; TIGR02334 428406012952 2-methylisocitrate dehydratase, Fe/S-dependent; Region: 2met_isocit_dHY; TIGR02333 428406012953 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 428406012954 substrate binding site [chemical binding]; other site 428406012955 ligand binding site [chemical binding]; other site 428406012956 Aconitase swivel domain. Aconitase (aconitate hydratase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. This is the aconitase swivel domain, which undergoes swivelling conformational change in the enzyme...; Region: Aconitase_swivel; cl00215 428406012957 substrate binding site [chemical binding]; other site 428406012958 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 428406012959 Subgroup of Escherichia coli (Ec) 2-methylcitrate synthase (2MCS)_like. 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and oxalacetate (OAA) to form 2-methylcitrate and coenzyme A (CoA) during propionate metabolism. Citrate synthase (CS)...; Region: Ec2MCS_like_1; cd06117 428406012960 dimer interface [polypeptide binding]; other site 428406012961 active site 428406012962 citrylCoA binding site [chemical binding]; other site 428406012963 oxalacetate/citrate binding site [chemical binding]; other site 428406012964 coenzyme A binding site [chemical binding]; other site 428406012965 catalytic triad [active] 428406012966 Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate...; Region: ICL_PEPM; cd00377 428406012967 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 428406012968 tetramer interface [polypeptide binding]; other site 428406012969 active site 428406012970 Mg2+/Mn2+ binding site [ion binding]; other site 428406012971 Propionate catabolism activator; Region: PrpR_N; pfam06506 428406012972 Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]; Region: RocR; COG3829 428406012973 PAS domain; Region: PAS; smart00091 428406012974 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406012975 Walker A motif; other site 428406012976 ATP binding site [chemical binding]; other site 428406012977 Walker B motif; other site 428406012978 arginine finger; other site 428406012979 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 428406012980 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 428406012981 Zn2+ binding site [ion binding]; other site 428406012982 Mg2+ binding site [ion binding]; other site 428406012983 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 428406012984 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 428406012985 metal binding site [ion binding]; metal-binding site 428406012986 active site 428406012987 I-site; other site 428406012988 Isochorismatase family; Region: Isochorismatase; pfam00857 428406012989 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cd00431 428406012990 catalytic triad [active] 428406012991 conserved cis-peptide bond; other site 428406012992 ClC chloride channel family. These protein sequences, closely related to the ClC Eric family, are putative halogen ion (Cl-, Br- and I-) transport proteins found in eubacteria. They belong to the ClC superfamily of chloride ion channels, which share a...; Region: EriC_like; cd01034 428406012993 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 428406012994 putative ion selectivity filter; other site 428406012995 putative pore gating glutamate residue; other site 428406012996 putative H+/Cl- coupling transport residue; other site 428406012997 Escherichia coli PhnB and similar proteins; the E. coli phnB gene is found next to an operon involved in the cleavage of carbon-phosphorus bonds in unactivated alkylphosphonates; Region: PhnB_like; cd06588 428406012998 dimer interface [polypeptide binding]; other site 428406012999 Uncharacterized protein conserved in bacteria (DUF2242); Region: DUF2242; pfam10001 428406013000 Restriction endonuclease; Region: Mrr_cat; pfam04471 428406013001 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 428406013002 DEAD-like helicases superfamily; Region: DEXDc; smart00487 428406013003 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 428406013004 ATP binding site [chemical binding]; other site 428406013005 putative Mg++ binding site [ion binding]; other site 428406013006 Predicted membrane protein [Function unknown]; Region: COG1289 428406013007 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 428406013008 Phosphotransferase system cellobiose-specific component IIC [Carbohydrate transport and metabolism]; Region: CelB; COG1455 428406013009 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 428406013010 putative DMT superfamily transporter inner membrane protein; Provisional; Region: PRK11272 428406013011 EamA-like transporter family; Region: EamA; pfam00892 428406013012 EamA-like transporter family; Region: EamA; pfam00892 428406013013 enoyl-CoA hydratase; Validated; Region: PRK08139 428406013014 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 428406013015 substrate binding site [chemical binding]; other site 428406013016 oxyanion hole (OAH) forming residues; other site 428406013017 trimer interface [polypeptide binding]; other site 428406013018 haloalkane dehalogenase; Provisional; Region: PRK00870 428406013019 Predicted transcriptional regulators [Transcription]; Region: COG1733 428406013020 HxlR-like helix-turn-helix; Region: HxlR; pfam01638 428406013021 Protein of unknown function DUF72; Region: DUF72; cl00777 428406013022 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 428406013023 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_1; cd03137 428406013024 conserved cys residue [active] 428406013025 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 428406013026 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_2; cd03139 428406013027 Putative intracellular protease/amidase [General function prediction only]; Region: ThiJ; COG0693 428406013028 conserved cys residue [active] 428406013029 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Validated; Region: PRK05584 428406013030 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Region: MTA/SAH-Nsdase; TIGR01704 428406013031 Protein of unknown function (DUF1311); Region: DUF1311; pfam07007 428406013032 Cytochrome c; Region: Cytochrom_C; cl11414 428406013033 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 428406013034 Cytochrome c; Region: Cytochrom_C; pfam00034 428406013035 Protein of unknown function (DUF1697); Region: DUF1697; pfam08002 428406013036 mercuric reductase; Validated; Region: PRK06370 428406013037 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 428406013038 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 428406013039 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 428406013040 Ca2+/H+ antiporter [Inorganic ion transport and metabolism]; Region: ChaA; COG0387 428406013041 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 428406013042 Spherulation-specific family 4; Region: Spherulin4; pfam12138 428406013043 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406013044 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406013045 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold; Region: PBP2_DntR_like_3; cd08461 428406013046 putative substrate binding pocket [chemical binding]; other site 428406013047 putative dimerization interface [polypeptide binding]; other site 428406013048 Putative NADPH-quinone reductase (modulator of drug activity B) [General function prediction only]; Region: MdaB; COG2249 428406013049 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 428406013050 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 428406013051 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 428406013052 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 428406013053 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis; Region: BFIT_BACH; cd03442 428406013054 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 428406013055 Putative multicopper oxidases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: SufI; COG2132 428406013056 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 428406013057 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 428406013058 Uncharacterized copper-binding protein [Inorganic ion transport and metabolism]; Region: COG4454 428406013059 Copper binding periplasmic protein CusF; Region: CusF_Ec; pfam11604 428406013060 Putative lipopolysaccharide-modifying enzyme; Region: CAP10; smart00672 428406013061 Phytanoyl-CoA dioxygenase (PhyH); Region: PhyH; cl17312 428406013062 Uncharacterized protein conserved in bacteria (DUF2141); Region: DUF2141; pfam09912 428406013063 Lignostilbene-alpha,beta-dioxygenase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3670 428406013064 Retinal pigment epithelial membrane protein; Region: RPE65; pfam03055 428406013065 hypothetical protein; Provisional; Region: PRK08201 428406013066 Uncharacterized M20 Dipeptidases; Region: M20_dipept_like_1; cd05678 428406013067 putative metal binding site [ion binding]; other site 428406013068 putative dimer interface [polypeptide binding]; other site 428406013069 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406013070 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406013071 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 428406013072 dimerization interface [polypeptide binding]; other site 428406013073 AMP nucleosidase; Provisional; Region: PRK08292 428406013074 Bacterial AMP nucleoside phosphorylase N-terminus; Region: AMNp_N; pfam10423 428406013075 Nucleoside phosphorylase [Nucleotide transport and metabolism]; Region: Pfs; COG0775 428406013076 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406013077 dimer interface [polypeptide binding]; other site 428406013078 conserved gate region; other site 428406013079 putative PBP binding loops; other site 428406013080 ABC-ATPase subunit interface; other site 428406013081 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 428406013082 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406013083 ABC-ATPase subunit interface; other site 428406013084 putative PBP binding loops; other site 428406013085 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 428406013086 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 428406013087 substrate binding pocket [chemical binding]; other site 428406013088 membrane-bound complex binding site; other site 428406013089 hinge residues; other site 428406013090 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 428406013091 active site 428406013092 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 428406013093 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 428406013094 dimer interface [polypeptide binding]; other site 428406013095 phosphorylation site [posttranslational modification] 428406013096 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406013097 ATP binding site [chemical binding]; other site 428406013098 Mg2+ binding site [ion binding]; other site 428406013099 G-X-G motif; other site 428406013100 Methyltransferase domain; Region: Methyltransf_31; pfam13847 428406013101 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 428406013102 S-adenosylmethionine binding site [chemical binding]; other site 428406013103 Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]; Region: COG3618 428406013104 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 428406013105 active site 428406013106 benzoate transport; Region: 2A0115; TIGR00895 428406013107 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406013108 putative substrate translocation pore; other site 428406013109 Maltooligosyl trehalose synthase [Carbohydrate transport and metabolism]; Region: TreY; COG3280 428406013110 Alpha amylase catalytic domain family; Region: AmyAc_family; cl07893 428406013111 Alpha amylase catalytic domain found in maltooligosyl trehalose synthase (MTSase); Region: AmyAc_MTSase; cd11336 428406013112 active site 428406013113 catalytic site [active] 428406013114 4-alpha-glucanotransferase; Provisional; Region: malQ; PRK11052 428406013115 4-alpha-glucanotransferase [Carbohydrate transport and metabolism]; Region: MalQ; COG1640 428406013116 N-terminal Early set domain associated with the catalytic domain of Maltooligosyl trehalose trehalohydrolase (also called Glycosyltrehalose trehalohydrolase) and similar proteins; Region: E_set_MTHase_like_N; cd02853 428406013117 malto-oligosyltrehalose trehalohydrolase; Region: trehalose_TreZ; TIGR02402 428406013118 Alpha amylase catalytic domain found in Glycosyltrehalose trehalohydrolase (also called Maltooligosyl trehalose Trehalohydrolase); Region: AmyAc_GTHase; cd11325 428406013119 catalytic site [active] 428406013120 active site 428406013121 Domain of unknown function (DUF3459); Region: DUF3459; pfam11941 428406013122 glycogen debranching enzyme GlgX; Region: glgX_debranch; TIGR02100 428406013123 N-terminal Early set domain associated with the catalytic domain of Glycogen debranching enzyme and bacterial isoamylase (also called glycogen 6-glucanohydrolase); Region: E_set_GDE_Isoamylase_N; cd02856 428406013124 Alpha amylase catalytic domain found in glycogen debranching enzymes; Region: AmyAc_Glg_debranch; cd11326 428406013125 active site 428406013126 catalytic site [active] 428406013127 glycogen branching enzyme; Provisional; Region: PRK05402 428406013128 N-terminal Early set domain associated with the catalytic domain of prokaryotic glycogen branching enzyme; Region: E_set_GBE_prok_N; cd02855 428406013129 Alpha amylase catalytic domain found in the Glycogen branching enzyme (also called 1,4-alpha-glucan branching enzyme); Region: AmyAc_Glg_BE; cd11322 428406013130 active site 428406013131 catalytic site [active] 428406013132 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; pfam02806 428406013133 trehalose synthase; Region: treS_nterm; TIGR02456 428406013134 Alpha amylase catalytic domain found in Trehalose synthetase; Region: AmyAc_TreS; cd11334 428406013135 active site 428406013136 catalytic site [active] 428406013137 trehalose synthase-fused probable maltokinase; Region: TreS_Cterm; TIGR02457 428406013138 Uncharacterized protein, probably involved in trehalose biosynthesis [Carbohydrate transport and metabolism]; Region: Ble; COG3281 428406013139 Alpha amylase catalytic domain family; Region: AmyAc_family; cl07893 428406013140 active site 428406013141 Domain of unknown function (DUF3416); Region: DUF3416; pfam11896 428406013142 Alpha amylase catalytic domain found in GlgE-like proteins; Region: AmyAc_GlgE_like; cd11344 428406013143 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 428406013144 active site 428406013145 homodimer interface [polypeptide binding]; other site 428406013146 catalytic site [active] 428406013147 acceptor binding site [chemical binding]; other site 428406013148 glycogen synthase; Provisional; Region: glgA; PRK00654 428406013149 This family is most closely related to the GT1 family of glycosyltransferases. Glycogen synthase catalyzes the formation and elongation of the alpha-1,4-glucose backbone using ADP-glucose, the second and key step of glycogen biosynthesis. This family...; Region: GT1_Glycogen_synthase_DULL1_like; cd03791 428406013150 ADP-binding pocket [chemical binding]; other site 428406013151 homodimer interface [polypeptide binding]; other site 428406013152 peroxiredoxin; Region: AhpC; TIGR03137 428406013153 Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic hydroperoxides; Region: PRX_Typ2cys; cd03015 428406013154 dimer interface [polypeptide binding]; other site 428406013155 decamer (pentamer of dimers) interface [polypeptide binding]; other site 428406013156 catalytic triad [active] 428406013157 peroxidatic and resolving cysteines [active] 428406013158 alkyl hydroperoxide reductase subunit F; Provisional; Region: PRK15317 428406013159 Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) family, N-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which in turn catalyzes the reduction...; Region: AhpF_NTD_N; cd02974 428406013160 catalytic residue [active] 428406013161 TRX-GRX-like family, Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) subfamily, C-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which then...; Region: AhpF_NTD_C; cd03026 428406013162 catalytic residues [active] 428406013163 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 428406013164 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 428406013165 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406013166 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406013167 LysR substrate binding domain; Region: LysR_substrate; pfam03466 428406013168 dimerization interface [polypeptide binding]; other site 428406013169 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 428406013170 metal binding site 2 [ion binding]; metal-binding site 428406013171 putative DNA binding helix; other site 428406013172 metal binding site 1 [ion binding]; metal-binding site 428406013173 dimer interface [polypeptide binding]; other site 428406013174 structural Zn2+ binding site [ion binding]; other site 428406013175 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 428406013176 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 428406013177 G1 box; other site 428406013178 GTP/Mg2+ binding site [chemical binding]; other site 428406013179 Switch I region; other site 428406013180 G2 box; other site 428406013181 G3 box; other site 428406013182 Switch II region; other site 428406013183 G4 box; other site 428406013184 G5 box; other site 428406013185 Nucleoside recognition; Region: Gate; pfam07670 428406013186 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 428406013187 Nucleoside recognition; Region: Gate; pfam07670 428406013188 Fe2+ transport system protein A [Inorganic ion transport and metabolism]; Region: FeoA; COG1918 428406013189 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 428406013190 dimerization interface [polypeptide binding]; other site 428406013191 