-- dump date 20140619_125818 -- class Genbank::misc_feature -- table misc_feature_note -- id note 557598000001 L-aspartate oxidase; Provisional; Region: PRK09077 557598000002 L-aspartate oxidase; Provisional; Region: PRK06175 557598000003 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 557598000004 DsrE/DsrF-like family; Region: DrsE; cl00672 557598000005 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 557598000006 active site 557598000007 HslU subunit interaction site [polypeptide binding]; other site 557598000008 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 557598000009 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 557598000010 Walker A motif; other site 557598000011 ATP binding site [chemical binding]; other site 557598000012 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 557598000013 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 557598000014 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 557598000015 RNA methyltransferase, RsmE family; Region: TIGR00046 557598000016 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 557598000017 Inositol-monophosphatase-like domains. This family of phosphatases is dependent on bivalent metal ions such as Mg++, and many members are inhibited by Li+ (which is thought to displace a bivalent ion in the active site). Substrates include fructose-1; Region: IMPase_like; cd01637 557598000018 active site 557598000019 aspartate carbamoyltransferase regulatory subunit; Reviewed; Region: PRK00893 557598000020 Aspartate carbamoyltransferase regulatory chain, allosteric domain; Region: PyrI; pfam01948 557598000021 Aspartate carbamoyltransferase regulatory chain, metal binding domain; Region: PyrI_C; pfam02748 557598000022 Aspartate carbamoyltransferase, catalytic chain [Nucleotide transport and metabolism]; Region: PyrB; COG0540 557598000023 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 557598000024 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 557598000025 Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: Pcm; COG2518 557598000026 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 557598000027 S-adenosylmethionine binding site [chemical binding]; other site 557598000028 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 557598000029 active site residue [active] 557598000030 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 557598000031 ligand binding site [chemical binding]; other site 557598000032 active site 557598000033 UGI interface [polypeptide binding]; other site 557598000034 catalytic site [active] 557598000035 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 557598000036 Glycosyltransferase family 9 (heptosyltransferase); Region: Glyco_transf_9; pfam01075 557598000037 putative active site [active] 557598000038 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 557598000039 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 557598000040 ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase; Region: ribokinase_pfkB_like; cl00192 557598000041 ATP binding site [chemical binding]; other site 557598000042 substrate binding site [chemical binding]; other site 557598000043 Uncharacterized protein family (UPF0093); Region: UPF0093; pfam03653 557598000044 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 557598000045 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 557598000046 inhibitor-cofactor binding pocket; inhibition site 557598000047 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557598000048 catalytic residue [active] 557598000049 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 557598000050 diaminopimelate decarboxylase; Region: lysA; TIGR01048 557598000051 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 557598000052 active site 557598000053 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 557598000054 substrate binding site [chemical binding]; other site 557598000055 catalytic residues [active] 557598000056 dimer interface [polypeptide binding]; other site 557598000057 iron donor protein CyaY; Region: FeS_CyaY; TIGR03421 557598000058 putative iron binding site [ion binding]; other site 557598000059 Predicted membrane protein [Function unknown]; Region: COG1238 557598000060 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 557598000061 Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]; Region: KsgA; COG0030 557598000062 S-adenosylmethionine binding site [chemical binding]; other site 557598000063 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 557598000064 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 557598000065 Walker A/P-loop; other site 557598000066 ATP binding site [chemical binding]; other site 557598000067 Q-loop/lid; other site 557598000068 ABC transporter signature motif; other site 557598000069 Walker B; other site 557598000070 D-loop; other site 557598000071 H-loop/switch region; other site 557598000072 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 557598000073 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 557598000074 substrate binding pocket [chemical binding]; other site 557598000075 membrane-bound complex binding site; other site 557598000076 hinge residues; other site 557598000077 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 557598000078 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 557598000079 dimer interface [polypeptide binding]; other site 557598000080 conserved gate region; other site 557598000081 putative PBP binding loops; other site 557598000082 ABC-ATPase subunit interface; other site 557598000083 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 557598000084 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 557598000085 dimer interface [polypeptide binding]; other site 557598000086 conserved gate region; other site 557598000087 putative PBP binding loops; other site 557598000088 ABC-ATPase subunit interface; other site 557598000089 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 557598000090 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 557598000091 Walker A/P-loop; other site 557598000092 ATP binding site [chemical binding]; other site 557598000093 Q-loop/lid; other site 557598000094 ABC transporter signature motif; other site 557598000095 Walker B; other site 557598000096 D-loop; other site 557598000097 H-loop/switch region; other site 557598000098 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 557598000099 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 557598000100 Walker A motif; other site 557598000101 ATP binding site [chemical binding]; other site 557598000102 Walker B motif; other site 557598000103 Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins; Region: PLPDE_III_Yggs_like; cd06824 557598000104 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 557598000105 catalytic residue [active] 557598000106 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 557598000107 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 557598000108 Cytochrome c; Region: Cytochrom_C; cl11414 557598000109 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 557598000110 phospho-2-dehydro-3-deoxyheptonate aldolase; Validated; Region: PRK09261 557598000111 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 557598000112 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 557598000113 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 557598000114 GTP binding site; other site 557598000115 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 557598000116 MoaE homodimer interface [polypeptide binding]; other site 557598000117 MoaD interaction [polypeptide binding]; other site 557598000118 active site residues [active] 557598000119 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 557598000120 MoaE interaction surface [polypeptide binding]; other site 557598000121 MoeB interaction surface [polypeptide binding]; other site 557598000122 thiocarboxylated glycine; other site 557598000123 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 557598000124 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 557598000125 intersubunit interface [polypeptide binding]; other site 557598000126 active site 557598000127 zinc binding site [ion binding]; other site 557598000128 Na+ binding site [ion binding]; other site 557598000129 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 557598000130 Phosphoglycerate kinase (PGK) is a monomeric enzyme which catalyzes the transfer of the high-energy phosphate group of 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate. This reaction represents the first of the two substrate-level...; Region: Phosphoglycerate_kinase; cd00318 557598000131 Phosphoglycerate kinase; Region: PGK; pfam00162 557598000132 substrate binding site [chemical binding]; other site 557598000133 hinge regions; other site 557598000134 ADP binding site [chemical binding]; other site 557598000135 catalytic site [active] 557598000136 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 557598000137 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 557598000138 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 557598000139 transketolase; Reviewed; Region: PRK12753 557598000140 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 557598000141 TPP-binding site [chemical binding]; other site 557598000142 dimer interface [polypeptide binding]; other site 557598000143 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 557598000144 PYR/PP interface [polypeptide binding]; other site 557598000145 dimer interface [polypeptide binding]; other site 557598000146 TPP binding site [chemical binding]; other site 557598000147 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 557598000148 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 557598000149 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 557598000150 active site 557598000151 FMN binding site [chemical binding]; other site 557598000152 2,4-decadienoyl-CoA binding site; other site 557598000153 catalytic residue [active] 557598000154 4Fe-4S cluster binding site [ion binding]; other site 557598000155 Uncharacterized NAD(FAD)-dependent dehydrogenases [General function prediction only]; Region: HcaD; COG0446 557598000156 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 557598000157 Major Facilitator Superfamily; Region: MFS_1; pfam07690 557598000158 putative substrate translocation pore; other site 557598000159 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 557598000160 TolQ protein; Region: tolQ; TIGR02796 557598000161 Aspartate racemase [Cell envelope biogenesis, outer membrane]; Region: RacX; COG1794 557598000162 aspartate racemase; Region: asp_race; TIGR00035 557598000163 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 557598000164 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 557598000165 gamma-glutamyl kinase; Provisional; Region: PRK05429 557598000166 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 557598000167 nucleotide binding site [chemical binding]; other site 557598000168 homotetrameric interface [polypeptide binding]; other site 557598000169 putative phosphate binding site [ion binding]; other site 557598000170 putative allosteric binding site; other site 557598000171 PUA domain; Region: PUA; pfam01472 557598000172 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 557598000173 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 557598000174 ATP binding site [chemical binding]; other site 557598000175 substrate interface [chemical binding]; other site 557598000176 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 557598000177 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 557598000178 active site 557598000179 phosphorylation site [posttranslational modification] 557598000180 intermolecular recognition site; other site 557598000181 dimerization interface [polypeptide binding]; other site 557598000182 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 557598000183 Walker A motif; other site 557598000184 ATP binding site [chemical binding]; other site 557598000185 Walker B motif; other site 557598000186 arginine finger; other site 557598000187 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 557598000188 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 557598000189 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 557598000190 dimerization interface [polypeptide binding]; other site 557598000191 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 557598000192 dimer interface [polypeptide binding]; other site 557598000193 phosphorylation site [posttranslational modification] 557598000194 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 557598000195 ATP binding site [chemical binding]; other site 557598000196 Mg2+ binding site [ion binding]; other site 557598000197 G-X-G motif; other site 557598000198 Domain of unknown function (DUF4390); Region: DUF4390; pfam14334 557598000199 16S rRNA methyltransferase B; Provisional; Region: PRK10901 