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 428406013192 PAS fold; Region: PAS_3; pfam08447 428406013193 heme pocket [chemical binding]; other site 428406013194 putative active site [active] 428406013195 PAS domain; Region: PAS_9; pfam13426 428406013196 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 428406013197 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 428406013198 PAS domain; Region: PAS_9; pfam13426 428406013199 putative active site [active] 428406013200 heme pocket [chemical binding]; other site 428406013201 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 428406013202 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 428406013203 metal binding site [ion binding]; metal-binding site 428406013204 active site 428406013205 I-site; other site 428406013206 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 428406013207 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 428406013208 PAS fold; Region: PAS_3; pfam08447 428406013209 putative active site [active] 428406013210 heme pocket [chemical binding]; other site 428406013211 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 428406013212 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 428406013213 dimer interface [polypeptide binding]; other site 428406013214 putative CheW interface [polypeptide binding]; other site 428406013215 Siderophore-interacting protein [Inorganic ion transport and metabolism]; Region: ViuB; COG2375 428406013216 Siderophore interacting proteins share the domain structure of the ferredoxin reductase like family. Siderophores are produced in various bacteria (and some plants) to extract iron from hosts. Binding constants are high, so iron can be pilfered from...; Region: siderophore_interacting; cd06193 428406013217 FAD binding pocket [chemical binding]; other site 428406013218 FAD binding motif [chemical binding]; other site 428406013219 phosphate binding motif [ion binding]; other site 428406013220 NAD binding pocket [chemical binding]; other site 428406013221 Predicted transcriptional regulators [Transcription]; Region: COG1695 428406013222 Transcriptional regulator PadR-like family; Region: PadR; pfam03551 428406013223 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 428406013224 MarR family; Region: MarR_2; pfam12802 428406013225 Uncharacterized conserved protein [Function unknown]; Region: COG2128 428406013226 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 428406013227 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 428406013228 Coenzyme A binding pocket [chemical binding]; other site 428406013229 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 428406013230 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 428406013231 Pyroglutamyl peptidase (PGP) type I, also known as pyrrolidone carboxyl peptidase (pcp) type I: Enzymes responsible for cleaving pyroglutamate (pGlu) from the N-terminal end of specialized proteins. The N-terminal pGlu protects these proteins from...; Region: Peptidase_C15; cd00501 428406013232 putative substrate binding pocket [chemical binding]; other site 428406013233 AC domain interface; other site 428406013234 catalytic triad [active] 428406013235 AB domain interface; other site 428406013236 interchain disulfide; other site 428406013237 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 428406013238 MarR family; Region: MarR_2; pfam12802 428406013239 Beta-lactamase class D [Defense mechanisms]; Region: COG2602 428406013240 Periplasmic glucans biosynthesis protein [Inorganic ion transport and metabolism]; Region: MdoG; COG3131 428406013241 glucan biosynthesis protein D; Provisional; Region: mdoD; PRK13273 428406013242 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 428406013243 Beta-lactamase; Region: Beta-lactamase; pfam00144 428406013244 Domain of unknown function (DUF1854); Region: DUF1854; pfam08909 428406013245 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 428406013246 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 428406013247 ATP-binding cassette domain of a mitochondrial protein MTABC3 and related proteins; Region: ABC_MTABC3_MDL1_MDL2; cd03249 428406013248 Walker A/P-loop; other site 428406013249 ATP binding site [chemical binding]; other site 428406013250 Q-loop/lid; other site 428406013251 ABC transporter signature motif; other site 428406013252 Walker B; other site 428406013253 D-loop; other site 428406013254 H-loop/switch region; other site 428406013255 cyanophycin synthetase; Provisional; Region: PRK14016 428406013256 ATP-grasp domain; Region: ATP-grasp_4; cl17255 428406013257 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 428406013258 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 428406013259 cyanophycin synthetase; Provisional; Region: PRK14016 428406013260 ATP-grasp domain; Region: ATP-grasp_4; pfam13535 428406013261 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 428406013262 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 428406013263 Conserved protein/domain typically associated with flavoprotein oxygenases, DIM6/NTAB family [General function prediction only]; Region: COG1853 428406013264 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 428406013265 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 428406013266 Coenzyme A binding pocket [chemical binding]; other site 428406013267 Arabinose-binding domain of AraC transcription regulator, N-term; Region: Arabinose_bd; pfam12625 428406013268 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 428406013269 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 428406013270 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 428406013271 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 428406013272 active site 428406013273 Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases [Lipid metabolism]; Region: Acs; COG0365 428406013274 Uncharacterized subfamily of medium-chain acyl-CoA synthetase (MACS); Region: MACS_like_1; cd05974 428406013275 active site 428406013276 acyl-activating enzyme (AAE) consensus motif; other site 428406013277 putative CoA binding site [chemical binding]; other site 428406013278 AMP binding site [chemical binding]; other site 428406013279 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 428406013280 methylmalonic acid semialdehyde dehydrogenase; Region: MMSDH; TIGR01722 428406013281 tetrameric interface [polypeptide binding]; other site 428406013282 NAD binding site [chemical binding]; other site 428406013283 catalytic residues [active] 428406013284 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 428406013285 3-hydroxyisobutyrate dehydrogenase; Region: HIBADH; TIGR01692 428406013286 enoyl-CoA hydratase; Provisional; Region: PRK09076 428406013287 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 428406013288 substrate binding site [chemical binding]; other site 428406013289 oxyanion hole (OAH) forming residues; other site 428406013290 trimer interface [polypeptide binding]; other site 428406013291 3-hydroxyisobutyryl-CoA hydrolase; Provisional; Region: PRK05617 428406013292 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 428406013293 substrate binding site [chemical binding]; other site 428406013294 oxyanion hole (OAH) forming residues; other site 428406013295 trimer interface [polypeptide binding]; other site 428406013296 2-enoyl-CoA Hydratase C-terminal region; Region: ECH_C; pfam13766 428406013297 Putative catalytic domain, repeat 1, of uncharacterized hypothetical proteins similar to Nuc, an endonuclease from Salmonella typhimurium; Region: PLDc_Nuc_like_unchar1_1; cd09172 428406013298 PLD-like domain; Region: PLDc_2; pfam13091 428406013299 putative active site [active] 428406013300 catalytic site [active] 428406013301 Putative catalytic domain, repeat 2, of uncharacterized hypothetical proteins similar to Nuc, an endonuclease from Salmonella typhimurium; Region: PLDc_Nuc_like_unchar1_2; cd09173 428406013302 PLD-like domain; Region: PLDc_2; pfam13091 428406013303 putative active site [active] 428406013304 catalytic site [active] 428406013305 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK08276 428406013306 Bacterial Bile acid CoA ligases and similar proteins; Region: BACL_like; cd05929 428406013307 acyl-activating enzyme (AAE) consensus motif; other site 428406013308 putative AMP binding site [chemical binding]; other site 428406013309 putative active site [active] 428406013310 putative CoA binding site [chemical binding]; other site 428406013311 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 428406013312 ClC sycA-like chloride channel proteins. This ClC family presents in bacteria, where it facilitates acid resistance in acidic soil. Mutation of this gene (sycA) in Rhizobium tropici CIAT899 causes serious deficiencies in nodule development, nodulation...; Region: ClC_sycA_like; cd03682 428406013313 putative Cl- selectivity filter; other site 428406013314 putative pore gating glutamate residue; other site 428406013315 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 428406013316 Transcriptional regulator [Transcription]; Region: IclR; COG1414 428406013317 hypothetical protein; Validated; Region: PRK06201 428406013318 Demethylmenaquinone methyltransferase [Coenzyme metabolism]; Region: MenG; COG0684 428406013319 Phosphoglycerate dehydrogenase and related dehydrogenases [Amino acid transport and metabolism]; Region: SerA; COG0111 428406013320 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_4; cd12173 428406013321 ligand binding site [chemical binding]; other site 428406013322 NAD binding site [chemical binding]; other site 428406013323 dimerization interface [polypeptide binding]; other site 428406013324 catalytic site [active] 428406013325 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 428406013326 Strictosidine synthase; Region: Str_synth; pfam03088 428406013327 4-hydroxyphenylacetate permease; Region: HpaX; TIGR02332 428406013328 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406013329 putative substrate translocation pore; other site 428406013330 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406013331 putative substrate translocation pore; other site 428406013332 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 428406013333 active site 428406013334 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 428406013335 active site 428406013336 catalytic residues [active] 428406013337 Proprotein convertase P-domain; Region: P_proprotein; pfam01483 428406013338 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 428406013339 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 428406013340 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 428406013341 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 428406013342 metal binding site [ion binding]; metal-binding site 428406013343 active site 428406013344 I-site; other site 428406013345 Predicted integral membrane protein [Function unknown]; Region: COG0392 428406013346 Uncharacterized conserved protein [Function unknown]; Region: COG2898 428406013347 Uncharacterized conserved protein (DUF2156); Region: DUF2156; pfam09924 428406013348 Type IV secretory pathway, VirJ component [Intracellular trafficking and secretion]; Region: VirJ; COG3946 428406013349 Bacterial virulence protein (VirJ); Region: VirJ; pfam06057 428406013350 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 428406013351 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 428406013352 Sulfate transporter family; Region: Sulfate_transp; pfam00916 428406013353 Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function; Region: STAS_SulP_like_sulfate_transporter; cd07042 428406013354 Protein of unknown function (DUF3761); Region: DUF3761; pfam12587 428406013355 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11074 428406013356 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406013357 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 428406013358 dimerization interface [polypeptide binding]; other site 428406013359 short chain dehydrogenase; Provisional; Region: PRK06500 428406013360 classical (c) SDRs; Region: SDR_c; cd05233 428406013361 NAD(P) binding site [chemical binding]; other site 428406013362 active site 428406013363 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2964 428406013364 YheO-like PAS domain; Region: PAS_6; pfam08348 428406013365 HTH domain; Region: HTH_22; pfam13309 428406013366 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 428406013367 Threonine dehydratase: The first step in amino acid degradation is the removal of nitrogen. Although the nitrogen atoms of most amino acids are transferred to alpha-ketoglutarate before removal, the alpha-amino group of threonine can be directly...; Region: Thr-dehyd; cd01562 428406013368 tetramer interface [polypeptide binding]; other site 428406013369 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406013370 catalytic residue [active] 428406013371 YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no...; Region: YjgF_YER057c_UK114_family; cd00448 428406013372 homotrimer interaction site [polypeptide binding]; other site 428406013373 putative active site [active] 428406013374 Flagellar protein YcgR; Region: YcgR_2; pfam12945 428406013375 PilZ domain; Region: PilZ; pfam07238 428406013376 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406013377 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406013378 LysR substrate binding domain; Region: LysR_substrate; pfam03466 428406013379 dimerization interface [polypeptide binding]; other site 428406013380 Predicted membrane protein [Function unknown]; Region: COG4125 428406013381 Bacterial Transmembrane Pair family; Region: BTP; pfam05232 428406013382 Bacterial Transmembrane Pair family; Region: BTP; pfam05232 428406013383 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 428406013384 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 428406013385 DNA binding residues [nucleotide binding] 428406013386 dimerization interface [polypeptide binding]; other site 428406013387 Protein of unknown function (DUF1059); Region: DUF1059; cl02284 428406013388 Protein of unknown function (DUF3455); Region: DUF3455; pfam11937 428406013389 Protein of unknown function, DUF488; Region: DUF488; cl01246 428406013390 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 428406013391 NMT1-like family; Region: NMT1_2; pfam13379 428406013392 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 428406013393 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406013394 putative PBP binding loops; other site 428406013395 ABC-ATPase subunit interface; other site 428406013396 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 428406013397 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 428406013398 Walker A/P-loop; other site 428406013399 ATP binding site [chemical binding]; other site 428406013400 Q-loop/lid; other site 428406013401 ABC transporter signature motif; other site 428406013402 Walker B; other site 428406013403 D-loop; other site 428406013404 H-loop/switch region; other site 428406013405 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 428406013406 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 428406013407 DNA-binding site [nucleotide binding]; DNA binding site 428406013408 UTRA domain; Region: UTRA; pfam07702 428406013409 Nitric oxide reductase large subunit [Inorganic ion transport and metabolism]; Region: NorB; COG3256 428406013410 Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is...; Region: Heme_Cu_Oxidase_I; cl00275 428406013411 Binuclear center (active site) [active] 428406013412 K-pathway; other site 428406013413 Putative proton exit pathway; other site 428406013414 Putative water exit pathway; other site 428406013415 Uncharacterized conserved protein [Function unknown]; Region: COG4309 428406013416 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 428406013417 Multicopper oxidase; Region: Cu-oxidase; pfam00394 428406013418 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 428406013419 Cytochrome c; Region: Cytochrom_C; pfam00034 428406013420 Uncharacterized conserved protein [Function unknown]; Region: COG1262 428406013421 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 428406013422 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 428406013423 SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c...; Region: SCO; cd02968 428406013424 Cu(I) binding site [ion binding]; other site 428406013425 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]; Region: MhpD; COG0179 428406013426 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 428406013427 Transcriptional regulators [Transcription]; Region: GntR; COG1802 428406013428 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 428406013429 DNA-binding site [nucleotide binding]; DNA binding site 428406013430 FCD domain; Region: FCD; pfam07729 428406013431 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406013432 D-galactonate transporter; Region: 2A0114; TIGR00893 428406013433 putative substrate translocation pore; other site 428406013434 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 428406013435 dihydropyrimidinase; Provisional; Region: PRK13404 428406013436 D-hydantoinases (D-HYD) also called dihydropyrimidases (DHPase) and related proteins; DHPases are a family of enzymes that catalyze the reversible hydrolytic ring opening of the amide bond in five- or six-membered cyclic diamides, like dihydropyrimidine...; Region: D-HYD; cd01314 428406013437 tetramer interface [polypeptide binding]; other site 428406013438 active site 428406013439 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 428406013440 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 428406013441 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 428406013442 ligand binding site [chemical binding]; other site 428406013443 flexible hinge region; other site 428406013444 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 428406013445 2-hydroxychromene-2-carboxylate isomerase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: NahD; COG3917 428406013446 DsbA family, 2-hydroxychromene-2-carboxylate (HCCA) isomerase subfamily; HCCA isomerase is a glutathione (GSH) dependent enzyme involved in the naphthalene catabolic pathway. It converts HCCA, a hemiketal formed spontaneously after ring cleavage of 1; Region: DsbA_HCCA_Iso; cd03022 428406013447 putative catalytic residue [active] 428406013448 Coenzyme A transferase; Region: CoA_trans; cl17247 428406013449 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 428406013450 Kef-type K+ transport system, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: RosB; COG4651 428406013451 Predicted flavoprotein [General function prediction only]; Region: COG0431 428406013452 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 428406013453 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 428406013454 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 428406013455 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 428406013456 Predicted periplasmic protein [Function unknown]; Region: COG3904 428406013457 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 428406013458 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 428406013459 Walker A/P-loop; other site 428406013460 ATP binding site [chemical binding]; other site 428406013461 Q-loop/lid; other site 428406013462 ABC transporter signature motif; other site 428406013463 Walker B; other site 428406013464 D-loop; other site 428406013465 H-loop/switch region; other site 428406013466 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 428406013467 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406013468 dimer interface [polypeptide binding]; other site 428406013469 conserved gate region; other site 428406013470 putative PBP binding loops; other site 428406013471 ABC-ATPase subunit interface; other site 428406013472 NMT1/THI5 like; Region: NMT1; pfam09084 428406013473 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 428406013474 substrate binding pocket [chemical binding]; other site 428406013475 membrane-bound complex binding site; other site 428406013476 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 428406013477 Transcriptional regulator [Transcription]; Region: IclR; COG1414 428406013478 Bacterial transcriptional regulator; Region: IclR; pfam01614 428406013479 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 428406013480 CoA-transferase family III; Region: CoA_transf_3; pfam02515 428406013481 Citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CCL cleaves citryl-CoA (CiCoA) to acetyl-CoA (AcCoA) and oxaloacetate (OAA); Region: CCL_ACL-C; cd06100 428406013482 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 428406013483 active site 428406013484 citrylCoA binding site [chemical binding]; other site 428406013485 oxalacetate binding site [chemical binding]; other site 428406013486 coenzyme A binding site [chemical binding]; other site 428406013487 catalytic triad [active] 428406013488 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 428406013489 Strictosidine synthase; Region: Str_synth; pfam03088 428406013490 transcriptional activator FlhD; Provisional; Region: PRK02909 428406013491 transcriptional activator FlhC; Provisional; Region: PRK12722 428406013492 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 428406013493 flagellar motor protein MotA; Validated; Region: PRK09110 428406013494 flagellar motor protein MotB; Validated; Region: motB; PRK09041 428406013495 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 428406013496 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 428406013497 ligand binding site [chemical binding]; other site 428406013498 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 428406013499 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406013500 active site 428406013501 phosphorylation site [posttranslational modification] 428406013502 intermolecular recognition site; other site 428406013503 dimerization interface [polypeptide binding]; other site 428406013504 chemotaxis protein CheA; Provisional; Region: PRK10547 428406013505 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cd00088 428406013506 putative binding surface; other site 428406013507 active site 428406013508 CheY binding; Region: CheY-binding; pfam09078 428406013509 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 428406013510 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406013511 ATP binding site [chemical binding]; other site 428406013512 Mg2+ binding site [ion binding]; other site 428406013513 G-X-G motif; other site 428406013514 CheA regulatory domain; CheA is a histidine protein kinase present in bacteria and archea. Activated by the chemotaxis receptor a histidine phosphoryl group from CheA is passed directly to an aspartate in the response regulator CheY. This signalling...; Region: CheA_reg; cd00731 428406013515 CheW, a small regulator protein, unique to the chemotaxis signalling in prokaryotes and archea. CheW interacts with the histidine kinase CheA, most likely with the related regulatory domain of CheA. CheW is proposed to form signalling arrays together...; Region: CheW; cd00732 428406013516 putative CheA interaction surface; other site 428406013517 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 428406013518 ligand binding domain of Tar- and Tsr-related chemoreceptors; Region: Tar_Tsr_LBD; cd00181 428406013519 dimer interface [polypeptide binding]; other site 428406013520 ligand binding site [chemical binding]; other site 428406013521 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 428406013522 dimerization interface [polypeptide binding]; other site 428406013523 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 428406013524 dimer interface [polypeptide binding]; other site 428406013525 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 428406013526 putative CheW interface [polypeptide binding]; other site 428406013527 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 428406013528 dimer interface [polypeptide binding]; other site 428406013529 putative CheW interface [polypeptide binding]; other site 428406013530 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 428406013531 chemotaxis methyltransferase CheR; Provisional; Region: PRK10611 428406013532 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 428406013533 CheD chemotactic sensory transduction; Region: CheD; cl00810 428406013534 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 428406013535 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406013536 active site 428406013537 phosphorylation site [posttranslational modification] 428406013538 intermolecular recognition site; other site 428406013539 dimerization interface [polypeptide binding]; other site 428406013540 CheB methylesterase; Region: CheB_methylest; pfam01339 428406013541 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 428406013542 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406013543 active site 428406013544 phosphorylation site [posttranslational modification] 428406013545 intermolecular recognition site; other site 428406013546 dimerization interface [polypeptide binding]; other site 428406013547 chemotaxis regulator CheZ; Provisional; Region: PRK11166 428406013548 ApbE family; Region: ApbE; pfam02424 428406013549 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 428406013550 Cytochrome c5 [Energy production and conversion]; Region: CycB; COG3245 428406013551 nitrous-oxide reductase; Validated; Region: PRK02888 428406013552 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 428406013553 Regulator of nitric oxide reductase transcription [Transcription]; Region: NosR; COG3901 428406013554 ferredoxin-type protein, NapH/MauN family; Region: napH_; TIGR02163 428406013555 4Fe-4S binding domain; Region: Fer4_5; pfam12801 428406013556 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 428406013557 Nitrous oxidase accessory protein [Inorganic ion transport and metabolism]; Region: NosD; COG3420 428406013558 parallel beta-helix repeat (two copies); Region: para_beta_helix; TIGR03804 428406013559 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 428406013560 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 428406013561 Walker A/P-loop; other site 428406013562 ATP binding site [chemical binding]; other site 428406013563 Q-loop/lid; other site 428406013564 ABC transporter signature motif; other site 428406013565 Walker B; other site 428406013566 D-loop; other site 428406013567 H-loop/switch region; other site 428406013568 ABC-type transport system involved in multi-copper enzyme maturation, permease component [General function prediction only]; Region: NosY; COG1277 428406013569 NosL; Region: NosL; pfam05573 428406013570 NosL; Region: NosL; cl01769 428406013571 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 428406013572 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257; cl15822 428406013573 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 428406013574 FHIPEP family; Region: FHIPEP; pfam00771 428406013575 flagellar biosynthetic protein FlhF; Region: FlhF; TIGR03499 428406013576 SRP54-type protein, GTPase domain; Region: SRP54; smart00962 428406013577 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 428406013578 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 428406013579 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 428406013580 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 428406013581 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 428406013582 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 428406013583 DNA binding residues [nucleotide binding] 428406013584 xanthine permease; Region: pbuX; TIGR03173 428406013585 galactose mutarotase_like; Region: galactose_mutarotase_like; cd09019 428406013586 active site 428406013587 catalytic residues [active] 428406013588 Transcriptional regulators [Transcription]; Region: PurR; COG1609 428406013589 Ligand-binding domain of DNA transcription repressor specific for xylose (XylR); Region: PBP1_XylR; cd01543 428406013590 putative dimerization interface [polypeptide binding]; other site 428406013591 putative ligand binding site [chemical binding]; other site 428406013592 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 428406013593 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 428406013594 D-xylose transporter subunit XylF; Provisional; Region: xylF; PRK10355 428406013595 Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily; Region: PBP1_ABC_xylose_binding; cd01538 428406013596 putative ligand binding site [chemical binding]; other site 428406013597 xylose transporter ATP-binding subunit; Provisional; Region: PRK13549 428406013598 First domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_I; cd03216 428406013599 Walker A/P-loop; other site 428406013600 ATP binding site [chemical binding]; other site 428406013601 Q-loop/lid; other site 428406013602 ABC transporter signature motif; other site 428406013603 Walker B; other site 428406013604 D-loop; other site 428406013605 H-loop/switch region; other site 428406013606 Second domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_II; cd03215 428406013607 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 428406013608 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 428406013609 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 428406013610 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 428406013611 TM-ABC transporter signature motif; other site 428406013612 3-hydroxybutyrate dehydrogenase; Region: PHB_DH; TIGR01963 428406013613 classical (c) SDRs; Region: SDR_c; cd05233 428406013614 NAD(P) binding site [chemical binding]; other site 428406013615 active site 428406013616 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 428406013617 Fumarylacetoacetate (FAA) hydrolase family protein [General function prediction only]; Region: COG3970 428406013618 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 428406013619 IclR helix-turn-helix domain; Region: HTH_IclR; cl17605 428406013620 Transcriptional regulator [Transcription]; Region: IclR; COG1414 428406013621 Bacterial transcriptional regulator; Region: IclR; pfam01614 428406013622 Transcriptional regulators [Transcription]; Region: PurR; COG1609 428406013623 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 428406013624 DNA binding site [nucleotide binding] 428406013625 domain linker motif; other site 428406013626 Ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators; Region: PBP1_GntR; cd01575 428406013627 putative dimerization interface [polypeptide binding]; other site 428406013628 putative ligand binding site [chemical binding]; other site 428406013629 dihydroxy-acid dehydratase; Provisional; Region: PRK13017 428406013630 Isochorismatase family; Region: Isochorismatase; pfam00857 428406013631 Nicotinamidase_ related amidohydrolases. Cysteine hydrolases of unknown function that share the catalytic triad with other amidohydrolases, like nicotinamidase, which converts nicotinamide to nicotinic acid and ammonia; Region: nicotinamidase_related; cd01014 428406013632 catalytic triad [active] 428406013633 conserved cis-peptide bond; other site 428406013634 transcriptional activator FtrA; Provisional; Region: ftrA; PRK09393 428406013635 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_1; cd03137 428406013636 conserved cys residue [active] 428406013637 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 428406013638 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 428406013639 YGGT family; Region: YGGT; pfam02325 428406013640 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 428406013641 substrate binding site [chemical binding]; other site 428406013642 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 428406013643 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 428406013644 substrate binding pocket [chemical binding]; other site 428406013645 membrane-bound complex binding site; other site 428406013646 hinge residues; other site 428406013647 Protein of unknown function (DUF971); Region: DUF971; pfam06155 428406013648 HEAT repeats; Region: HEAT_2; pfam13646 428406013649 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 428406013650 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 428406013651 putative oxidoreductase; Provisional; Region: PRK08275 428406013652 L-aspartate oxidase; Provisional; Region: PRK06175 428406013653 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 428406013654 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 428406013655 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 428406013656 DNA-binding site [nucleotide binding]; DNA binding site 428406013657 UTRA domain; Region: UTRA; pfam07702 428406013658 Periplasmic binding domain of ABC-type YtfQ-like transport systems; Region: PBP1_YtfQ_like; cd06309 428406013659 Periplasmic binding protein domain; Region: Peripla_BP_4; pfam13407 428406013660 putative ligand binding site [chemical binding]; other site 428406013661 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 428406013662 First domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_I; cd03216 428406013663 Walker A/P-loop; other site 428406013664 ATP binding site [chemical binding]; other site 428406013665 Q-loop/lid; other site 428406013666 ABC transporter signature motif; other site 428406013667 Walker B; other site 428406013668 D-loop; other site 428406013669 H-loop/switch region; other site 428406013670 Second domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_II; cd03215 428406013671 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 428406013672 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 428406013673 TM-ABC transporter signature motif; other site 428406013674 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 428406013675 Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group...; Region: TM_PBP1_transp_AraH_like; cd06579 428406013676 TM-ABC transporter signature motif; other site 428406013677 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4430 428406013678 Bacteriocin-protection, YdeI or OmpD-Associated; Region: OmdA; pfam13376 428406013679 Lipocalin-like domain; Region: Lipocalin_5; pfam13924 428406013680 RibD C-terminal domain; Region: RibD_C; cl17279 428406013681 recombination associated protein; Reviewed; Region: rdgC; PRK00321 428406013682 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 428406013683 branched-chain amino acid aminotransferase; Provisional; Region: PRK13357 428406013684 BCAT_beta_family: Branched-chain aminotransferase catalyses the transamination of the branched-chain amino acids leusine, isoleucine and valine to their respective alpha-keto acids, alpha-ketoisocaproate, alpha-keto-beta-methylvalerate and...; Region: BCAT_beta_family; cd01557 428406013685 homodimer interface [polypeptide binding]; other site 428406013686 substrate-cofactor binding pocket; other site 428406013687 catalytic residue [active] 428406013688 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 428406013689 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 428406013690 Choline/Carnitine o-acyltransferase; Region: Carn_acyltransf; pfam00755 428406013691 Alkane hydroxylase is a bacterial, integral-membrane di-iron enzyme that shares a requirement for iron and oxygen for activity similar to that of the non-heme integral-membrane acyl coenzyme A (CoA) desaturases and acyl lipid desaturases. The alk genes...; Region: Alkane-hydroxylase; cd03512 428406013692 Fatty acid desaturase; Region: FA_desaturase; pfam00487 428406013693 Di-iron ligands [ion binding]; other site 428406013694 Cupin domain; Region: Cupin_2; cl17218 428406013695 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 428406013696 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 