557598000200 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 557598000201 NOL1/NOP2/sun family putative RNA methylase; Region: nop2p; TIGR00446 557598000202 M48 family peptidase; Provisional; Region: PRK03001 557598000203 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 557598000204 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 557598000205 active site 557598000206 phosphorylation site [posttranslational modification] 557598000207 intermolecular recognition site; other site 557598000208 dimerization interface [polypeptide binding]; other site 557598000209 LytTr DNA-binding domain; Region: LytTR; smart00850 557598000210 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 557598000211 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 557598000212 active site 557598000213 phosphorylation site [posttranslational modification] 557598000214 intermolecular recognition site; other site 557598000215 dimerization interface [polypeptide binding]; other site 557598000216 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 557598000217 binding surface 557598000218 TPR motif; other site 557598000219 Tetratricopeptide repeat; Region: TPR_16; pfam13432 557598000220 DNA-dependent helicase II; Provisional; Region: uvrD; PRK11773 557598000221 Part of AAA domain; Region: AAA_19; pfam13245 557598000222 Family description; Region: UvrD_C_2; pfam13538 557598000223 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 557598000224 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 557598000225 substrate binding site [chemical binding]; other site 557598000226 oxyanion hole (OAH) forming residues; other site 557598000227 trimer interface [polypeptide binding]; other site 557598000228 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 557598000229 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 557598000230 RNA binding surface [nucleotide binding]; other site 557598000231 Pseudouridine synthase, Escherichia coli RsuA like; Region: PseudoU_synth_RsuA; cd02553 557598000232 active site 557598000233 uracil binding [chemical binding]; other site 557598000234 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 557598000235 Na2 binding site [ion binding]; other site 557598000236 putative substrate binding site 1 [chemical binding]; other site 557598000237 Na binding site 1 [ion binding]; other site 557598000238 putative substrate binding site 2 [chemical binding]; other site 557598000239 heme biosynthesis-associated TPR protein; Region: TPR_hemY_coli; TIGR00540 557598000240 HemY protein N-terminus; Region: HemY_N; pfam07219 557598000241 putative uroporphyrinogen III C-methyltransferase; Provisional; Region: PRK10920 557598000242 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 557598000243 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 557598000244 active site 557598000245 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 557598000246 active site residue [active] 557598000247 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3224 557598000248 chromosome condensation membrane protein; Provisional; Region: PRK14196 557598000249 Maf-like protein; Region: Maf; pfam02545 557598000250 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 557598000251 active site 557598000252 dimer interface [polypeptide binding]; other site 557598000253 ribonuclease G; Provisional; Region: PRK11712 557598000254 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 557598000255 homodimer interface [polypeptide binding]; other site 557598000256 oligonucleotide binding site [chemical binding]; other site 557598000257 tRNA pseudouridine isomerase C; Region: PseudoU_synth_TruC; cd02563 557598000258 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 557598000259 probable active site [active] 557598000260 putative monooxygenase; Provisional; Region: PRK11118 557598000261 Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Escherichia coli Hsp31 protein; Region: GATase1_Hsp31_like; cd03141 557598000262 Putative intracellular protease/amidase [General function prediction only]; Region: ThiJ; COG0693 557598000263 potential catalytic triad [active] 557598000264 conserved cys residue [active] 557598000265 AraC-like ligand binding domain; Region: AraC_binding; pfam02311 557598000266 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 557598000267 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557598000268 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557598000269 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 557598000270 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 557598000271 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 557598000272 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 557598000273 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 557598000274 Walker A motif; other site 557598000275 ATP binding site [chemical binding]; other site 557598000276 Walker B motif; other site 557598000277 arginine finger; other site 557598000278 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 557598000279 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 557598000280 substrate binding site [chemical binding]; other site 557598000281 Protein of unknown function (DUF1275); Region: DUF1275; cl01453 557598000282 This domain is the catalytic domain of ribonuclease II; Region: RNB; smart00955 557598000283 RNB domain; Region: RNB; pfam00773 557598000284 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 557598000285 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 557598000286 active site 557598000287 phosphorylation site [posttranslational modification] 557598000288 intermolecular recognition site; other site 557598000289 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 557598000290 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557598000291 metal binding site [ion binding]; metal-binding site 557598000292 active site 557598000293 I-site; other site 557598000294 arginine-ornithine antiporter; Region: arg_ornith_anti; TIGR03810 557598000295 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 557598000296 Coenzyme A binding pocket [chemical binding]; other site 557598000297 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 557598000298 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 557598000299 CAP-like domain; other site 557598000300 active site 557598000301 primary dimer interface [polypeptide binding]; other site 557598000302 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 557598000303 active site 557598000304 8-amino-7-oxononanoate synthase; Reviewed; Region: PRK05958 557598000305 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 557598000306 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 557598000307 catalytic residue [active] 557598000308 Biotin synthase and related enzymes [Coenzyme metabolism]; Region: BioB; COG0502 557598000309 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 557598000310 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 557598000311 Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]; Region: CspR; COG0219 557598000312 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 557598000313 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 557598000314 Sporulation related domain; Region: SPOR; pfam05036 557598000315 Uncharacterized protein family (UPF0227); Region: UPF0227; cl14886 557598000316 serine acetyltransferase; Provisional; Region: cysE; PRK11132 557598000317 Serine acetyltransferase, N-terminal; Region: SATase_N; pfam06426 557598000318 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 557598000319 trimer interface [polypeptide binding]; other site 557598000320 active site 557598000321 substrate binding site [chemical binding]; other site 557598000322 CoA binding site [chemical binding]; other site 557598000323 Quinone oxidoreductase (QOR); Region: QOR2; cd05286 557598000324 quinone oxidoreductase, NADPH-dependent; Provisional; Region: PRK10754 557598000325 NADP binding site [chemical binding]; other site 557598000326 dimer interface [polypeptide binding]; other site 557598000327 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 557598000328 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 557598000329 dimer interface [polypeptide binding]; other site 557598000330 phosphorylation site [posttranslational modification] 557598000331 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 557598000332 ATP binding site [chemical binding]; other site 557598000333 Mg2+ binding site [ion binding]; other site 557598000334 G-X-G motif; other site 557598000335 Response regulator receiver domain; Region: Response_reg; pfam00072 557598000336 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 557598000337 active site 557598000338 phosphorylation site [posttranslational modification] 557598000339 intermolecular recognition site; other site 557598000340 dimerization interface [polypeptide binding]; other site 557598000341 B12-dependent methionine synthase; Provisional; Region: metH; PRK09490 557598000342 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; COG0646 557598000343 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 557598000344 substrate binding pocket [chemical binding]; other site 557598000345 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 557598000346 B12 binding site [chemical binding]; other site 557598000347 cobalt ligand [ion binding]; other site 557598000348 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 557598000349 futalosine nucleosidase; Region: fut_nucase; TIGR03664 557598000350 DoxX; Region: DoxX; cl17842 557598000351 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 557598000352 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 557598000353 non-specific DNA binding site [nucleotide binding]; other site 557598000354 salt bridge; other site 557598000355 sequence-specific DNA binding site [nucleotide binding]; other site 557598000356 YaeQ protein; Region: YaeQ; pfam07152 557598000357 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 557598000358 fructokinase; Reviewed; Region: PRK09557 557598000359 oxalate/formate antiporter family transporter; Region: 2A0111; TIGR00890 557598000360 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 557598000361 putative substrate translocation pore; other site 557598000362 Cache domain; Region: Cache_1; pfam02743 557598000363 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 557598000364 dimerization interface [polypeptide binding]; other site 557598000365 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 557598000366 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557598000367 dimer interface [polypeptide binding]; other site 557598000368 putative CheW interface [polypeptide binding]; other site 557598000369 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: COG4667 557598000370 Hypothetical patatin similar to yjju protein of Escherichia coli; Region: Pat_hypo_Ecoli_yjju_like; cd07208 557598000371 active site 557598000372 nucleophile elbow; other site 557598000373 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK05574 557598000374 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 557598000375 Lipopolysaccharide-assembly; Region: LptE; cl01125 557598000376 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 557598000377 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 557598000378 HIGH motif; other site 557598000379 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 557598000380 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 557598000381 active site 557598000382 KMSKS motif; other site 557598000383 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 557598000384 tRNA binding surface [nucleotide binding]; other site 557598000385 K+ transporter [Inorganic ion transport and metabolism]; Region: Kup; COG3158 557598000386 potassium uptake protein; Region: kup; TIGR00794 557598000387 M20 Peptidase Glutamate carboxypeptidase, a periplasmic enzyme; Region: M20_CPDG2; cd03885 557598000388 hypothetical protein; Provisional; Region: PRK07338 557598000389 metal binding site [ion binding]; metal-binding site 557598000390 dimer interface [polypeptide binding]; other site 557598000391 C4-dicarboxylate anaerobic carrier; Region: DcuC; pfam03606 557598000392 C4-dicarboxylate transporter [Energy production and conversion]; Region: DcuC; COG3069 557598000393 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 557598000394 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 557598000395 amidase catalytic site [active] 557598000396 Zn binding residues [ion binding]; other site 557598000397 substrate binding site [chemical binding]; other site 557598000398 Hemerythrin-like domain; Region: Hr-like; cd12108 557598000399 Fe binding site [ion binding]; other site 557598000400 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557598000401 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 557598000402 