428406013697 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 428406013698 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 428406013699 NAD(P) binding site [chemical binding]; other site 428406013700 active site 428406013701 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 428406013702 substrate binding site [chemical binding]; other site 428406013703 Protein of unknown function (DUF1304); Region: DUF1304; pfam06993 428406013704 Dienelactone hydrolase and related enzymes [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG0412 428406013705 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 428406013706 Flavin containing amine oxidoreductase; Region: Amino_oxidase; pfam01593 428406013707 Predicted spermidine synthase with an N-terminal membrane domain [General function prediction only]; Region: COG4262 428406013708 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 428406013709 Predicted membrane protein [Function unknown]; Region: COG3766 428406013710 Domain of Unknown Function (DUF350); Region: DUF350; pfam03994 428406013711 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]; Region: COG4260 428406013712 A subgroup of the band 7 domain of flotillin (reggie) like proteins. This subgroup contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. Many of these band 7 domain-containing proteins are lipid raft-associated. Individual...; Region: Band_7_5; cd03408 428406013713 Short C-terminal domain; Region: SHOCT; pfam09851 428406013714 Domain of unknown function (DUF4178); Region: DUF4178; pfam13785 428406013715 Double zinc ribbon; Region: DZR; pfam12773 428406013716 Domain of unknown function (DUF4178); Region: DUF4178; pfam13785 428406013717 S-adenosylmethionine decarboxylase; Region: AdoMet_dc; pfam02675 428406013718 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 428406013719 GAF domain; Region: GAF; pfam01590 428406013720 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 428406013721 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 428406013722 metal binding site [ion binding]; metal-binding site 428406013723 active site 428406013724 I-site; other site 428406013725 fumarate hydratase; Reviewed; Region: fumC; PRK00485 428406013726 Class II fumarases; Region: Fumarase_classII; cd01362 428406013727 active site 428406013728 tetramer interface [polypeptide binding]; other site 428406013729 putative transporter; Provisional; Region: PRK10504 428406013730 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406013731 putative substrate translocation pore; other site 428406013732 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 428406013733 Part of AAA domain; Region: AAA_19; pfam13245 428406013734 Family description; Region: UvrD_C_2; pfam13538 428406013735 hypothetical protein; Provisional; Region: PRK02237 428406013736 TraB family; Region: TraB; pfam01963 428406013737 AAA domain; Region: AAA_14; pfam13173 428406013738 Protein of unknown function (DUF2946); Region: DUF2946; pfam11162 428406013739 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 428406013740 N-terminal plug; other site 428406013741 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 428406013742 ligand-binding site [chemical binding]; other site 428406013743 BNR repeat-like domain; Region: BNR_2; pfam13088 428406013744 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 428406013745 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 428406013746 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 428406013747 hypothetical protein; Provisional; Region: PRK10621 428406013748 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406013749 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406013750 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold; Region: PBP2_LTTR_like_1; cd08421 428406013751 putative dimerization interface [polypeptide binding]; other site 428406013752 Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases [Lipid metabolism]; Region: Acs; COG0365 428406013753 Uncharacterized subfamily of medium-chain acyl-CoA synthetase (MACS); Region: MACS_like_1; cd05974 428406013754 active site 428406013755 acyl-activating enzyme (AAE) consensus motif; other site 428406013756 putative CoA binding site [chemical binding]; other site 428406013757 AMP binding site [chemical binding]; other site 428406013758 Protein of unknown function (DUF1488); Region: DUF1488; pfam07369 428406013759 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 428406013760 Acyl carrier protein phosphodiesterase [Lipid metabolism]; Region: AcpD; COG1182 428406013761 LysR family transcriptional regulator; Provisional; Region: PRK14997 428406013762 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406013763 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_4; cd08473 428406013764 putative effector binding pocket; other site 428406013765 putative dimerization interface [polypeptide binding]; other site 428406013766 Major Facilitator Superfamily; Region: MFS_1; pfam07690 428406013767 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406013768 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406013769 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3662 428406013770 PGDYG protein; Region: PGDYG; pfam14083 428406013771 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 428406013772 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 428406013773 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 428406013774 Predicted transcriptional regulators [Transcription]; Region: COG1510 428406013775 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 428406013776 dimerization interface [polypeptide binding]; other site 428406013777 putative DNA binding site [nucleotide binding]; other site 428406013778 putative Zn2+ binding site [ion binding]; other site 428406013779 Nitrate/nitrite transporter [Inorganic ion transport and metabolism]; Region: NarK; COG2223 428406013780 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406013781 putative substrate translocation pore; other site 428406013782 nitrite reductase subunit NirD; Provisional; Region: PRK14989 428406013783 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 428406013784 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 428406013785 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 428406013786 Assimilatory nitrite reductase (NirD) family, Rieske domain; Assimilatory nitrate and nitrite reductases convert nitrate through nitrite to ammonium. Members include bacterial and fungal proteins. The bacterial NirD contains a single Rieske domain while...; Region: Rieske_NirD; cd03529 428406013787 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_2; pfam07992 428406013788 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 428406013789 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 428406013790 Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol...; Region: MopB_Nitrate-R-NapA-like; cd02754 428406013791 [4Fe-4S] binding site [ion binding]; other site 428406013792 molybdopterin cofactor binding site; other site 428406013793 Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol...; Region: MopB_CT_Nitrate-R-NapA-like; cd02791 428406013794 molybdopterin cofactor binding site; other site 428406013795 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 428406013796 Uncharacterized protein conserved in bacteria (DUF2239); Region: DUF2239; pfam09998 428406013797 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 428406013798 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Bacillus subtilis yoeA; Region: MATE_yoeA_like; cd13138 428406013799 H+ Antiporter protein; Region: 2A0121; TIGR00900 428406013800 cardiolipin synthetase; Reviewed; Region: cls; PRK01642 428406013801 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 428406013802 putative active site [active] 428406013803 catalytic site [active] 428406013804 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 428406013805 putative active site [active] 428406013806 catalytic site [active] 428406013807 Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_1; cd09111 428406013808 PLD-like domain; Region: PLDc_2; pfam13091 428406013809 putative active site [active] 428406013810 catalytic site [active] 428406013811 Protein of unknown function (DUF3729); Region: DUF3729; pfam12526 428406013812 Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_2; cd09113 428406013813 PLD-like domain; Region: PLDc_2; pfam13091 428406013814 putative active site [active] 428406013815 catalytic site [active] 428406013816 Entericidin EcnA/B family; Region: Entericidin; pfam08085 428406013817 Tar ligand binding domain homologue; Region: TarH; pfam02203 428406013818 dimer interface [polypeptide binding]; other site 428406013819 ligand binding site [chemical binding]; other site 428406013820 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 428406013821 dimerization interface [polypeptide binding]; other site 428406013822 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 428406013823 dimer interface [polypeptide binding]; other site 428406013824 putative CheW interface [polypeptide binding]; other site 428406013825 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 428406013826 metal binding site [ion binding]; metal-binding site 428406013827 active site 428406013828 I-site; other site 428406013829 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 428406013830 Flagellar protein YcgR; Region: YcgR_2; pfam12945 428406013831 PilZ domain; Region: PilZ; pfam07238 428406013832 Predicted membrane protein [Function unknown]; Region: COG2246 428406013833 GtrA-like protein; Region: GtrA; pfam04138 428406013834 PAS domain S-box; Region: sensory_box; TIGR00229 428406013835 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 428406013836 putative active site [active] 428406013837 heme pocket [chemical binding]; other site 428406013838 PAS fold; Region: PAS_3; pfam08447 428406013839 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 428406013840 putative active site [active] 428406013841 heme pocket [chemical binding]; other site 428406013842 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 428406013843 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 428406013844 metal binding site [ion binding]; metal-binding site 428406013845 active site 428406013846 I-site; other site 428406013847 Lipid A 3-O-deacylase (PagL); Region: PagL; pfam09411 428406013848 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 428406013849 multidrug efflux system subunit MdtC; Provisional; Region: PRK10614 428406013850 Protein export membrane protein; Region: SecD_SecF; cl14618 428406013851 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 428406013852 Protein export membrane protein; Region: SecD_SecF; cl14618 428406013853 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 428406013854 HlyD family secretion protein; Region: HlyD_3; pfam13437 428406013855 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 428406013856 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406013857 active site 428406013858 phosphorylation site [posttranslational modification] 428406013859 intermolecular recognition site; other site 428406013860 dimerization interface [polypeptide binding]; other site 428406013861 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 428406013862 DNA binding site [nucleotide binding] 428406013863 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 428406013864 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 428406013865 dimer interface [polypeptide binding]; other site 428406013866 phosphorylation site [posttranslational modification] 428406013867 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406013868 ATP binding site [chemical binding]; other site 428406013869 Mg2+ binding site [ion binding]; other site 428406013870 G-X-G motif; other site 428406013871 Putative hemolysin [General function prediction only]; Region: Hlx; COG3042 428406013872 Domain of unknown function (DUF333); Region: DUF333; pfam03891 428406013873 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 428406013874 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl17364 428406013875 3,4-dihydroxy-2-butanone 4-phosphate synthase; Provisional; Region: ribB; PRK03353 428406013876 3,4-dihydroxy-2-butanone 4-phosphate synthase [Coenzyme metabolism]; Region: RibB; COG0108 428406013877 keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase; Provisional; Region: PRK05718 428406013878 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 428406013879 active site 428406013880 intersubunit interface [polypeptide binding]; other site 428406013881 catalytic residue [active] 428406013882 GntP family permease; Region: GntP_permease; pfam02447 428406013883 fructuronate transporter; Provisional; Region: PRK10034; cl15264 428406013884 YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no...; Region: YjgF_YER057c_UK114_family; cd00448 428406013885 homotrimer interaction site [polypeptide binding]; other site 428406013886 putative active site [active] 428406013887 N-acyl-D-aspartate/D-glutamate deacylase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3653 428406013888 D-aminoacylases (N-acyl-D-Amino acid amidohydrolases) catalyze the hydrolysis of N-acyl-D-amino acids to produce the corresponding D-amino acids, which are used as intermediates in the synthesis of pesticides, bioactive peptides, and antibiotics; Region: D-aminoacylase; cd01297 428406013889 active site 428406013890 putative substrate binding pocket [chemical binding]; other site 428406013891 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 428406013892 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 428406013893 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 428406013894 RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate...; Region: SIS_RpiR; cd05013 428406013895 putative active site [active] 428406013896 Predicted amino acid aldolase or racemase [Amino acid transport and metabolism]; Region: COG3616 428406013897 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Bacterial Cryptic D-Serine Dehydratase; Region: PLPDE_III_cryptic_DSD; cd06818 428406013898 dimer interface [polypeptide binding]; other site 428406013899 active site 428406013900 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 428406013901 substrate binding site [chemical binding]; other site 428406013902 catalytic residue [active] 428406013903 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 428406013904 2-keto-3-deoxygluconate kinase (KdgK) phosphorylates 2-keto-3-deoxygluconate (KDG) to form 2-keto-3-deoxy-6-phosphogluconate (KDGP). KDG is the common intermediate product, that allows organisms to channel D-glucuronate and/or D-galacturinate into the...; Region: KdgK; cd01166 428406013905 substrate binding site [chemical binding]; other site 428406013906 ATP binding site [chemical binding]; other site 428406013907 Protein related to penicillin acylase [General function prediction only]; Region: COG2366 428406013908 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a...; Region: Ntn_hydrolase; cl00467 428406013909 Penicillin G acylase (PGA) belongs to a family of beta-lactam acylases that includes cephalosporin acylase (CA) and aculeacin A acylase. PGA and CA are crucial for the production of backbone chemicals like 6-aminopenicillanic acid and...; Region: Ntn_PGA_like; cd03747 428406013910 active site 428406013911 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 428406013912 PAS domain; Region: PAS_9; pfam13426 428406013913 putative active site [active] 428406013914 heme pocket [chemical binding]; other site 428406013915 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 428406013916 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 428406013917 dimer interface [polypeptide binding]; other site 428406013918 phosphorylation site [posttranslational modification] 428406013919 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406013920 ATP binding site [chemical binding]; other site 428406013921 Mg2+ binding site [ion binding]; other site 428406013922 G-X-G motif; other site 428406013923 Response regulator receiver domain; Region: Response_reg; pfam00072 428406013924 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406013925 active site 428406013926 phosphorylation site [posttranslational modification] 428406013927 intermolecular recognition site; other site 428406013928 dimerization interface [polypeptide binding]; other site 428406013929 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406013930 H+ Antiporter protein; Region: 2A0121; TIGR00900 428406013931 putative substrate translocation pore; other site 428406013932 Protein of unknown function (DUF3175); Region: DUF3175; pfam11373 428406013933 Dodecin; Region: Dodecin; pfam07311 428406013934 Phospholipase C [Cell envelope biogenesis, outer membrane]; Region: PlcC; COG3511 428406013935 acid phosphatase, Burkholderia-type; Region: acid_phos_Burk; TIGR03397 428406013936 Di-haem cytochrome c peroxidase; Region: CCP_MauG; pfam03150 428406013937 Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]; Region: TerC; COG0861 428406013938 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 428406013939 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the CorC_HlyC domain. CorC_HlyC is a transporter associated domain. This small domain is found in Na+/H+ antiporters, in proteins involved in...; Region: CBS_pair_CorC_HlyC_assoc; cd04590 428406013940 Transporter associated domain; Region: CorC_HlyC; pfam03471 428406013941 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 428406013942 EamA-like transporter family; Region: EamA; pfam00892 428406013943 EamA-like transporter family; Region: EamA; pfam00892 428406013944 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 428406013945 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 428406013946 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 428406013947 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 428406013948 dimerization interface [polypeptide binding]; other site 428406013949 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 428406013950 dimer interface [polypeptide binding]; other site 428406013951 phosphorylation site [posttranslational modification] 428406013952 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406013953 ATP binding site [chemical binding]; other site 428406013954 Mg2+ binding site [ion binding]; other site 428406013955 G-X-G motif; other site 428406013956 DNA-binding transcriptional regulator BaeR; Provisional; Region: PRK10710 428406013957 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406013958 active site 428406013959 phosphorylation site [posttranslational modification] 428406013960 intermolecular recognition site; other site 428406013961 dimerization interface [polypeptide binding]; other site 428406013962 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 428406013963 DNA binding site [nucleotide binding] 428406013964 CpxP component of the bacterial Cpx-two-component system and related proteins; Region: CpxP_like; cd09916 428406013965 dimer interface [polypeptide binding]; other site 428406013966 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 428406013967 Ligand Binding Site [chemical binding]; other site 428406013968 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 428406013969 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 428406013970 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 428406013971 PAS domain S-box; Region: sensory_box; TIGR00229 428406013972 PAS domain; Region: PAS; smart00091 428406013973 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 428406013974 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 428406013975 metal binding site [ion binding]; metal-binding site 428406013976 active site 428406013977 I-site; other site 428406013978 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 428406013979 N-terminal domain of molybdenum-binding protein [General function prediction only]; Region: ModE; COG2005 428406013980 molybdenum-pterin binding domain; Region: Mop; TIGR00638 428406013981 TOBE domain; Region: TOBE; cl01440 428406013982 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 428406013983 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 428406013984 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 428406013985 Walker A/P-loop; other site 428406013986 ATP binding site [chemical binding]; other site 428406013987 ABC transporter; Region: ABC_tran; pfam00005 428406013988 Q-loop/lid; other site 428406013989 AAA domain; Region: AAA_21; pfam13304 428406013990 ABC transporter signature motif; other site 428406013991 Walker B; other site 428406013992 D-loop; other site 428406013993 H-loop/switch region; other site 428406013994 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 428406013995 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406013996 putative PBP binding loops; other site 428406013997 dimer interface [polypeptide binding]; other site 428406013998 ABC-ATPase subunit interface; other site 428406013999 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 428406014000 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 428406014001 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 428406014002 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 428406014003 HlyD family secretion protein; Region: HlyD_3; pfam13437 428406014004 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 428406014005 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406014006 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406014007 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold; Region: PBP2_CrgA_like_3; cd08472 428406014008 putative effector binding pocket; other site 428406014009 putative dimerization interface [polypeptide binding]; other site 428406014010 Predicted secreted protein [Function unknown]; Region: COG5445 428406014011 Ub domain fused to Mut7-C; Region: Ub-Mut7C; pfam14451 428406014012 Uncharacterized conserved protein [Function unknown]; Region: COG1656 428406014013 Protein of unknown function DUF82; Region: DUF82; pfam01927 428406014014 Trehalose-6-Phosphate Synthase (TPS) is a glycosyltransferase that catalyses the synthesis of alpha,alpha-1,1-trehalose-6-phosphate from glucose-6-phosphate using a UDP-glucose donor. It is a key enzyme in the trehalose synthesis pathway. Trehalose is a...; Region: GT1_TPS; cd03788 428406014015 alpha,alpha-trehalose-phosphate synthase [UDP-forming]; Region: trehalose_OtsA; TIGR02400 428406014016 active site 428406014017 homotetramer interface [polypeptide binding]; other site 428406014018 trehalose-6-phosphate phosphatase; Provisional; Region: PRK10187; cl17105 428406014019 Trehalose-phosphatase; Region: Trehalose_PPase; pfam02358 428406014020 2,4-dienoyl-CoA reductase (DCR) FMN-binding domain. DCR in E. coli is an iron-sulfur flavoenzyme which contains FMN, FAD, and a 4Fe-4S cluster. It is also a monomer, unlike that of its eukaryotic counterparts which form homotetramers and lack the...; Region: DCR_FMN; cd02930 428406014021 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 428406014022 active site 428406014023 FMN binding site [chemical binding]; other site 428406014024 2,4-decadienoyl-CoA binding site; other site 428406014025 catalytic residue [active] 428406014026 4Fe-4S cluster binding site [ion binding]; other site 428406014027 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 428406014028 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 428406014029 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 428406014030 active site 428406014031 Int/Topo IB signature motif; other site 428406014032 catalytic residues [active] 428406014033 DNA binding site [nucleotide binding] 428406014034 UDP-glucose 4-epimerase; Region: PLN02240 428406014035 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 428406014036 NAD binding site [chemical binding]; other site 428406014037 homodimer interface [polypeptide binding]; other site 428406014038 active site 428406014039 substrate binding site [chemical binding]; other site 428406014040 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 428406014041 putative active site [active] 428406014042 PAS fold; Region: PAS_3; pfam08447 428406014043 heme pocket [chemical binding]; other site 428406014044 Cache domain; Region: Cache_2; pfam08269 428406014045 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 428406014046 dimer interface [polypeptide binding]; other site 428406014047 putative CheW interface [polypeptide binding]; other site 428406014048 H-NS histone family; Region: Histone_HNS; pfam00816 428406014049 Domain in histone-like proteins of HNS family; Region: HNS; smart00528 428406014050 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 428406014051 metal binding site [ion binding]; metal-binding site 428406014052 active site 428406014053 I-site; other site 428406014054 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 428406014055 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 428406014056 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 428406014057 DNA binding residues [nucleotide binding] 428406014058 dimerization interface [polypeptide binding]; other site 428406014059 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 428406014060 POTRA domain, ShlB-type; Region: POTRA_2; pfam08479 428406014061 Flp pilus assembly protein, pilin Flp [Intracellular trafficking and secretion]; Region: Flp; COG3847 428406014062 Flp pilus assembly protein, protease CpaA [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: CpaA; COG4960 428406014063 Flp pilus assembly protein CpaB [Intracellular trafficking and secretion]; Region: CpaB; COG3745 428406014064 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 428406014065 Flp pilus assembly protein, secretin CpaC [Intracellular trafficking and secretion]; Region: CpaC; COG4964 428406014066 Pilus formation protein N terminal region; Region: T2SS-T3SS_pil_N; pfam13629 428406014067 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 428406014068 Flp pilus assembly protein, ATPase CpaE [Intracellular trafficking and secretion]; Region: CpaE; COG4963 428406014069 Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]; Region: CpaF; COG4962 428406014070 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 428406014071 ATP binding site [chemical binding]; other site 428406014072 Walker A motif; other site 428406014073 hexamer interface [polypeptide binding]; other site 428406014074 Walker B motif; other site 428406014075 Flp pilus assembly protein TadB [Intracellular trafficking and secretion]; Region: TadB; COG4965 428406014076 Flp pilus assembly protein TadC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: TadC; COG2064 428406014077 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 428406014078 TPR repeat; Region: TPR_11; pfam13414 428406014079 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 428406014080 binding surface 428406014081 TPR motif; other site 428406014082 Protein of unknown function (DUF3613); Region: DUF3613; pfam12266 428406014083 Predicted membrane protein [Function unknown]; Region: COG4655 428406014084 Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]; Region: PspF; COG1221 428406014085 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406014086 Walker A motif; other site 428406014087 ATP binding site [chemical binding]; other site 428406014088 Walker B motif; other site 428406014089 arginine finger; other site 428406014090 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 428406014091 Protein of unknown function (DUF2968); Region: DUF2968; pfam11180 428406014092 Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism]; Region: CypX; COG2124 428406014093 Cytochrome P450; Region: p450; pfam00067 428406014094 Sulfite reductase, alpha subunit (flavoprotein) [Inorganic ion transport and metabolism]; Region: CysJ; COG0369 428406014095 Flavodoxin; Region: Flavodoxin_1; pfam00258 428406014096 These bifunctional proteins fuse N-terminal cytochrome p450 with a cytochrome p450 reductase (CYPOR). NADPH cytochrome p450 reductase serves as an electron donor in several oxygenase systems and is a component of nitric oxide synthases and methionine...; Region: bifunctional_CYPOR; cd06206 428406014097 FAD binding pocket [chemical binding]; other site 428406014098 FAD binding motif [chemical binding]; other site 428406014099 catalytic residues [active] 428406014100 NAD binding pocket [chemical binding]; other site 428406014101 phosphate binding motif [ion binding]; other site 428406014102 beta-alpha-beta structure motif; other site 428406014103 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 428406014104 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 428406014105 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 428406014106 Uncharacterized enzyme involved in biosynthesis of extracellular polysaccharides [General function prediction only]; Region: COG2329 428406014107 Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism]; Region: CypX; COG2124 428406014108 Cytochrome P450; Region: p450; cl12078 428406014109 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 428406014110 dimerization interface [polypeptide binding]; other site 428406014111 putative DNA binding site [nucleotide binding]; other site 428406014112 putative Zn2+ binding site [ion binding]; other site 428406014113 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 428406014114 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 428406014115 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 428406014116 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 428406014117 Outer membrane receptor for monomeric catechols [Inorganic ion transport and metabolism]; Region: Fiu; COG4774 428406014118 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 428406014119 N-terminal plug; other site 428406014120 ligand-binding site [chemical binding]; other site 428406014121 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 428406014122 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 428406014123 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 428406014124 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 428406014125 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 428406014126 active site 428406014127 nucleophile elbow; other site 428406014128 Patatin phospholipase; Region: DUF3734; pfam12536 428406014129 3-hydroxybutyrate dehydrogenase; Provisional; Region: PRK13394 428406014130 classical (c) SDRs; Region: SDR_c; cd05233 428406014131 NAD(P) binding site [chemical binding]; other site 428406014132 active site 428406014133 acetoacetate decarboxylase; Provisional; Region: PRK02265 428406014134 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]; Region: ARO8; COG1167 428406014135 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 428406014136 DNA-binding site [nucleotide binding]; DNA binding site 428406014137 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 428406014138 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406014139 homodimer interface [polypeptide binding]; other site 428406014140 catalytic residue [active] 428406014141 beta alanine--pyruvate transaminase; Provisional; Region: PRK09221 428406014142 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 428406014143 inhibitor-cofactor binding pocket; inhibition site 428406014144 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406014145 catalytic residue [active] 428406014146 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 428406014147 methylmalonic acid semialdehyde dehydrogenase; Region: MMSDH; TIGR01722 428406014148 tetrameric interface [polypeptide binding]; other site 428406014149 NAD binding site [chemical binding]; other site 428406014150 catalytic residues [active] 428406014151 Cold shock proteins [Transcription]; Region: CspC; COG1278 428406014152 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 428406014153 DNA-binding site [nucleotide binding]; DNA binding site 428406014154 RNA-binding motif; other site 428406014155 K+ transporter [Inorganic ion transport and metabolism]; Region: Kup; COG3158 428406014156 potassium uptake protein; Region: kup; TIGR00794 428406014157 formate dehydrogenase accessory protein; Reviewed; Region: PRK00724 428406014158 oxidoreductase alpha (molybdopterin) subunit; Region: Fdhalpha-like; TIGR01701 428406014159 The MopB_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins; Region: MopB_ydeP; cd02767 428406014160 putative molybdopterin cofactor binding site [chemical binding]; other site 428406014161 The MopB_CT_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region...; Region: MopB_CT_ydeP; cd02787 428406014162 putative molybdopterin cofactor binding site; other site 428406014163 oxalate/formate antiporter family transporter; Region: 2A0111; TIGR00890 428406014164 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406014165 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cd00088 428406014166 putative binding surface; other site 428406014167 active site 428406014168 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 428406014169 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 428406014170 HlyD family secretion protein; Region: HlyD_3; pfam13437 428406014171 Outer membrane efflux protein; Region: OEP; pfam02321 428406014172 Outer membrane efflux protein; Region: OEP; pfam02321 428406014173 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 428406014174 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 428406014175 DNA binding residues [nucleotide binding] 428406014176 bacterial OsmY and nodulation domain; Region: BON; smart00749 428406014177 Predicted membrane protein [Function unknown]; Region: COG2259 428406014178 Uncharacterized protein conserved in bacteria (DUF2063); Region: DUF2063; pfam09836 428406014179 hypothetical protein; Provisional; Region: PRK05409 428406014180 Predicted integral membrane protein (DUF2282); Region: DUF2282; pfam10048 428406014181 DNA-binding protein H-NS [General function prediction only]; Region: Hns; COG2916 428406014182 Domain in histone-like proteins of HNS family; Region: HNS; smart00528 428406014183 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 428406014184 EamA-like transporter family; Region: EamA; pfam00892 428406014185 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 428406014186 AsnC-type helix-turn-helix domain; Region: HTH_AsnC-type; pfam13404 428406014187 AsnC family; Region: AsnC_trans_reg; pfam01037 428406014188 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 428406014189 Winged helix-turn-helix DNA-binding; Region: HTH_24; pfam13412 428406014190 AsnC family; Region: AsnC_trans_reg; pfam01037 428406014191 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 428406014192 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 428406014193 4-hydroxyphenylpyruvate dioxygenase and related hemolysins [Amino acid transport and metabolism / General function prediction only]; Region: COG3185 428406014194 N-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate Synthase (HmaS); Region: HPPD_N_like; cd08342 428406014195 dimer interface [polypeptide binding]; other site 428406014196 C-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HppD) and hydroxymandelate Synthase (HmaS); Region: HPPD_C_like; cd07250 428406014197 active site 428406014198 Fe binding site [ion binding]; other site 428406014199 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 428406014200 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406014201 putative substrate translocation pore; other site 428406014202 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 428406014203 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 