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557598000403 2-isopropylmalate synthase; Validated; Region: PRK00915 557598000404 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 557598000405 active site 557598000406 catalytic residues [active] 557598000407 metal binding site [ion binding]; metal-binding site 557598000408 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 557598000409 PAS fold; Region: PAS_4; pfam08448 557598000410 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 557598000411 putative active site [active] 557598000412 heme pocket [chemical binding]; other site 557598000413 PAS fold; Region: PAS_3; pfam08447 557598000414 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 557598000415 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557598000416 metal binding site [ion binding]; metal-binding site 557598000417 active site 557598000418 I-site; other site 557598000419 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 557598000420 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 557598000421 E3 interaction surface; other site 557598000422 lipoyl attachment site [posttranslational modification]; other site 557598000423 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 557598000424 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 557598000425 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 557598000426 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 557598000427 dihydrolipoamide acetyltransferase; Reviewed; Region: PRK11855 557598000428 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 557598000429 E3 interaction surface; other site 557598000430 lipoyl attachment site [posttranslational modification]; other site 557598000431 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 557598000432 E3 interaction surface; other site 557598000433 lipoyl attachment site [posttranslational modification]; other site 557598000434 e3 binding domain; Region: E3_binding; pfam02817 557598000435 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 557598000436 pyruvate dehydrogenase subunit E1; Reviewed; Region: aceE; PRK09405 557598000437 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 557598000438 dimer interface [polypeptide binding]; other site 557598000439 TPP-binding site [chemical binding]; other site 557598000440 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]; Region: COG4783 557598000441 Peptidase family M48; Region: Peptidase_M48; cl12018 557598000442 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 557598000443 binding surface 557598000444 TPR motif; other site 557598000445 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 557598000446 active site residue [active] 557598000447 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 557598000448 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 557598000449 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 557598000450 HlyD family secretion protein; Region: HlyD_3; pfam13437 557598000451 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 557598000452 putative DNA binding site [nucleotide binding]; other site 557598000453 dimerization interface [polypeptide binding]; other site 557598000454 putative Zn2+ binding site [ion binding]; other site 557598000455 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 557598000456 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 557598000457 active site 557598000458 (T/H)XGH motif; other site 557598000459 Oligomerisation domain; Region: Oligomerisation; cl00519 557598000460 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 557598000461 Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnA; COG2824 557598000462 PhnA protein; Region: PhnA; pfam03831 557598000463 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 557598000464 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 557598000465 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 557598000466 DNA binding site [nucleotide binding] 557598000467 active site 557598000468 Bacterial protein of unknown function (DUF937); Region: DUF937; cl01528 557598000469 hypothetical protein; Provisional; Region: PRK10621 557598000470 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 557598000471 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 557598000472 guanine deaminase; Provisional; Region: PRK09228 557598000473 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 557598000474 active site 557598000475 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 557598000476 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 557598000477 N-acetyl-D-glucosamine binding site [chemical binding]; other site 557598000478 catalytic residue [active] 557598000479 RDD family; Region: RDD; pfam06271 557598000480 Protein of unknown function (DUF3106); Region: DUF3106; pfam11304 557598000481 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK06965 557598000482 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 557598000483 PYR/PP interface [polypeptide binding]; other site 557598000484 dimer interface [polypeptide binding]; other site 557598000485 TPP binding site [chemical binding]; other site 557598000486 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 557598000487 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 557598000488 TPP-binding site [chemical binding]; other site 557598000489 dimer interface [polypeptide binding]; other site 557598000490 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 557598000491 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 557598000492 putative valine binding site [chemical binding]; other site 557598000493 dimer interface [polypeptide binding]; other site 557598000494 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 557598000495 ketol-acid reductoisomerase; Provisional; Region: PRK05479 557598000496 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 557598000497 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 557598000498 Putative MetA-pathway of phenol degradation; Region: Phenol_MetA_deg; cl01768 557598000499 phosphatidylserine decarboxylase; Provisional; Region: PRK05305 557598000500 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 557598000501 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 557598000502 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 557598000503 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 557598000504 active site 557598000505 phosphorylation site [posttranslational modification] 557598000506 intermolecular recognition site; other site 557598000507 dimerization interface [polypeptide binding]; other site 557598000508 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 557598000509 DNA binding site [nucleotide binding] 557598000510 Domain of unknown function (DUF3329); Region: DUF3329; pfam11808 557598000511 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 557598000512 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 557598000513 putative active site [active] 557598000514 heme pocket [chemical binding]; other site 557598000515 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 557598000516 dimer interface [polypeptide binding]; other site 557598000517 phosphorylation site [posttranslational modification] 557598000518 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 557598000519 ATP binding site [chemical binding]; other site 557598000520 Mg2+ binding site [ion binding]; other site 557598000521 G-X-G motif; other site 557598000522 Transaldolase-like proteins from plants and bacteria; Region: Transaldolase_like; cd00955 557598000523 putative active site [active] 557598000524 catalytic residue [active] 557598000525 AAA domain; Region: AAA_26; pfam13500 557598000526 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 557598000527 cytochrome c oxidase subunit II; Provisional; Region: COX2; MTH00140 557598000528 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 557598000529 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 557598000530 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 557598000531 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 557598000532 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 557598000533 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 557598000534 Subunit I/III interface [polypeptide binding]; other site 557598000535 D-pathway; other site 557598000536 Subunit I/VIIc interface [polypeptide binding]; other site 557598000537 Subunit I/IV interface [polypeptide binding]; other site 557598000538 Subunit I/II interface [polypeptide binding]; other site 557598000539 Low-spin heme (heme a) binding site [chemical binding]; other site 557598000540 Subunit I/VIIa interface [polypeptide binding]; other site 557598000541 Subunit I/VIa interface [polypeptide binding]; other site 557598000542 Dimer interface; other site 557598000543 Putative water exit pathway; other site 557598000544 Binuclear center (heme a3/CuB) [ion binding]; other site 557598000545 K-pathway; other site 557598000546 Subunit I/Vb interface [polypeptide binding]; other site 557598000547 Putative proton exit pathway; other site 557598000548 Subunit I/VIb interface; other site 557598000549 Subunit I/VIc interface [polypeptide binding]; other site 557598000550 Electron transfer pathway; other site 557598000551 Subunit I/VIIIb interface [polypeptide binding]; other site 557598000552 Subunit I/VIIb interface [polypeptide binding]; other site 557598000553 Cytochrome c oxidase assembly protein CtaG/Cox11; Region: CtaG_Cox11; cl01240 557598000554 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 557598000555 Subunit III/VIIa interface [polypeptide binding]; other site 557598000556 Phospholipid binding site [chemical binding]; other site 557598000557 Subunit I/III interface [polypeptide binding]; other site 557598000558 Subunit III/VIb interface [polypeptide binding]; other site 557598000559 Subunit III/VIa interface; other site 557598000560 Subunit III/Vb interface [polypeptide binding]; other site 557598000561 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; cl01321 557598000562 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 557598000563 Cytochrome oxidase assembly protein; Region: COX15-CtaA; pfam02628 557598000564 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 557598000565 UbiA prenyltransferase family; Region: UbiA; pfam01040 557598000566 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 557598000567 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 557598000568 Cu(I) binding site [ion binding]; other site 557598000569 Flagellar regulator YcgR; Region: YcgR; pfam07317 557598000570 c-di-GMP-binding protein [Signal transduction mechanisms]; Region: COG5581 557598000571 PilZ domain; Region: PilZ; pfam07238 557598000572 ATP phosphoribosyltransferase [Amino acid transport and metabolism]; Region: HisG; COG0040 557598000573 ATP phosphoribosyltransferase catalytic subunit; Reviewed; Region: hisG; PRK01686 557598000574 LysE type translocator; Region: LysE; cl00565 557598000575 Histidinol dehydrogenase [Amino acid transport and metabolism]; Region: HisD; COG0141 557598000576 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 557598000577 NAD binding site [chemical binding]; other site 557598000578 dimerization interface [polypeptide binding]; other site 557598000579 product binding site; other site 557598000580 substrate binding site [chemical binding]; other site 557598000581 zinc binding site [ion binding]; other site 557598000582 catalytic residues [active] 557598000583 histidinol-phosphate aminotransferase; Provisional; Region: PRK04870 557598000584 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 557598000585 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557598000586 homodimer interface [polypeptide binding]; other site 557598000587 catalytic residue [active] 557598000588 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 557598000589 putative active site pocket [active] 557598000590 4-fold oligomerization interface [polypeptide binding]; other site 557598000591 metal binding residues [ion binding]; metal-binding site 557598000592 3-fold/trimer interface [polypeptide binding]; other site 557598000593 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13146 557598000594 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 557598000595 putative active site [active] 557598000596 oxyanion strand; other site 557598000597 catalytic triad [active] 557598000598 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 557598000599 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 557598000600 catalytic residues [active] 557598000601 GlpM protein; Region: GlpM; pfam06942 557598000602 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 557598000603 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 557598000604 substrate binding site [chemical binding]; other site 557598000605 glutamase interaction surface [polypeptide binding]; other site 557598000606 phosphoribosyl-AMP