428406014204 NAD(P) binding site [chemical binding]; other site 428406014205 shikimate binding site; other site 428406014206 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406014207 metabolite-proton symporter; Region: 2A0106; TIGR00883 428406014208 putative substrate translocation pore; other site 428406014209 beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family; Region: pcaR_pcaU; TIGR02431 428406014210 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 428406014211 Bacterial transcriptional regulator; Region: IclR; pfam01614 428406014212 Sugar phosphate isomerases/epimerases [Carbohydrate transport and metabolism]; Region: IolE; COG1082 428406014213 4-hydroxyphenylpyruvate dioxygenase; Region: 4HPPD; TIGR01263 428406014214 N-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate Synthase (HmaS); Region: HPPD_N_like; cd08342 428406014215 dimer interface [polypeptide binding]; other site 428406014216 C-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HppD) and hydroxymandelate Synthase (HmaS); Region: HPPD_C_like; cd07250 428406014217 active site 428406014218 Fe binding site [ion binding]; other site 428406014219 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 428406014220 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 428406014221 trimer interface [polypeptide binding]; other site 428406014222 eyelet of channel; other site 428406014223 D-amino acid dehydrogenase small subunit; Provisional; Region: PRK12409 428406014224 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 428406014225 hydroxyglutarate oxidase; Provisional; Region: PRK11728 428406014226 ethanolamine ammonia-lyase small subunit; Provisional; Region: PRK05465 428406014227 ethanolamine ammonia lyase large subunit; Provisional; Region: PRK15067 428406014228 Ethanolamine ammonia lyase large subunit (EutB); Region: EutB; pfam06751 428406014229 Chromate transport protein ChrA [Inorganic ion transport and metabolism]; Region: ChrA; COG2059 428406014230 chromate transporter, chromate ion transporter (CHR) family; Region: 2A51; TIGR00937 428406014231 Chromate transporter; Region: Chromate_transp; pfam02417 428406014232 ATP-dependent RNA helicase DbpA; Provisional; Region: PRK11776 428406014233 DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif; Region: DEADc; cd00268 428406014234 ATP binding site [chemical binding]; other site 428406014235 Mg++ binding site [ion binding]; other site 428406014236 motif III; other site 428406014237 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 428406014238 nucleotide binding region [chemical binding]; other site 428406014239 ATP-binding site [chemical binding]; other site 428406014240 RNA recognition motif in Escherichia coli RNA helicase dbpA and similar proteins; Region: RRM_EcDbpA_like; cd12501 428406014241 putative RNA binding site [nucleotide binding]; other site 428406014242 Poly-beta-hydroxybutyrate polymerase N terminal; Region: PHBC_N; pfam12551 428406014243 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 428406014244 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 428406014245 bifunctional enoyl-CoA hydratase/phosphate acetyltransferase; Validated; Region: PRK08190 428406014246 (R)-hydratase [(R)-specific enoyl-CoA hydratase] catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. (R)-hydratase contains a hot-dog fold similar to those of thioesterase...; Region: R_hydratase; cd03449 428406014247 dimer interaction site [polypeptide binding]; other site 428406014248 substrate-binding tunnel; other site 428406014249 active site 428406014250 catalytic site [active] 428406014251 substrate binding site [chemical binding]; other site 428406014252 phosphate acetyltransferase; Provisional; Region: PRK11890 428406014253 propionate/acetate kinase; Provisional; Region: PRK12379 428406014254 Acetokinase family; Region: Acetate_kinase; cl17229 428406014255 succinic semialdehyde dehydrogenase; Region: PLN02278 428406014256 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 428406014257 tetramerization interface [polypeptide binding]; other site 428406014258 NAD(P) binding site [chemical binding]; other site 428406014259 catalytic residues [active] 428406014260 Alcohol dehydrogenase, class IV [Energy production and conversion]; Region: EutG; COG1454 428406014261 5-hydroxyvalerate dehydrogenase (HVD) catalyzes the oxidation of 5-hydroxyvalerate to 5-oxovalerate with NAD+ as cofactor; Region: HVD; cd08193 428406014262 putative active site [active] 428406014263 metal binding site [ion binding]; metal-binding site 428406014264 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 428406014265 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 428406014266 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cd00312 428406014267 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 428406014268 substrate binding pocket [chemical binding]; other site 428406014269 YjgH belongs to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no...; Region: YjgH_like; cd02198 428406014270 homotrimer interaction site [polypeptide binding]; other site 428406014271 putative active site [active] 428406014272 Protein of unknown function (DUF1329); Region: DUF1329; pfam07044 428406014273 Protein of unknown function (DUF1302); Region: DUF1302; pfam06980 428406014274 Predicted exporters of the RND superfamily [General function prediction only]; Region: COG1033 428406014275 Uncharacterized protein related to plant photosystem II stability/assembly factor [General function prediction only]; Region: COG4447 428406014276 Phytanoyl-CoA dioxygenase (PhyH); Region: PhyH; pfam05721 428406014277 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 428406014278 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 428406014279 Bacterial transcriptional repressor; Region: TetR_C_6; pfam13977 428406014280 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 428406014281 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 428406014282 Bacterial transcriptional repressor; Region: TetR_C_6; pfam13977 428406014283 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 428406014284 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 428406014285 Phytanoyl-CoA dioxygenase (PhyH); Region: PhyH; pfam05721 428406014286 Monoamine oxidase [Amino acid transport and metabolism]; Region: COG1231 428406014287 hydroxyglutarate oxidase; Provisional; Region: PRK11728 428406014288 Domain of unknown function (DUF4158); Region: DUF4158; pfam13700 428406014289 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; pfam01526 428406014290 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 428406014291 INT_SG1, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 1, C-terminal catalytic domain. The CD contains mainly predicted integrase/recombinase and site-specific XerD recombinases. The members of this CD are found predominantly in...; Region: INT_SG1_C; cd01183 428406014292 Int/Topo IB signature motif; other site 428406014293 Plasmid stabilisation system protein; Region: Plasmid_stabil; pfam05016 428406014294 Predicted transcriptional regulator [Transcription]; Region: COG3905 428406014295 Protein of unknown function (DUF2807); Region: DUF2807; pfam10988 428406014296 Domain of unknown function (DUF4098); Region: DUF4098; pfam13345 428406014297 Plasmid replication region DNA-binding N-term; Region: KfrA_N; pfam11740 428406014298 Cytochrome c; Region: Cytochrom_C; cl11414 428406014299 Cytochrome c; Region: Cytochrom_C; pfam00034 428406014300 Monoamine oxidase [Amino acid transport and metabolism]; Region: COG1231 428406014301 Cytochrome c; Region: Cytochrom_C; cl11414 428406014302 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 428406014303 Cytochrome c; Region: Cytochrom_C; cl11414 428406014304 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 428406014305 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 428406014306 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK08314 428406014307 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 428406014308 Putative long-chain fatty acid CoA ligase; Region: LC_FACS_like; cd05935 428406014309 acyl-activating enzyme (AAE) consensus motif; other site 428406014310 putative AMP binding site [chemical binding]; other site 428406014311 putative active site [active] 428406014312 putative CoA binding site [chemical binding]; other site 428406014313 choline dehydrogenase; Validated; Region: PRK02106 428406014314 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 428406014315 aldehyde dehydrogenase family protein; Provisional; Region: PTZ00381 428406014316 Coniferyl aldehyde dehydrogenase-like; Region: ALDH_CALDH_CalB; cd07133 428406014317 NAD(P) binding site [chemical binding]; other site 428406014318 catalytic residues [active] 428406014319 3-oxoadipate enol-lactonase; Region: protocat_pcaD; TIGR02427 428406014320 Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]; Region: TrkA; COG2072 428406014321 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_3; pfam13738 428406014322 Replication initiation factor; Region: Rep_trans; pfam02486 428406014323 Zonular occludens toxin (Zot); Region: Zot; cl17485 428406014324 Domain of unknown function (DUF4158); Region: DUF4158; pfam13700 428406014325 Tn3 transposase DDE domain; Region: DDE_Tnp_Tn3; pfam01526 428406014326 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 428406014327 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 428406014328 catalytic residues [active] 428406014329 catalytic nucleophile [active] 428406014330 Presynaptic Site I dimer interface [polypeptide binding]; other site 428406014331 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 428406014332 Synaptic Flat tetramer interface [polypeptide binding]; other site 428406014333 Synaptic Site I dimer interface [polypeptide binding]; other site 428406014334 DNA binding site [nucleotide binding] 428406014335 Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed...; Region: HTH_Hin_like; cd00569 428406014336 DNA-binding interface [nucleotide binding]; DNA binding site 428406014337 Plasmid stabilisation system protein; Region: Plasmid_stabil; pfam05016 428406014338 Chlorite dismutase; Region: Chlor_dismutase; cl01280 428406014339 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 428406014340 Type I phosphodiesterase / nucleotide pyrophosphatase; Region: Phosphodiest; pfam01663 428406014341 Type I phosphodiesterase / nucleotide pyrophosphatase; Region: Phosphodiest; pfam01663 428406014342 Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; Region: HTH_MlrA-CarA; cd01104 428406014343 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 428406014344 DNA binding residues [nucleotide binding] 428406014345 classical (c) SDRs; Region: SDR_c; cd05233 428406014346 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 428406014347 NAD(P) binding site [chemical binding]; other site 428406014348 active site 428406014349 Protein of unknown function (DUF3429); Region: DUF3429; pfam11911 428406014350 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase C (SdhC) subunit; composed of bacterial SdhC and eukaryotic large cytochrome b binding (CybL) proteins. SQR catalyzes the oxidation of succinate to fumarate coupled to the...; Region: SQR_TypeC_SdhC; cd03499 428406014351 Iron-sulfur protein interface; other site 428406014352 proximal quinone binding site [chemical binding]; other site 428406014353 SdhD (CybS) interface [polypeptide binding]; other site 428406014354 proximal heme binding site [chemical binding]; other site 428406014355 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase D (SdhD) subunit; SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. E. coli SQR, a member of this subfamily, reduces the...; Region: SQR_TypeC_SdhD; cd03494 428406014356 SdhC subunit interface [polypeptide binding]; other site 428406014357 proximal heme binding site [chemical binding]; other site 428406014358 cardiolipin binding site; other site 428406014359 Iron-sulfur protein interface; other site 428406014360 proximal quinone binding site [chemical binding]; other site 428406014361 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK07057 428406014362 L-aspartate oxidase; Provisional; Region: PRK06175 428406014363 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 428406014364 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 428406014365 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 428406014366 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5343 428406014367 Anti-sigma-K factor rskA; Region: RskA; pfam10099 428406014368 RNA polymerase sigma factor; Provisional; Region: PRK12514 428406014369 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 428406014370 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 428406014371 DNA binding residues [nucleotide binding] 428406014372 Secreted and surface protein containing fasciclin-like repeats [Cell envelope biogenesis, outer membrane]; Region: COG2335 428406014373 Fasciclin domain; Region: Fasciclin; pfam02469 428406014374 superfamily containing globins and truncated hemoglobins; Region: globin_like; cl00280 428406014375 heme-binding site [chemical binding]; other site 428406014376 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 428406014377 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 428406014378 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 428406014379 FtsX-like permease family; Region: FtsX; pfam02687 428406014380 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 428406014381 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 428406014382 Walker A/P-loop; other site 428406014383 ATP binding site [chemical binding]; other site 428406014384 Q-loop/lid; other site 428406014385 ABC transporter signature motif; other site 428406014386 Walker B; other site 428406014387 D-loop; other site 428406014388 H-loop/switch region; other site 428406014389 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK08974 428406014390 heavy metal-(Cd/Co/Hg/Pb/Zn)-translocating P-type ATPase; Region: ATPase-IB2_Cd; TIGR01512 428406014391 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 428406014392 Soluble P-type ATPase [General function prediction only]; Region: COG4087 428406014393 Hemerythrin HHE cation binding domain; Region: Hemerythrin; pfam01814 428406014394 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 428406014395 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 428406014396 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 428406014397 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 428406014398 HlyD family secretion protein; Region: HlyD_3; pfam13437 428406014399 thymidine phosphorylase; Provisional; Region: PRK04350 428406014400 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 428406014401 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 428406014402 Pyrimidine nucleoside phosphorylase C-terminal domain; Region: PYNP_C; smart00941 428406014403 Protein of unknown function (DUF1488); Region: DUF1488; pfam07369 428406014404 phosphoribosylpyrophosphate synthetase; Provisional; Region: PRK07199 428406014405 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 428406014406 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 428406014407 active site 428406014408 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 428406014409 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 428406014410 Beta-Casp domain; Region: Beta-Casp; smart01027 428406014411 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 428406014412 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 428406014413 Group of bacterial proteins containing an alpha crystallin domain (ACD) similar to Lactobacillus plantarum (Lp) small heat shock proteins (sHsp) HSP 18.5, HSP 18.55 and HSP 19.3. sHsps are molecular chaperones that suppress protein aggregation and...; Region: ACD_LpsHSP_like; cd06471 428406014414 putative dimer interface [polypeptide binding]; other site 428406014415 Lecithin retinol acyltransferase; Region: LRAT; pfam04970 428406014416 FtsH Extracellular; Region: FtsH_ext; pfam06480 428406014417 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 428406014418 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 428406014419 Walker A motif; other site 428406014420 ATP binding site [chemical binding]; other site 428406014421 Walker B motif; other site 428406014422 arginine finger; other site 428406014423 Peptidase family M41; Region: Peptidase_M41; pfam01434 428406014424 Erythromycin esterase; Region: Erythro_esteras; pfam05139 428406014425 Fructose-1-phosphate kinase and related fructose-6-phosphate kinase (PfkB) [Carbohydrate transport and metabolism]; Region: FruK; COG1105 428406014426 1-phosphofructokinase (FruK), minor 6-phosphofructokinase (pfkB) and related sugar kinases. FruK plays an important role in the predominant pathway for fructose utilisation.This group also contains tagatose-6-phophate kinase, an enzyme of the tagatose...; Region: FruK_PfkB_like; cd01164 428406014427 putative substrate binding site [chemical binding]; other site 428406014428 putative ATP binding site [chemical binding]; other site 428406014429 Activation domain of S53 peptidases; Region: Pro-peptidase_S53; cl07889 428406014430 phosphoenolpyruvate synthase; Validated; Region: PRK06464 428406014431 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 428406014432 Phosphohistidine swiveling domain [Signal transduction mechanisms]; Region: COG3848 428406014433 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 428406014434 Uncharacterized anaerobic dehydrogenase [General function prediction only]; Region: COG3383 428406014435 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 428406014436 catalytic loop [active] 428406014437 iron binding site [ion binding]; other site 428406014438 Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is...; Region: MopB_Formate-Dh-H; cd02753 428406014439 [4Fe-4S] binding site [ion binding]; other site 428406014440 molybdopterin cofactor binding site; other site 428406014441 This CD includes formate dehydrogenases (Fdh) H and N; nitrate reductases, Nap and Nas; and other related proteins. Formate dehydrogenase H is a component of the anaerobic formate hydrogen lyase complex and catalyzes the reversible oxidation of formate...; Region: MopB_CT_Fdh-Nap-like; cd00508 428406014442 molybdopterin cofactor binding site; other site 428406014443 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 428406014444 SLBB domain; Region: SLBB; pfam10531 428406014445 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; pfam10589 428406014446 Histidine kinase; Region: HisKA_3; pfam07730 428406014447 Histidine kinase-like ATPase domain; Region: HATPase_c_2; pfam13581 428406014448 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406014449 ATP binding site [chemical binding]; other site 428406014450 Mg2+ binding site [ion binding]; other site 428406014451 G-X-G motif; other site 428406014452 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 428406014453 Alpha-crystallin domain (ACD) of alpha-crystallin-type small(s) heat shock proteins (Hsps). sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is the Alpha-crystallin domain (ACD). sHsps are generally...; Region: ACD_sHsps-like; cd06464 428406014454 putative dimer interface [polypeptide binding]; other site 428406014455 RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal...; Region: RaiA; cl00250 428406014456 30S subunit binding site; other site 428406014457 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 428406014458 GroEL_like type I chaperonin. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings, each composed of 7-9 subunits. The symmetry of type I is seven-fold and they are found...; Region: GroEL; cd03344 428406014459 ring oligomerisation interface [polypeptide binding]; other site 428406014460 ATP/Mg binding site [chemical binding]; other site 428406014461 stacking interactions; other site 428406014462 hinge regions; other site 428406014463 L-lactate dehydrogenase; Provisional; Region: lldD; PRK11197 428406014464 ribonucleotide reductase-like protein; Provisional; Region: PRK06948 428406014465 Ribonucleotide reductase, all-alpha domain; Region: Ribonuc_red_lgN; pfam00317 428406014466 Class II ribonucleotide reductase, dimeric form; Region: RNR_II_dimer; cd02888 428406014467 active site 428406014468 dimer interface [polypeptide binding]; other site 428406014469 effector binding site; other site 428406014470 Beta-lactamase; Region: Beta-lactamase; pfam00144 428406014471 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 428406014472 Protein of unknown function (DUF1343); Region: DUF1343; pfam07075 428406014473 Putative glycosyl hydrolase domain; Region: DUF4015; pfam13200 428406014474 Putative catalytic NodB homology domain of PgaB, IcaB, and similar proteins which consist of a deformed (beta/alpha)8 barrel fold with 5- or 6-strands; Region: CE4_NodB_like_5s_6s; cd10918 428406014475 putative active site [active] 428406014476 putative metal binding site [ion binding]; other site 428406014477 Membrane associated serine protease [Amino acid transport and metabolism]; Region: COG0705 428406014478 Nucleotidyltransferase (NT) domain of family X DNA Polymerases; Region: NT_POLXc; cd00141 428406014479 hypothetical protein; Provisional; Region: PRK08609 428406014480 active site 428406014481 primer binding site [nucleotide binding]; other site 428406014482 NTP binding site [chemical binding]; other site 428406014483 metal binding triad [ion binding]; metal-binding site 428406014484 Polymerase and Histidinol Phosphatase domain of bacterial polymerase X; Region: PHP_PolX; cd07436 428406014485 active site 428406014486 RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal...; Region: RaiA; cd00552 428406014487 30S subunit binding site; other site 428406014488 acetoacetyl-CoA reductase; Region: AcAcCoA_reduct; TIGR01829 428406014489 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 428406014490 NAD(P) binding site [chemical binding]; other site 428406014491 homotetramer interface [polypeptide binding]; other site 428406014492 homodimer interface [polypeptide binding]; other site 428406014493 active site 428406014494 This family is the oxydase domain of NRPS (non-ribosomal peptide synthetase) and other proteins that modify polypeptides by cyclizing a thioester to form a ring. These include epoB, part of the epothilone biosynthesis pathway; tubD, part of the tubulysin...; Region: mcbC-like_oxidoreductase; cd02142 428406014495 putative FMN binding site [chemical binding]; other site 428406014496 NADPH bind site [chemical binding]; other site 428406014497 formaldehyde dehydrogenase (FDH)-like; Region: FDH_like_ADH2; cd08286 428406014498 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 428406014499 catalytic Zn binding site [ion binding]; other site 428406014500 structural Zn binding site [ion binding]; other site 428406014501 NAD(P) binding site [chemical binding]; other site 428406014502 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2187 428406014503 AAA domain; Region: AAA_33; pfam13671 428406014504 Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates...; Region: NK; cl17190 428406014505 active site 428406014506 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair_9; cd04622 428406014507 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 428406014508 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 428406014509 active site 428406014510 magnesium-transporting ATPase MgtA; Provisional; Region: PRK10517 428406014511 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; smart00831 428406014512 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 428406014513 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 428406014514 Soluble P-type ATPase [General function prediction only]; Region: COG4087 428406014515 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 428406014516 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 428406014517 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 428406014518 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 428406014519 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 428406014520 Walker A/P-loop; other site 428406014521 ATP binding site [chemical binding]; other site 428406014522 Q-loop/lid; other site 428406014523 ABC transporter signature motif; other site 428406014524 Walker B; other site 428406014525 D-loop; other site 428406014526 H-loop/switch region; other site 428406014527 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 428406014528 FtsX-like permease family; Region: FtsX; pfam02687 428406014529 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 428406014530 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 428406014531 active site 428406014532 phosphorylation site [posttranslational modification] 428406014533 intermolecular recognition site; other site 428406014534 dimerization interface [polypeptide binding]; other site 428406014535 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 428406014536 DNA binding residues [nucleotide binding] 428406014537 dimerization interface [polypeptide binding]; other site 428406014538 PAS domain S-box; Region: sensory_box; TIGR00229 428406014539 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 428406014540 putative active site [active] 428406014541 heme pocket [chemical binding]; other site 428406014542 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: COG3920 428406014543 Histidine kinase; Region: HisKA_3; pfam07730 428406014544 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 428406014545 ATP binding site [chemical binding]; other site 428406014546 Mg2+ binding site [ion binding]; other site 428406014547 G-X-G motif; other site 428406014548 fumarate/nitrate reduction transcriptional regulator; Provisional; Region: PRK11161 428406014549 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 428406014550 ligand binding site [chemical binding]; other site 428406014551 flexible hinge region; other site 428406014552 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 428406014553 putative switch regulator; other site 428406014554 non-specific DNA interactions [nucleotide binding]; other site 428406014555 DNA binding site [nucleotide binding] 428406014556 sequence specific DNA binding site [nucleotide binding]; other site 428406014557 putative cAMP binding site [chemical binding]; other site 428406014558 Predicted periplasmic or secreted lipoprotein [General function prediction only]; Region: OsmY; COG2823 428406014559 BON domain; Region: BON; pfam04972 428406014560 BON domain; Region: BON; pfam04972 428406014561 BON domain; Region: BON; pfam04972 428406014562 DnaK suppressor protein [Signal transduction mechanisms]; Region: DksA; COG1734 428406014563 Flavodoxins [Energy production and conversion]; Region: FldA; COG0716 428406014564 Predicted periplasmic or secreted lipoprotein [General function prediction only]; Region: OsmY; COG2823 428406014565 BON domain; Region: BON; pfam04972 428406014566 BON domain; Region: BON; pfam04972 428406014567 BON domain; Region: BON; pfam04972 428406014568 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 428406014569 Ligand Binding Site [chemical binding]; other site 428406014570 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 428406014571 Ligand Binding Site [chemical binding]; other site 428406014572 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 428406014573 Ligand Binding Site [chemical binding]; other site 428406014574 FOG: CBS domain [General function prediction only]; Region: COG0517 428406014575 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair_9; cd04622 428406014576 Predicted membrane protein [Function unknown]; Region: COG3174 428406014577 Domain of unknown function (DUF4010); Region: DUF4010; pfam13194 428406014578 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 428406014579 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD2; cd08298 428406014580 putative NAD(P) binding site [chemical binding]; other site 428406014581 putative substrate binding site [chemical binding]; other site 428406014582 catalytic Zn binding site [ion binding]; other site 428406014583 structural Zn binding site [ion binding]; other site 428406014584 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 428406014585 Ligand Binding Site [chemical binding]; other site 428406014586 Glutamine amidotransferases class-II (Gn-AT)_YafJ-type. YafJ is a glutamine amidotransferase-like protein of unknown function found in prokaryotes, eukaryotes and archaea. YafJ has a conserved structural fold similar to those of other class II...; Region: YafJ; cd01908 428406014587 ergothioneine biosynthesis protein EgtC; Region: TIGR03442 428406014588 putative active site [active] 428406014589 putative dimer interface [polypeptide binding]; other site 428406014590 Excinuclease ATPase subunit [DNA replication, recombination, and repair]; Region: UvrA; COG0178 428406014591 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 428406014592 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 428406014593 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 428406014594 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 428406014595 Walker A/P-loop; other site 428406014596 ATP binding site [chemical binding]; other site 428406014597 Q-loop/lid; other site 428406014598 Excinuclease ATPase subunit [DNA replication, recombination, and repair]; Region: UvrA; COG0178 428406014599 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 428406014600 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 428406014601 Walker A/P-loop; other site 428406014602 ATP binding site [chemical binding]; other site 428406014603 Q-loop/lid; other site 428406014604 ABC transporter signature motif; other site 428406014605 Walker B; other site 428406014606 D-loop; other site 428406014607 H-loop/switch region; other site 428406014608 Flagellar capping protein [Cell motility and secretion]; Region: FliD; COG1345 428406014609 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 428406014610 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 428406014611 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 428406014612 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 428406014613 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 428406014614 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406014615 D-galactonate transporter; Region: 2A0114; TIGR00893 428406014616 putative substrate translocation pore; other site 428406014617 SMP-30/Gluconolaconase/LRE-like region; Region: SGL; pfam08450 428406014618 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 428406014619 extended (e) SDRs; Region: SDR_e; cd08946 428406014620 NAD(P) binding site [chemical binding]; other site 428406014621 active site 428406014622 substrate binding site [chemical binding]; other site 428406014623 galactarate dehydratase; Region: galactar-dH20; TIGR03248 428406014624 Domains similar to fish antifreeze type III protein; Region: SAF_AH_GD; cd11613 428406014625 D-galactarate dehydratase / Altronate hydrolase, C terminus; Region: GD_AH_C; pfam04295 428406014626 glucarate dehydratase; Region: glucar-dehydr; TIGR03247 428406014627 D-Glucarate dehydratase (GlucD) catalyzes the dehydration of both D-glucarate and L-idarate to form 5-keto-4-deoxy-D-glucarate (5-KDG) , the initial reaction of the catabolic pathway for (D)-glucarate. GlucD belongs to the enolase superfamily of enzymes; Region: D-glucarate_dehydratase; cd03323 428406014628 active site 428406014629 tetramer interface [polypeptide binding]; other site 428406014630 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406014631 D-galactonate transporter; Region: 2A0114; TIGR00893 428406014632 putative substrate translocation pore; other site 428406014633 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406014634 NAD-dependent aldehyde dehydrogenases [Energy production and conversion]; Region: PutA; COG1012 428406014635 Alpha-Ketoglutaric Semialdehyde Dehydrogenase; Region: ALDH_KGSADH; cd07129 428406014636 dimer interface [polypeptide binding]; other site 428406014637 NADP binding site [chemical binding]; other site 428406014638 catalytic residues [active] 428406014639 5-dehydro-4-deoxyglucarate dehydratase, also called 5-keto-4-deoxy-glucarate dehydratase (KDGDH); Region: KDGDH; cd00951 428406014640 Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: DapA; COG0329 428406014641 putative active site [active] 428406014642 catalytic residue [active] 428406014643 DNA-binding transcriptional activator XapR; Provisional; Region: PRK09986 428406014644 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406014645 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold; Region: PBP2_LTTR_aromatics_like_1; cd08447 428406014646 putative dimerization interface [polypeptide binding]; other site 428406014647 putative substrate binding pocket [chemical binding]; other site 428406014648 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 428406014649 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 428406014650 membrane-bound complex binding site; other site 428406014651 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 428406014652 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 428406014653 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 428406014654 Walker A/P-loop; other site 428406014655 ATP binding site [chemical binding]; other site 428406014656 Q-loop/lid; other site 428406014657 ABC transporter signature motif; other site 428406014658 Walker B; other site 428406014659 D-loop; other site 428406014660 H-loop/switch region; other site 428406014661 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 428406014662 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406014663 dimer interface [polypeptide binding]; other site 428406014664 conserved gate region; other site 428406014665 putative PBP binding loops; other site 428406014666 ABC-ATPase subunit interface; other site 428406014667 NMT1-like family; Region: NMT1_2; pfam13379 428406014668 NMT1/THI5 like; Region: NMT1; pfam09084 428406014669 hypothetical protein; Provisional; Region: PRK06208 428406014670 intersubunit interface [polypeptide binding]; other site 428406014671 active site 428406014672 Zn2+ binding site [ion binding]; other site 428406014673 Alkanesulfonate monoxygenase is the monoxygenase of a two-component system that catalyzes the conversion of alkanesulfonates to the corresponding aldehyde and sulfite. Alkanesulfonate monoxygenase (SsuD) has an absolute requirement for reduced flavin...; Region: Alkanesulfonate_monoxygenase; cd01094 428406014674 active site 428406014675 alkanesulfonate monooxygenase, FMNH(2)-dependent; Region: alk_sulf_monoox; TIGR03565 428406014676 dimer interface [polypeptide binding]; other site 428406014677 non-prolyl cis peptide bond; other site 428406014678 insertion regions; other site 428406014679 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 428406014680 Acyl-CoA dehydrogenase; Region: ACAD; cd00567 428406014681 active site 428406014682 Predicted metal-dependent enzyme of the double-stranded beta helix superfamily [General function prediction only]; Region: COG5553 428406014683 Member of the Rhodanese Homology Domain superfamily, repeat 1. This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 1st repeat which does not contain the putative...; Region: 4RHOD_Repeat_1; cd01532 428406014684 active site residue [active] 428406014685 Member of the Rhodanese Homology Domain superfamily, repeat 2. This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 2nd repeat which does contain the putative catalytic...; Region: 4RHOD_Repeat_2; cd01533 428406014686 active site residue [active] 428406014687 Member of the Rhodanese Homology Domain superfamily, repeat 3. This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 3rd repeat which does not contain the putative...; Region: 4RHOD_Repeat_3; cd01534 428406014688 active site residue [active] 428406014689 Member of the Rhodanese Homology Domain superfamily, repeat 4. This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 4th repeat which, in general, contains the putative...; Region: 4RHOD_Repeat_4; cd01535 428406014690 active site residue [active] 428406014691 EamA-like transporter family; Region: EamA; pfam00892 428406014692 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 428406014693 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 428406014694 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 428406014695 metal binding site [ion binding]; metal-binding site 428406014696 active site 428406014697 I-site; other site 428406014698 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 428406014699 Domain of unknown function (DUF4154); Region: DUF4154; pfam13689 428406014700 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 428406014701 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 428406014702 N-terminal plug; other site 428406014703 ligand-binding site [chemical binding]; other site 428406014704 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 428406014705 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 428406014706 gamma subunit interface [polypeptide binding]; other site 428406014707 epsilon subunit interface [polypeptide binding]; other site 428406014708 LBP interface [polypeptide binding]; other site 428406014709 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406014710 aminoethylphosphonate catabolism associated LysR family transcriptional regulator; Region: phn_lysR; TIGR03339 428406014711 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 428406014712 dimerization interface [polypeptide binding]; other site 428406014713 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 428406014714 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 428406014715 FAD dependent oxidoreductase TIGR03364; Region: HpnW_proposed 428406014716 putative 2-aminoethylphosphonate ABC transporter, periplasmic 2-aminoethylphosphonate-binding protein; Region: phnS2; TIGR03261 428406014717 ABC-type thiamine transport system, periplasmic component [Coenzyme metabolism]; Region: TbpA; COG4143 428406014718 phosphonoacetaldehyde hydrolase; Provisional; Region: PRK13478 428406014719 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 428406014720 motif II; other site 428406014721 putative 2-aminoethylphosphonate ABC transporter, permease protein; Region: PhnU2; TIGR03262 428406014722 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406014723 dimer interface [polypeptide binding]; other site 428406014724 conserved gate region; other site 428406014725 putative PBP binding loops; other site 428406014726 ABC-ATPase subunit interface; other site 428406014727 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 428406014728 dimer interface [polypeptide binding]; other site 428406014729 conserved gate region; other site 428406014730 putative PBP binding loops; other site 428406014731 ABC-ATPase subunit interface; other site 428406014732 putative 2-aminoethylphosphonate ABC transporter, ATP-binding protein; Region: PhnT2; TIGR03265 428406014733 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 428406014734 Walker A/P-loop; other site 428406014735 ATP binding site [chemical binding]; other site 428406014736 Q-loop/lid; other site 428406014737 ABC transporter signature motif; other site 428406014738 Walker B; other site 428406014739 D-loop; other site 428406014740 H-loop/switch region; other site 428406014741 TOBE domain; Region: TOBE_2; pfam08402 428406014742 aminoethylphosphonate catabolism associated LysR family transcriptional regulator; Region: phn_lysR; TIGR03339 428406014743 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406014744 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cd05466 428406014745 dimerization interface [polypeptide binding]; other site 428406014746 Peptidase M30; Region: Peptidase_M30; pfam10460 428406014747 Peptidase MA superfamily; Region: Peptidase_MA_2; pfam13485 428406014748 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 428406014749 Aconitase B swivel domain. Aconitate hydratase B is involved in energy metabolism as part of the TCA cycle. It catalyses the formation of cis-aconitate from citrate. This is the aconitase swivel domain, which undergoes swivelling conformational change in...; Region: AcnB_Swivel; cd01576 428406014750 substrate binding site [chemical binding]; other site 428406014751 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 428406014752 substrate binding site [chemical binding]; other site 428406014753 ligand binding site [chemical binding]; other site 428406014754 Ferredoxin [Energy production and conversion]; Region: COG1146 428406014755 4Fe-4S binding domain; Region: Fer4; pfam00037 428406014756 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 428406014757 enoyl-CoA hydratase; Provisional; Region: PRK07509 428406014758 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 428406014759 substrate binding site [chemical binding]; other site 428406014760 oxyanion hole (OAH) forming residues; other site 428406014761 trimer interface [polypeptide binding]; other site 428406014762 Predicted membrane protein [Function unknown]; Region: COG4539 428406014763 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 428406014764 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 428406014765 ligand binding site [chemical binding]; other site 428406014766 flexible hinge region; other site 428406014767 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 428406014768 putative switch regulator; other site 428406014769 non-specific DNA interactions [nucleotide binding]; other site 428406014770 DNA binding site [nucleotide binding] 428406014771 sequence specific DNA binding site [nucleotide binding]; other site 428406014772 putative cAMP binding site [chemical binding]; other site 428406014773 elongation factor G; Reviewed; Region: PRK00007 428406014774 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 428406014775 G1 box; other site 428406014776 putative GEF interaction site [polypeptide binding]; other site 428406014777 GTP/Mg2+ binding site [chemical binding]; other site 428406014778 Switch I region; other site 428406014779 G2 box; other site 428406014780 G3 box; other site 428406014781 Switch II region; other site 428406014782 G4 box; other site 428406014783 G5 box; other site 428406014784 EFG_mtEFG_II: this subfamily represents the domain II of elongation factor G (EF-G) in bacteria and, the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2)_like proteins found in eukaryotes. During the process of peptide synthesis...; Region: EFG_mtEFG_II; cd04088 428406014785 EFG_mtEFG1_IV: domains similar to domain IV of the bacterial translational elongation factor (EF) EF-G. Included in this group is a domain of mitochondrial Elongation factor G1 (mtEFG1) proteins homologous to domain IV of EF-G. Eukaryotic cells harbor 2...; Region: EFG_mtEFG1_IV; cd01434 428406014786 EFG_mtEFG_C: domains similar to the C-terminal domain of the bacterial translational elongation factor (EF) EF-G. Included in this group is the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2) proteins. Eukaryotic cells harbor 2...; Region: EFG_mtEFG_C; cd03713 428406014787 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 428406014788 Putative anion permease YbiR. Based on sequence similarity, YbiR proteins are predicted to function as anion translocating permeases in eubacteria, archaea and plants. They belong to ArsB/NhaD superfamily of permeases that have been shown to translocate...; Region: YbiR_permease; cd01117 428406014789 transmembrane helices; other site 428406014790 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 428406014791 non-specific DNA binding site [nucleotide binding]; other site 428406014792 salt bridge; other site 428406014793 sequence-specific DNA binding site [nucleotide binding]; other site 428406014794 error-prone DNA polymerase; Validated; Region: dnaE2; PRK05672 428406014795 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at DnaE2 gene; Region: PHP_PolIIIA_DnaE2; cd07434 428406014796 putative active site [active] 428406014797 putative PHP Thumb interface [polypeptide binding]; other site 428406014798 DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains...; Region: DnaE_OBF; cd04485 428406014799 generic binding surface II; other site 428406014800 generic binding surface I; other site 428406014801 DNA Polymerase Y-family; Region: PolY_like; cd03468 428406014802 active site 428406014803 Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]; Region: DinP; COG0389 428406014804 DNA binding site [nucleotide binding] 428406014805 Domain of unknown function (DUF4337); Region: DUF4337; pfam14235 428406014806 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 428406014807 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; pfam04116 428406014808 Uncharacterized conserved protein [Function unknown]; Region: COG3542 428406014809 tartronate semialdehyde reductase; Provisional; Region: PRK15059 428406014810 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 428406014811 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 428406014812 benzoate transport; Region: 2A0115; TIGR00895 428406014813 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406014814 putative substrate translocation pore; other site 428406014815 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 428406014816 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 428406014817 Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers...; Region: gram_neg_porins; cd00342 428406014818 trimer interface [polypeptide binding]; other site 428406014819 eyelet of channel; other site 428406014820 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 428406014821 Phthalate dioxygenase reductase (PDR) is an FMN-dependent reductase that mediates electron transfer from NADH to FMN to an iron sulfur cluster. PDR has an an N-terminal ferrredoxin reductase (FNR)-like NAD(H) binding domain and a C-terminal iron-sulfur; Region: PDR_like; cd06185 428406014822 FMN-binding pocket [chemical binding]; other site 428406014823 flavin binding motif; other site 428406014824 phosphate binding motif [ion binding]; other site 428406014825 beta-alpha-beta structure motif; other site 428406014826 NAD binding pocket [chemical binding]; other site 428406014827 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 428406014828 catalytic loop [active] 428406014829 iron binding site [ion binding]; other site 428406014830 C-terminal domain of Burkholderia sp. NF100 MhqB and similar proteins; MhqB is a type I extradiol dioxygenase involved in the catabolism of methylhydroquinone, an intermediate in the degradation of fenitrothion; Region: MhqB_like_C; cd08360 428406014831 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 428406014832 putative active site [active] 428406014833 putative metal binding site [ion binding]; other site 428406014834 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 428406014835 Uncharacterized Candidatus pelagibacter aldehyde dehydrogenase, DhaS-like; Region: ALDH_DhaS; cd07114 428406014836 NAD(P) binding site [chemical binding]; other site 428406014837 catalytic residues [active] 428406014838 L-aspartate dehydrogenase; Provisional; Region: PRK13303 428406014839 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 428406014840 Domain of unknown function DUF108; Region: DUF108; pfam01958 428406014841 hypothetical protein; Provisional; Region: PRK07064 428406014842 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 428406014843 PYR/PP interface [polypeptide binding]; other site 428406014844 dimer interface [polypeptide binding]; other site 428406014845 TPP binding site [chemical binding]; other site 428406014846 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 428406014847 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cd00568 428406014848 TPP-binding site [chemical binding]; other site 428406014849 short chain dehydrogenase; Provisional; Region: PRK07062 428406014850 putative beta-ketoacyl acyl carrier protein [ACP] reductase (BKR)-like, SDR; Region: BKR_like_SDR_like; cd05344 428406014851 putative NAD(P) binding site [chemical binding]; other site 428406014852 putative active site [active] 428406014853 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 428406014854 Transcriptional regulator [Transcription]; Region: IclR; COG1414 428406014855 Bacterial transcriptional regulator; Region: IclR; pfam01614 428406014856 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 428406014857 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 428406014858 Cupin domain; Region: Cupin_2; pfam07883 428406014859 short chain dehydrogenase; Provisional; Region: PRK12939 428406014860 classical (c) SDRs; Region: SDR_c; cd05233 428406014861 NAD(P) binding site [chemical binding]; other site 428406014862 active site 428406014863 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 428406014864 Rieske non-heme iron oxygenase (RO) family, N-terminal Rieske domain of the oxygenase alpha subunit; The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable...; Region: Rieske_RO_Alpha_N; cd03469 428406014865 [2Fe-2S] cluster binding site [ion binding]; other site 428406014866 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 428406014867 hydrophobic ligand binding site; other site 428406014868 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 428406014869 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 428406014870 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 428406014871 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 428406014872 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 428406014873 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3558 428406014874 SnoaL-like domain; Region: SnoaL_2; pfam12680 428406014875 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 428406014876 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 428406014877 Coenzyme A binding pocket [chemical binding]; other site 428406014878 Protein of unknown function (DUF2798); Region: DUF2798; pfam11391 428406014879 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406014880 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406014881 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 428406014882 putative effector binding pocket; other site 428406014883 dimerization interface [polypeptide binding]; other site 428406014884 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 428406014885 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 428406014886 D-Alanine aminotransferase (D-AAT_like): D-amino acid aminotransferase catalyzes transamination between D-amino acids and their respective alpha-keto acids. It plays a major role in the synthesis of bacterial cell wall components like D-alanine and...; Region: D-AAT_like; cd01558 428406014887 homodimer interface [polypeptide binding]; other site 428406014888 substrate-cofactor binding pocket; other site 428406014889 pyridoxal 5'-phosphate binding site [chemical binding]; other site 428406014890 catalytic residue [active] 428406014891 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 428406014892 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 428406014893 Walker A/P-loop; other site 428406014894 ATP binding site [chemical binding]; other site 428406014895 Q-loop/lid; other site 428406014896 ABC transporter signature motif; other site 428406014897 Walker B; other site 428406014898 D-loop; other site 428406014899 H-loop/switch region; other site 428406014900 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 428406014901 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 428406014902 TM-ABC transporter signature motif; other site 428406014903 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 428406014904 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 428406014905 Walker A/P-loop; other site 428406014906 ATP binding site [chemical binding]; other site 428406014907 Q-loop/lid; other site 428406014908 ABC transporter signature motif; other site 428406014909 Walker B; other site 428406014910 D-loop; other site 428406014911 H-loop/switch region; other site 428406014912 Transmembrane subunit (TM) of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which are involved in the uptake of branched-chain amino acids (AAs), as well as TMs of transporters involved in the uptake of...; Region: TM_PBP1_branched-chain-AA_like; cl00454 428406014913 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 428406014914 TM-ABC transporter signature motif; other site 428406014915 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 428406014916 Transcriptional regulator [Transcription]; Region: IclR; COG1414 428406014917 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 428406014918 FAD-dependent oxidoreductase; Provisional; Region: PRK08132 428406014919 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 428406014920 Protein of unknown function (DUF2783); Region: DUF2783; pfam10932 428406014921 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 428406014922 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 428406014923 active site 428406014924 catalytic tetrad [active] 428406014925 Transcriptional regulator [Transcription]; Region: LysR; COG0583 428406014926 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 428406014927 The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold; Region: PBP2_DntR_NahR_LinR_like; cd08459 428406014928 substrate binding pocket [chemical binding]; other site 428406014929 dimerization interface [polypeptide binding]; other site