cyclohydrolase; Reviewed; Region: hisI; PRK00051 557598000607 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 557598000608 metal binding site [ion binding]; metal-binding site 557598000609 Protein Kinase C Interacting protein related (PKCI): PKCI and related proteins belong to the ubiquitous HIT family of hydrolases that act on alpha-phosphates of ribonucleotides. The members of this subgroup have a conserved HxHxHxx motif (x is a...; Region: PKCI_related; cd01276 557598000610 nucleotide binding site/active site [active] 557598000611 HIT family signature motif; other site 557598000612 catalytic residue [active] 557598000613 twin arginine translocase protein A; Provisional; Region: tatA; PRK02958 557598000614 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 557598000615 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 557598000616 Predicted membrane protein (DUF2069); Region: DUF2069; cl01299 557598000617 Putative phosphatase (DUF442); Region: DUF442; cl17385 557598000618 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 557598000619 Predicted metal-dependent hydrolases with the TIM-barrel fold [General function prediction only]; Region: COG1099 557598000620 active site 557598000621 sensor protein RstB; Provisional; Region: PRK10604 557598000622 HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain; Region: HAMP; smart00304 557598000623 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 557598000624 dimer interface [polypeptide binding]; other site 557598000625 phosphorylation site [posttranslational modification] 557598000626 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 557598000627 ATP binding site [chemical binding]; other site 557598000628 Mg2+ binding site [ion binding]; other site 557598000629 G-X-G motif; other site 557598000630 DNA-binding transcriptional regulator RstA; Provisional; Region: PRK10701 557598000631 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 557598000632 active site 557598000633 phosphorylation site [posttranslational modification] 557598000634 intermolecular recognition site; other site 557598000635 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 557598000636 DNA binding site [nucleotide binding] 557598000637 Cytochrome c [Energy production and conversion]; Region: COG3258 557598000638 Cytochrome c; Region: Cytochrom_C; pfam00034 557598000639 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 557598000640 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 557598000641 active site 557598000642 phosphorylation site [posttranslational modification] 557598000643 intermolecular recognition site; other site 557598000644 dimerization interface [polypeptide binding]; other site 557598000645 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 557598000646 DNA binding residues [nucleotide binding] 557598000647 dimerization interface [polypeptide binding]; other site 557598000648 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 557598000649 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 557598000650 dimer interface [polypeptide binding]; other site 557598000651 phosphorylation site [posttranslational modification] 557598000652 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 557598000653 ATP binding site [chemical binding]; other site 557598000654 Mg2+ binding site [ion binding]; other site 557598000655 G-X-G motif; other site 557598000656 acetyl-CoA acetyltransferase; Provisional; Region: PRK06954 557598000657 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 557598000658 dimer interface [polypeptide binding]; other site 557598000659 active site 557598000660 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 557598000661 Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR; Region: HTH_GnyR; cd04776 557598000662 DNA binding residues [nucleotide binding] 557598000663 putative dimer interface [polypeptide binding]; other site 557598000664 3-hydroxybutyryl-CoA dehydrogenase; Validated; Region: PRK05808 557598000665 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 557598000666 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 557598000667 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 557598000668 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 557598000669 Long-chain fatty acid CoA synthetases and Bubblegum-like very long-chain fatty acid CoA synthetases; Region: VL_LC_FACS_like; cd05907 557598000670 acyl-activating enzyme (AAE) consensus motif; other site 557598000671 putative AMP binding site [chemical binding]; other site 557598000672 putative active site [active] 557598000673 putative CoA binding site [chemical binding]; other site 557598000674 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 557598000675 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 557598000676 Walker A/P-loop; other site 557598000677 ATP binding site [chemical binding]; other site 557598000678 Q-loop/lid; other site 557598000679 ABC transporter signature motif; other site 557598000680 Walker B; other site 557598000681 D-loop; other site 557598000682 H-loop/switch region; other site 557598000683 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 557598000684 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 557598000685 TM-ABC transporter signature motif; other site 557598000686 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 557598000687 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 557598000688 TM-ABC transporter signature motif; other site 557598000689 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions; Region: PBP1_ABC_ligand_binding_like_1; cd06334 557598000690 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 557598000691 putative ligand binding site [chemical binding]; other site 557598000692 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 557598000693 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 557598000694 Walker A/P-loop; other site 557598000695 ATP binding site [chemical binding]; other site 557598000696 Q-loop/lid; other site 557598000697 ABC transporter signature motif; other site 557598000698 Walker B; other site 557598000699 D-loop; other site 557598000700 H-loop/switch region; other site 557598000701 Coenzyme F390 synthetase [Coenzyme metabolism]; Region: PaaK; COG1541 557598000702 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 557598000703 acyl-activating enzyme (AAE) consensus motif; other site 557598000704 active site 557598000705 AMP binding site [chemical binding]; other site 557598000706 CoA binding site [chemical binding]; other site 557598000707 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 557598000708 methylmalonic acid semialdehyde dehydrogenase; Region: MMSDH; TIGR01722 557598000709 tetrameric interface [polypeptide binding]; other site 557598000710 NAD binding site [chemical binding]; other site 557598000711 catalytic residues [active] 557598000712 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 557598000713 Isobutyryl-CoA dehydrogenase; Region: IBD; cd01162 557598000714 substrate binding pocket [chemical binding]; other site 557598000715 FAD binding site [chemical binding]; other site 557598000716 catalytic base [active] 557598000717 enoyl-CoA hydratase; Provisional; Region: PRK09076 557598000718 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 557598000719 substrate binding site [chemical binding]; other site 557598000720 oxyanion hole (OAH) forming residues; other site 557598000721 trimer interface [polypeptide binding]; other site 557598000722 3-hydroxyisobutyryl-CoA hydrolase; Provisional; Region: PRK05617 557598000723 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 557598000724 substrate binding site [chemical binding]; other site 557598000725 oxyanion hole (OAH) forming residues; other site 557598000726 trimer interface [polypeptide binding]; other site 557598000727 2-enoyl-CoA Hydratase C-terminal region; Region: ECH_C; pfam13766 557598000728 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 557598000729 3-hydroxyisobutyrate dehydrogenase; Region: HIBADH; TIGR01692 557598000730 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 557598000731 macrolide transporter ATP-binding /permease protein; Provisional; Region: PRK10535 557598000732 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 557598000733 Walker A/P-loop; other site 557598000734 ATP binding site [chemical binding]; other site 557598000735 Q-loop/lid; other site 557598000736 ABC transporter signature motif; other site 557598000737 Walker B; other site 557598000738 D-loop; other site 557598000739 H-loop/switch region; other site 557598000740 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 557598000741 FtsX-like permease family; Region: FtsX; pfam02687 557598000742 macrolide transporter subunit MacA; Provisional; Region: PRK11578 557598000743 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 557598000744 HlyD family secretion protein; Region: HlyD_3; pfam13437 557598000745 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 557598000746 Ca2+ binding site [ion binding]; other site 557598000747 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 557598000748 pseudo EF-hand loop; other site 557598000749 peptide binding pocket; other site 557598000750 EF-hand domain pair; Region: EF_hand_5; pfam13499 557598000751 Ca2+ binding site [ion binding]; other site 557598000752 Eps15 homology domain; found in proteins implicated in endocytosis, vesicle transport, and signal transduction. The alignment contains a pair of EF-hand motifs, typically one of them is canonical and binds to Ca2+, while the other may not bind to Ca2+. A...; Region: EH; cd00052 557598000753 pseudo EF-hand loop; other site 557598000754 peptide binding pocket; other site 557598000755 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 557598000756 EF-hand domain pair; Region: EF_hand_5; pfam13499 557598000757 Ca2+ binding site [ion binding]; other site 557598000758 Ca2+ binding site [ion binding]; other site 557598000759 DNA-binding transcriptional regulator BaeR; Provisional; Region: PRK10710 557598000760 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 557598000761 active site 557598000762 phosphorylation site [posttranslational modification] 557598000763 intermolecular recognition site; other site 557598000764 dimerization interface [polypeptide binding]; other site 557598000765 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 557598000766 DNA binding site [nucleotide binding] 557598000767 signal transduction histidine-protein kinase BaeS; Provisional; Region: PRK10549 557598000768 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 557598000769 dimerization interface [polypeptide binding]; other site 557598000770 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 557598000771 dimer interface [polypeptide binding]; other site 557598000772 phosphorylation site [posttranslational modification] 557598000773 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 557598000774 ATP binding site [chemical binding]; other site 557598000775 Mg2+ binding site [ion binding]; other site 557598000776 G-X-G motif; other site 557598000777 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557598000778 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 557598000779 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 557598000780 putative effector binding pocket; other site 557598000781 putative dimerization interface [polypeptide binding]; other site 557598000782 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 557598000783 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 557598000784 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 557598000785 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 557598000786 DNA binding residues [nucleotide binding] 557598000787 putative protein insertion permease FtsX; Region: ftsX; TIGR00439 557598000788 cell division ABC transporter subunit FtsX; Provisional; Region: ftsX; PRK11026 557598000789 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 557598000790 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 557598000791 Walker A/P-loop; other site 557598000792 ATP binding site [chemical binding]; other site 557598000793 Q-loop/lid; other site 557598000794 ABC transporter signature motif; other site 557598000795 Walker B; other site 557598000796 D-loop; other site 557598000797 H-loop/switch region; other site 557598000798 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 557598000799 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 557598000800 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 557598000801 P loop; other site 557598000802 GTP binding site [chemical binding]; other site 557598000803 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 557598000804 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 557598000805 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 557598000806 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 557598000807 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 557598000808 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 557598000809 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 557598000810 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 557598000811 S-adenosylmethionine binding site [chemical binding]; other site 557598000812 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 557598000813 elongation factor Tu; Reviewed; Region: PRK00049 557598000814 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 557598000815 G1 box; other site 557598000816 GEF interaction site [polypeptide binding]; other site 557598000817 GTP/Mg2+ binding site [chemical binding]; other site 557598000818 Switch I region; other site 557598000819 G2 box; other site 557598000820 G3 box; other site 557598000821 Switch II region; other site 557598000822 G4 box; other site 557598000823 G5 box; other site 557598000824 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 557598000825 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 557598000826 Antibiotic Binding Site [chemical binding]; other site 557598000827 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK05740 557598000828 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 557598000829 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 557598000830 putative homodimer interface [polypeptide binding]; other site 557598000831 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 557598000832 heterodimer interface [polypeptide binding]; other site 557598000833 homodimer interface [polypeptide binding]; other site 557598000834 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 557598000835 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 557598000836 23S rRNA interface [nucleotide binding]; other site 557598000837 L7/L12 interface [polypeptide binding]; other site 557598000838 putative thiostrepton binding site; other site 557598000839 L25 interface [polypeptide binding]; other site 557598000840 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 557598000841 mRNA/rRNA interface [nucleotide binding]; other site 557598000842 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 557598000843 23S rRNA interface [nucleotide binding]; other site 557598000844 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 557598000845 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 557598000846 core dimer interface [polypeptide binding]; other site 557598000847 peripheral dimer interface [polypeptide binding]; other site 557598000848 L10 interface [polypeptide binding]; other site 557598000849 L11 interface [polypeptide binding]; other site 557598000850 putative EF-Tu interaction site [polypeptide binding]; other site 557598000851 putative EF-G interaction site [polypeptide binding]; other site 557598000852 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 557598000853 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 557598000854 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 557598000855 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 557598000856 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 557598000857 RPB3 interaction site [polypeptide binding]; other site 557598000858 RPB1 interaction site [polypeptide binding]; other site 557598000859 RPB11 interaction site [polypeptide binding]; other site 557598000860 RPB10 interaction site [polypeptide binding]; other site 557598000861 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 557598000862 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 557598000863 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 557598000864 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 557598000865 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 557598000866 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 557598000867 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 557598000868 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 557598000869 DNA binding site [nucleotide binding] 557598000870 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 557598000871 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 557598000872 S17 interaction site [polypeptide binding]; other site 557598000873 S8 interaction site; other site 557598000874 16S rRNA interaction site [nucleotide binding]; other site 557598000875 streptomycin interaction site [chemical binding]; other site 557598000876 23S rRNA interaction site [nucleotide binding]; other site 557598000877 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 557598000878 30S ribosomal protein S7; Validated; Region: PRK05302 557598000879 elongation factor G; Reviewed; Region: PRK00007 557598000880 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 557598000881 G1 box; other site 557598000882 putative GEF interaction site [polypeptide binding]; other site 557598000883 GTP/Mg2+ binding site [chemical binding]; other site 557598000884 Switch I region; other site 557598000885 G2 box; other site 557598000886 G3 box; other site 557598000887 Switch II region; other site 557598000888 G4 box; other site 557598000889 G5 box; other site 557598000890 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 557598000891 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 557598000892 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 557598000893 elongation factor Tu; Reviewed; Region: PRK00049 557598000894 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 557598000895 G1 box; other site 557598000896 GEF interaction site [polypeptide binding]; other site 557598000897 GTP/Mg2+ binding site [chemical binding]; other site 557598000898 Switch I region; other site 557598000899 G2 box; other site 557598000900 G3 box; other site 557598000901 Switch II region; other site 557598000902 G4 box; other site 557598000903 G5 box; other site 557598000904 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 557598000905 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 557598000906 Antibiotic Binding Site [chemical binding]; other site 557598000907 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 557598000908 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 557598000909 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 557598000910 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 557598000911 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 557598000912 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 557598000913 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 557598000914 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 557598000915 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 557598000916 putative translocon binding site; other site 557598000917 protein-rRNA interface [nucleotide binding]; other site 557598000918 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 557598000919 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 557598000920 G-X-X-G motif; other site 557598000921 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 557598000922 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 557598000923 23S rRNA interface [nucleotide binding]; other site 557598000924 5S rRNA interface [nucleotide binding]; other site 557598000925 putative antibiotic binding site [chemical binding]; other site 557598000926 L25 interface [polypeptide binding]; other site 557598000927 L27 interface [polypeptide binding]; other site 557598000928 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 557598000929 23S rRNA interface [nucleotide binding]; other site 557598000930 putative translocon interaction site; other site 557598000931 signal recognition particle (SRP54) interaction site; other site 557598000932 L23 interface [polypeptide binding]; other site 557598000933 trigger factor interaction site; other site 557598000934 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 557598000935 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 557598000936 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 557598000937 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 557598000938 RNA binding site [nucleotide binding]; other site 557598000939 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 557598000940 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 557598000941 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 557598000942 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 557598000943 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 557598000944 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 557598000945 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 557598000946 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 557598000947 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 557598000948 5S rRNA interface [nucleotide binding]; other site 557598000949 23S rRNA interface [nucleotide binding]; other site 557598000950 L5 interface [polypeptide binding]; other site 557598000951 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 557598000952 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 557598000953 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 557598000954 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 557598000955 23S rRNA binding site [nucleotide binding]; other site 557598000956 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 557598000957 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 557598000958 SecY translocase; Region: SecY; pfam00344 557598000959 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 557598000960 rRNA binding site [nucleotide binding]; other site 557598000961 predicted 30S ribosome binding site; other site 557598000962 50S ribosomal protein L36; Reviewed; Region: rpmJ; PRK00465 557598000963 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 557598000964 30S ribosomal protein S13; Region: bact_S13; TIGR03631 557598000965 30S ribosomal protein S11; Validated; Region: PRK05309 557598000966 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 557598000967 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 557598000968 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 557598000969 RNA binding surface [nucleotide binding]; other site 557598000970 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 557598000971 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 557598000972 alphaNTD homodimer interface [polypeptide binding]; other site 557598000973 alphaNTD - beta interaction site [polypeptide binding]; other site 557598000974 alphaNTD - beta' interaction site [polypeptide binding]; other site 557598000975 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 557598000976 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 557598000977 pteridine reductase; Provisional; Region: PRK09135 557598000978 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557598000979 NAD(P) binding site [chemical binding]; other site 557598000980 active site 557598000981 Uncharacterized conserved protein [Function unknown]; Region: COG1565 557598000982 Uncharacterized anaerobic dehydrogenase [General function prediction only]; Region: COG3383 557598000983 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 557598000984 catalytic loop [active] 557598000985 iron binding site [ion binding]; other site 557598000986 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; smart00929 557598000987 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 557598000988 [4Fe-4S] binding site [ion binding]; other site 557598000989 molybdopterin cofactor binding site; other site 557598000990 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 557598000991 molybdopterin cofactor binding site; other site 557598000992 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 557598000993 SLBB domain; Region: SLBB; pfam10531 557598000994 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; pfam10589 557598000995 formate dehydrogenase subunit gamma; Validated; Region: PRK05988 557598000996 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 557598000997 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NAD-dependent formate dehydrogenase (FDH) beta subunit; composed of proteins similar to the beta subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of...; Region: TRX_Fd_FDH_beta; cd03063 557598000998 putative dimer interface [polypeptide binding]; other site 557598000999 MgtC family; Region: MgtC; pfam02308 557598001000 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 557598001001 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 557598001002 putative active site [active] 557598001003 catalytic triad [active] 557598001004 putative dimer interface [polypeptide binding]; other site 557598001005 Putative Mg2+ and Co2+ transporter CorC [Inorganic ion transport and metabolism]; Region: CorC; COG4535 557598001006 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 557598001007 Transporter associated domain; Region: CorC_HlyC; smart01091 557598001008 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG0319 557598001009 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 557598001010 PhoH-like protein; Region: PhoH; pfam02562 557598001011 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 557598001012 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 557598001013 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 557598001014 FeS/SAM binding site; other site 557598001015 TRAM domain; Region: TRAM; pfam01938 557598001016 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557598001017 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 557598001018 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 557598001019 dimerization interface [polypeptide binding]; other site 557598001020 arginine-ornithine antiporter; Region: arg_ornith_anti; TIGR03810 557598001021 Predicted amino acid racemase [Amino acid transport and metabolism]; Region: COG3457 557598001022 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase-like 1; Region: PLPDE_III_AR_like_1; cd06815 557598001023 dimer interface [polypeptide binding]; other site 557598001024 active site 557598001025 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 557598001026 substrate binding site [chemical binding]; other site 557598001027 catalytic residue [active] 557598001028 C4-dicarboxylate transporter [Energy production and conversion]; Region: DcuC; cl17322 557598001029 Predicted membrane protein [Function unknown]; Region: COG1288 557598001030 C4-dicarboxylate anaerobic carrier; Region: DcuC; pfam03606 557598001031 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557598001032 LysR substrate binding domain; Region: LysR_substrate; pfam03466 557598001033 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 557598001034 active site 557598001035 SCP-2 sterol transfer family; Region: SCP2; cl01225 557598001036 putative protease; Provisional; Region: PRK15447 557598001037 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 557598001038 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 557598001039 Peptidase family U32; Region: Peptidase_U32; pfam01136 557598001040 Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; Region: HTH_MlrA-CarA; cd01104 557598001041 DNA binding residues [nucleotide binding] 557598001042 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 557598001043 B12 binding domain; Region: B12-binding_2; pfam02607 557598001044 B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase; Region: B12-binding_like; cl00293 557598001045 B12 binding site [chemical binding]; other site 557598001046 Predicted integral membrane protein (DUF2189); Region: DUF2189; pfam09955 557598001047 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 557598001048 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 557598001049 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 557598001050 putative active site [active] 557598001051 catalytic residue [active] 557598001052 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 557598001053 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 557598001054 5S rRNA interface [nucleotide binding]; other site 557598001055 CTC domain interface [polypeptide binding]; other site 557598001056 L16 interface [polypeptide binding]; other site 557598001057 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 557598001058 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 557598001059 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 557598001060 active site 557598001061 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00343 557598001062 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 557598001063 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 557598001064 outer membrane lipoprotein LolB; Provisional; Region: lolB; PRK00022 557598001065 Outer membrane lipoprotein LolB; Region: LolB; pfam03550 557598001066 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 557598001067 binding surface 557598001068 TPR motif; other site 557598001069 TPR repeat; Region: TPR_11; pfam13414 557598001070 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 557598001071 binding surface 557598001072 TPR motif; other site 557598001073 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 557598001074 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 557598001075 DNA binding site [nucleotide binding] 557598001076 catalytic residue [active] 557598001077 H2TH interface [polypeptide binding]; other site 557598001078 putative catalytic residues [active] 557598001079 turnover-facilitating residue; other site 557598001080 intercalation triad [nucleotide binding]; other site 557598001081 8OG recognition residue [nucleotide binding]; other site 557598001082 putative reading head residues; other site 557598001083 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 557598001084 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 557598001085 diadenosine tetraphosphatase; Reviewed; Region: apaH; PRK00166 557598001086 Escherichia coli ApaH and related proteins, metallophosphatase domain; Region: MPP_ApaH; cd07422 557598001087 active site 557598001088 metal binding site [ion binding]; metal-binding site 557598001089 ATP-dependent DNA helicase Rep; Region: rep; TIGR01074 557598001090 Part of AAA domain; Region: AAA_19; pfam13245 557598001091 Family description; Region: UvrD_C_2; pfam13538 557598001092 polyphosphate:AMP phosphotransferase; Region: poly_P_AMP_trns; TIGR03708 557598001093 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 557598001094 Polyphosphate kinase 2 (PPK2); Region: PPK2; cl11971 557598001095 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 557598001096 nudix motif; other site 557598001097 4-hydroxybenzoate polyprenyltransferase and related prenyltransferases [Coenzyme metabolism]; Region: UbiA; cl00337 557598001098 UbiA prenyltransferase family; Region: UbiA; pfam01040 557598001099 Chorismate lyase; Region: Chor_lyase; cl01230 557598001100 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 557598001101 catalytic core [active] 557598001102 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 557598001103 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 557598001104 dimer interface [polypeptide binding]; other site 557598001105 phosphorylation site [posttranslational modification] 557598001106 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 557598001107 ATP binding site [chemical binding]; other site 557598001108 G-X-G motif; other site 557598001109 DNA-binding transcriptional regulator QseB; Provisional; Region: PRK10336 557598001110 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 557598001111 active site 557598001112 phosphorylation site [posttranslational modification] 557598001113 intermolecular recognition site; other site 557598001114 dimerization interface [polypeptide binding]; other site 557598001115 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 557598001116 DNA binding site [nucleotide binding] 557598001117 Peptidase propeptide and YPEB domain; Region: PepSY_2; pfam13670 557598001118 Serine hydrolase; Region: Ser_hydrolase; pfam06821 557598001119 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 557598001120 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 557598001121 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 557598001122 dimer interface [polypeptide binding]; other site 557598001123 conserved gate region; other site 557598001124 putative PBP binding loops; other site 557598001125 ABC-ATPase subunit interface; other site 557598001126 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 557598001127 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 557598001128 sulfate transport protein; Provisional; Region: cysT; CHL00187 557598001129 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 557598001130 dimer interface [polypeptide binding]; other site 557598001131 conserved gate region; other site 557598001132 putative PBP binding loops; other site 557598001133 ABC-ATPase subunit interface; other site 557598001134 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 557598001135 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 557598001136 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 557598001137 dimerization interface [polypeptide binding]; other site 557598001138 DsrE/DsrF-like family; Region: DrsE; cl00672 557598001139 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 557598001140 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 557598001141 Domain of unknown function (DUF1853); Region: DUF1853; cl01545 557598001142 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 557598001143 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 557598001144 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 557598001145 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 557598001146 active site 557598001147 dimerization interface [polypeptide binding]; other site 557598001148 GTP-binding protein YchF; Reviewed; Region: PRK09601 557598001149 YchF GTPase; Region: YchF; cd01900 557598001150 G1 box; other site 557598001151 GTP/Mg2+ binding site [chemical binding]; other site 557598001152 Switch I region; other site 557598001153 G2 box; other site 557598001154 Switch II region; other site 557598001155 G3 box; other site 557598001156 G4 box; other site 557598001157 G5 box; other site 557598001158 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 557598001159 Cache domain; Region: Cache_1; pfam02743 557598001160 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 557598001161 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557598001162 metal binding site [ion binding]; metal-binding site 557598001163 active site 557598001164 I-site; other site 557598001165 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 557598001166 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 557598001167 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 557598001168 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 557598001169 alanine racemase; Reviewed; Region: alr; PRK00053 557598001170 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 557598001171 active site 557598001172 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 557598001173 substrate binding site [chemical binding]; other site 557598001174 catalytic residues [active] 557598001175 dimer interface [polypeptide binding]; other site 557598001176 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 557598001177 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 557598001178 FeS/SAM binding site; other site 557598001179 HemN C-terminal domain; Region: HemN_C; pfam06969 557598001180 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 557598001181 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 557598001182 ligand binding site [chemical binding]; other site 557598001183 flexible hinge region; other site 557598001184 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 557598001185 putative switch regulator; other site 557598001186 non-specific DNA interactions [nucleotide binding]; other site 557598001187 DNA binding site [nucleotide binding] 557598001188 sequence specific DNA binding site [nucleotide binding]; other site 557598001189 putative cAMP binding site [chemical binding]; other site 557598001190 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 557598001191 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 557598001192 DNA binding residues [nucleotide binding] 557598001193 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 557598001194 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 557598001195 Peptidase family M23; Region: Peptidase_M23; pfam01551 557598001196 protein-L-isoaspartate O-methyltransferase; Reviewed; Region: pcm; PRK00312 557598001197 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 557598001198 S-adenosylmethionine binding site [chemical binding]; other site 557598001199 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 557598001200 quinolinate synthetase; Provisional; Region: PRK09375 557598001201 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 557598001202 CoA binding domain; Region: CoA_binding_2; pfam13380 557598001203 Succinyl-CoA ligase like flavodoxin domain; Region: Succ_CoA_lig; pfam13607 557598001204 ATP-grasp domain; Region: ATP-grasp_5; pfam13549 557598001205 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 557598001206 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 557598001207 Coenzyme A binding pocket [chemical binding]; other site 557598001208 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 557598001209 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 557598001210 RimM N-terminal domain; Region: RimM; pfam01782 557598001211 PRC-barrel domain; Region: PRC; pfam05239 557598001212 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 557598001213 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 557598001214 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 557598001215 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 557598001216 DNA binding site [nucleotide binding] 557598001217 active site 557598001218 ATP-dependent Clp protease ATP-binding subunit clpA; Region: ClpA; TIGR02639 557598001219 Clp amino terminal domain; Region: Clp_N; pfam02861 557598001220 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 557598001221 Walker A motif; other site 557598001222 ATP binding site [chemical binding]; other site 557598001223 Walker B motif; other site 557598001224 arginine finger; other site 557598001225 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 557598001226 Walker A motif; other site 557598001227 ATP binding site [chemical binding]; other site 557598001228 Walker B motif; other site 557598001229 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 557598001230 Uncharacterized conserved protein [Function unknown]; Region: COG2127 557598001231 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 557598001232 DNA-binding site [nucleotide binding]; DNA binding site 557598001233 RNA-binding motif; other site 557598001234 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 557598001235 bifunctional isocitrate dehydrogenase kinase/phosphatase protein; Validated; Region: aceK; PRK02946 557598001236 Isocitrate dehydrogenase kinase/phosphatase [Signal transduction mechanisms]; Region: COG4579 557598001237 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 557598001238 pseudouridine synthase; Region: TIGR00093 557598001239 active site 557598001240 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 557598001241 MutS domain I; Region: MutS_I; pfam01624 557598001242 MutS domain II; Region: MutS_II; pfam05188 557598001243 MutS domain III; Region: MutS_III; pfam05192 557598001244 MutS domain V; Region: MutS_V; pfam00488 557598001245 Walker A/P-loop; other site 557598001246 ATP binding site [chemical binding]; other site 557598001247 Q-loop/lid; other site 557598001248 ABC transporter signature motif; other site 557598001249 Walker B; other site 557598001250 D-loop; other site 557598001251 H-loop/switch region; other site 557598001252 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 557598001253 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 557598001254 active site 557598001255 DNA binding site [nucleotide binding] 557598001256 Int/Topo IB signature motif; other site 557598001257 potential protein location (hypothetical protein) that overlaps protein (hypothetical protein) 557598001258 potential protein location (hypothetical protein) that overlaps protein (hypothetical protein) 557598001259 Bacteriophage replication gene A protein (GPA); Region: Phage_GPA; cl15276 557598001260 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 557598001261 non-specific DNA binding site [nucleotide binding]; other site 557598001262 salt bridge; other site 557598001263 sequence-specific DNA binding site [nucleotide binding]; other site 557598001264 Ogr/Delta-like zinc finger; Region: Ogr_Delta; pfam04606 557598001265 Archaea-specific editing domain of threonyl-tRNA synthetase; Region: tRNA-Thr_ED; pfam08915 557598001266 Predicted nucleotide-binding protein containing TIR-like domain; Region: TIR-like; pfam10137 557598001267 Uncharacterized small protein (DUF2158); Region: DUF2158; pfam09926 557598001268 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 557598001269 Phage P2 GpU; Region: Phage_P2_GpU; pfam06995 557598001270 phage tail tape measure protein, TP901 family, core region; Region: tape_meas_TP901; TIGR01760 557598001271 Phage P2 GpE; Region: Phage_P2_GpE; pfam06528 557598001272 Mu-like prophage FluMu protein gp41; Region: FluMu_gp41; pfam10109 557598001273 major tail tube protein; Provisional; Region: FII; PHA02600 557598001274 major tail sheath protein; Provisional; Region: FI; PHA02560 557598001275 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dam; COG0338 557598001276 Mu-like prophage protein Com; Region: Mu-like_Com; cl11540 557598001277 Domain of unknown function (DUF4376); Region: DUF4376; pfam14301 557598001278 Phage tail-collar fibre protein; Region: DUF3751; pfam12571 557598001279 Bacteriophage P2-related tail formation protein [General function prediction only]; Region: gpI; COG4385 557598001280 Baseplate J-like protein; Region: Baseplate_J; cl01294 557598001281 Gene 25-like lysozyme; Region: GPW_gp25; cl01403 557598001282 phage baseplate assembly protein V; Region: phage_P2_V; TIGR01644 557598001283 Phage-related baseplate assembly protein; Region: Phage_base_V; cl17812 557598001284 Phage virion morphogenesis family; Region: Phage_tail_S; pfam05069 557598001285 P2 phage tail completion protein R (GpR); Region: P2_Phage_GpR; pfam06891 557598001286 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 557598001287 phage lysis regulatory protein, LysB family; Region: phage_LysB; TIGR03495 557598001288 Putative peptidoglycan-binding domain-containing protein [Cell envelope biogenesis, outer membrane]; Region: COG3409 557598001289 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 557598001290 Protein of unknown function (DUF3380); Region: DUF3380; pfam11860 557598001291 Protein of unknown function (DUF754); Region: DUF754; pfam05449 557598001292 Phage Tail Protein X; Region: Phage_tail_X; cl02088 557598001293 Phage head completion protein (GPL); Region: Phage_GPL; pfam05926 557598001294 terminase endonuclease subunit; Provisional; Region: M; PHA02537 557598001295 Phage small terminase subunit; Region: Phage_term_smal; pfam05944 557598001296 capsid protein; Provisional; Region: N; PHA02538 557598001297 Phage capsid scaffolding protein (GPO) serine peptidase; Region: Phage_GPO; cl15838 557598001298 terminase ATPase subunit; Provisional; Region: P; PHA02535 557598001299 Putative ATPase subunit of terminase (gpP-like); Region: Terminase_5; pfam06056 557598001300 Mu-like prophage FluMu protein gp28 [General function prediction only]; Region: COG4373 557598001301 portal vertex protein; Provisional; Region: Q; PHA02536 557598001302 Phage portal protein; Region: Phage_portal; pfam04860 557598001303 Protein of unknown function (DUF2798); Region: DUF2798; pfam11391 557598001304 Domain of unknown function (DUF1841); Region: DUF1841; pfam08897 557598001305 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 557598001306 catalytic residues [active] 557598001307 dimer interface [polypeptide binding]; other site 557598001308 tRNA (guanine-N(7)-)-methyltransferase; Reviewed; Region: trmB; PRK00121 557598001309 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557598001310 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 557598001311 NAD(P) binding site [chemical binding]; other site 557598001312 active site 557598001313 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 557598001314 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 557598001315 catalytic loop [active] 557598001316 iron binding site [ion binding]; other site 557598001317 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 557598001318 FAD binding pocket [chemical binding]; other site 557598001319 FAD binding motif [chemical binding]; other site 557598001320 phosphate binding motif [ion binding]; other site 557598001321 beta-alpha-beta structure motif; other site 557598001322 NAD binding pocket [chemical binding]; other site 557598001323 Spore germination protein; Region: Spore_permease; cl17796 557598001324 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 557598001325 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 557598001326 eyelet of channel; other site 557598001327 trimer interface [polypeptide binding]; other site 557598001328 Uncharacterized protein conserved in bacteria containing a pentein-type domain [Function unknown]; Region: COG4874 557598001329 Amidinotransferase; Region: Amidinotransf; pfam02274 557598001330 lysine transporter; Provisional; Region: PRK10836 557598001331 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 557598001332 active site 557598001333 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 557598001334 Clp amino terminal domain; Region: Clp_N; pfam02861 557598001335 Clp amino terminal domain; Region: Clp_N; pfam02861 557598001336 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 557598001337 Walker A motif; other site 557598001338 ATP binding site [chemical binding]; other site 557598001339 Walker B motif; other site 557598001340 arginine finger; other site 557598001341 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 557598001342 Walker A motif; other site 557598001343 ATP binding site [chemical binding]; other site 557598001344 Walker B motif; other site 557598001345 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 557598001346 flagellar hook-associated protein FlgL; Reviewed; Region: flgL; PRK07192 557598001347 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 557598001348 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK06945 557598001349 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 557598001350 flagellar rod assembly protein/muramidase FlgJ; Validated; Region: flgJ; PRK05684 557598001351 Rod binding protein; Region: Rod-binding; cl01626 557598001352 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; Region: Glucosaminidase; pfam01832 557598001353 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 557598001354 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 557598001355 Flagellar basal body L-ring protein [Cell motility and secretion]; Region: FlgH; COG2063 557598001356 Flagellar L-ring protein; Region: FlgH; pfam02107 557598001357 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 557598001358 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 557598001359 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 557598001360 flagellar basal body rod protein FlgF; Reviewed; Region: flgF; PRK12640 557598001361 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 557598001362 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 557598001363 flagellar hook protein FlgE; Provisional; Region: flgE; PRK12637 557598001364 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 557598001365 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 557598001366 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 557598001367 flagellar basal body rod modification protein; Reviewed; Region: flgD; PRK06655 557598001368 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 557598001369 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 557598001370 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 557598001371 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 557598001372 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 557598001373 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK05680 557598001374 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK07182 557598001375 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 557598001376 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 557598001377 Walker A/P-loop; other site 557598001378 ATP binding site [chemical binding]; other site 557598001379 Q-loop/lid; other site 557598001380 ABC transporter signature motif; other site 557598001381 Walker B; other site 557598001382 D-loop; other site 557598001383 H-loop/switch region; other site 557598001384 ABC nitrate/sulfonate/bicarbonate family transporter, ATPase subunit; Region: ABC_transp; pfam09821 557598001385 ABC-type anion transport system, duplicated permease component [Inorganic ion transport and metabolism]; Region: COG4986 557598001386 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 557598001387 dimer interface [polypeptide binding]; other site 557598001388 conserved gate region; other site 557598001389 putative PBP binding loops; other site 557598001390 ABC-ATPase subunit interface; other site 557598001391 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 557598001392 Heavy-metal-associated domain; Region: HMA; pfam00403 557598001393 metal-binding site [ion binding] 557598001394 heavy metal translocating P-type ATPase; Region: ATPase-IB_hvy; TIGR01525 557598001395 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 557598001396 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 557598001397 Cd(II)/Pb(II)-responsive transcriptional regulator; Region: CadR-PbrR; TIGR02047 557598001398 Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators; Region: HTH_CadR-PbrR; cd04784 557598001399 DNA binding residues [nucleotide binding] 557598001400 dimer interface [polypeptide binding]; other site 557598001401 putative metal binding site [ion binding]; other site 557598001402 putative protease; Provisional; Region: PRK15452 557598001403 Peptidase family U32; Region: Peptidase_U32; pfam01136 557598001404 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 557598001405 dinuclear metal binding motif [ion binding]; other site 557598001406 flagellar assembly protein FliW; Provisional; Region: PRK13284 557598001407 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 557598001408 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 557598001409 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 557598001410 catalytic site [active] 557598001411 G-X2-G-X-G-K; other site 557598001412 DNA-directed RNA polymerase subunit omega; Reviewed; Region: rpoZ; PRK00392 557598001413 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 557598001414 HD domain; Region: HD_4; pfam13328 557598001415 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 557598001416 synthetase active site [active] 557598001417 NTP binding site [chemical binding]; other site 557598001418 metal binding site [ion binding]; metal-binding site 557598001419 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 557598001420 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 557598001421 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 557598001422 thiS-thiF/thiG interaction site; other site 557598001423 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 557598001424 ThiS interaction site; other site 557598001425 putative active site [active] 557598001426 tetramer interface [polypeptide binding]; other site 557598001427 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 557598001428 Yqey-like protein; Region: YqeY; pfam09424 557598001429 DNA primase, catalytic core; Region: dnaG; TIGR01391 557598001430 CHC2 zinc finger; Region: zf-CHC2; pfam01807 557598001431 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 557598001432 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 557598001433 active site 557598001434 metal binding site [ion binding]; metal-binding site 557598001435 interdomain interaction site; other site 557598001436 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 557598001437 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 557598001438 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 557598001439 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 557598001440 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 557598001441 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 557598001442 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 557598001443 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 557598001444 DNA binding residues [nucleotide binding] 557598001445 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 557598001446 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA; Region: MATE_MepA_like; cd13143 557598001447 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557598001448 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 557598001449 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 557598001450 putative effector binding pocket; other site 557598001451 dimerization interface [polypeptide binding]; other site 557598001452 DNA-binding transcriptional regulator MetR; Provisional; Region: PRK15421 557598001453 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 557598001454 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 557598001455 putative dimerization interface [polypeptide binding]; other site 557598001456 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional; Region: PRK05222 557598001457 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 557598001458 THF binding site; other site 557598001459 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 557598001460 substrate binding site [chemical binding]; other site 557598001461 THF binding site; other site 557598001462 zinc-binding site [ion binding]; other site 557598001463 Protein of unknown function (DUF3079); Region: DUF3079; pfam11278 557598001464 Esterase PHB depolymerase; Region: Esterase_phd; pfam10503 557598001465 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_2; cd07253 557598001466 dimer interface [polypeptide binding]; other site 557598001467 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 557598001468 metal binding site [ion binding]; metal-binding site 557598001469 Domain of unknown function (DUF202); Region: DUF202; cl09954 557598001470 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 557598001471 putative substrate binding site 2 [chemical binding]; other site 557598001472 putative substrate binding site 1 [chemical binding]; other site 557598001473 Na binding site 1 [ion binding]; other site 557598001474 Na2 binding site [ion binding]; other site 557598001475 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 557598001476 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 557598001477 dimerization interface [polypeptide binding]; other site 557598001478 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557598001479 dimer interface [polypeptide binding]; other site 557598001480 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 557598001481 putative CheW interface [polypeptide binding]; other site 557598001482 heat shock protein 90; Provisional; Region: PRK05218 557598001483 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 557598001484 ATP binding site [chemical binding]; other site 557598001485 Mg2+ binding site [ion binding]; other site 557598001486 G-X-G motif; other site 557598001487 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 557598001488 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; smart00831 557598001489 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 557598001490 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 557598001491 Soluble P-type ATPase [General function prediction only]; Region: COG4087 557598001492 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 557598001493 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 557598001494 Ligand Binding Site [chemical binding]; other site 557598001495 BCCT family transporter; Region: BCCT; pfam02028 557598001496 Creatinine amidohydrolase; Region: Creatininase; pfam02633 557598001497 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 557598001498 EamA-like transporter family; Region: EamA; pfam00892 557598001499 EamA-like transporter family; Region: EamA; pfam00892 557598001500 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 557598001501 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557598001502 fumarate hydratase; Reviewed; Region: fumC; PRK00485 557598001503 Class II fumarases; Region: Fumarase_classII; cd01362 557598001504 active site 557598001505 tetramer interface [polypeptide binding]; other site 557598001506 Fe(II)-dependent oxygenase superfamily protein; Provisional; Region: PRK05467 557598001507 Outer membrane receptor for monomeric catechols [Inorganic ion transport and metabolism]; Region: Fiu; COG4774 557598001508 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 557598001509 N-terminal plug; other site 557598001510 ligand-binding site [chemical binding]; other site 557598001511 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 557598001512 TolR protein; Region: tolR; TIGR02801 557598001513 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 557598001514 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 557598001515 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 557598001516 Xanthine/uracil permeases [Nucleotide transport and metabolism]; Region: UraA; COG2233 557598001517 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 557598001518 active site 557598001519 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 557598001520 putative GSH binding site [chemical binding]; other site 557598001521 catalytic residues [active] 557598001522 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 557598001523 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 557598001524 putative ion selectivity filter; other site 557598001525 putative pore gating glutamate residue; other site 557598001526 putative H+/Cl- coupling transport residue; other site 557598001527 tRNA and rRNA cytosine-C5-methylases [Translation, ribosomal structure and biogenesis]; Region: Sun; COG0144 557598001528 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 557598001529 S-adenosylmethionine binding site [chemical binding]; other site 557598001530 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 557598001531 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 557598001532 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 557598001533 active site 557598001534 substrate binding site [chemical binding]; other site 557598001535 cosubstrate binding site; other site 557598001536 catalytic site [active] 557598001537 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 557598001538 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 557598001539 dimerization interface [polypeptide binding]; other site 557598001540 putative ATP binding site [chemical binding]; other site 557598001541 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 557598001542 Domain of unknown function DUF20; Region: UPF0118; pfam01594 557598001543 DnaA regulatory inactivator Hda; Validated; Region: PRK08903 557598001544 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 557598001545 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 557598001546 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 557598001547 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3165 557598001548 SCP-2 sterol transfer family; Region: SCP2; pfam02036 557598001549 putative ubiquinone biosynthesis protein UbiB; Reviewed; Region: ubiB; PRK04750 557598001550 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 557598001551 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 557598001552 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 557598001553 FeS/SAM binding site; other site 557598001554 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 557598001555 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_cladeB; cd00884 557598001556 active site clefts [active] 557598001557 zinc binding site [ion binding]; other site 557598001558 dimer interface [polypeptide binding]; other site 557598001559 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 557598001560 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557598001561 dimer interface [polypeptide binding]; other site 557598001562 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 557598001563 putative CheW interface [polypeptide binding]; other site 557598001564 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 557598001565 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 557598001566 Surface antigen; Region: Bac_surface_Ag; pfam01103 557598001567 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2911 557598001568 Family of unknown function (DUF490); Region: DUF490; pfam04357 557598001569 phosphate transporter ATP-binding protein; Provisional; Region: pstB; PRK10744 557598001570 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 557598001571 Walker A/P-loop; other site 557598001572 ATP binding site [chemical binding]; other site 557598001573 Q-loop/lid; other site 557598001574 ABC transporter signature motif; other site 557598001575 Walker B; other site 557598001576 D-loop; other site 557598001577 H-loop/switch region; other site 557598001578 phosphate transporter permease subunit PtsA; Provisional; Region: pstA; PRK11268 557598001579 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 557598001580 dimer interface [polypeptide binding]; other site 557598001581 conserved gate region; other site 557598001582 putative PBP binding loops; other site 557598001583 ABC-ATPase subunit interface; other site 557598001584 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstC; COG0573 557598001585 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 557598001586 dimer interface [polypeptide binding]; other site 557598001587 conserved gate region; other site 557598001588 putative PBP binding loops; other site 557598001589 ABC-ATPase subunit interface; other site 557598001590 PBP superfamily domain; Region: PBP_like_2; cl17296 557598001591 triosephosphate isomerase; Provisional; Region: PRK14567 557598001592 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 557598001593 substrate binding site [chemical binding]; other site 557598001594 dimer interface [polypeptide binding]; other site 557598001595 catalytic triad [active] 557598001596 Preprotein translocase SecG subunit; Region: SecG; pfam03840 557598001597 NADH:ubiquinone oxidoreductase subunit A; Validated; Region: PRK06602 557598001598 NADH dehydrogenase subunit B; Validated; Region: PRK06411 557598001599 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 557598001600 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 557598001601 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 557598001602 NADH dehydrogenase subunit D; Validated; Region: PRK06075 557598001603 NADH dehydrogenase subunit E; Validated; Region: PRK07539 557598001604 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 557598001605 putative dimer interface [polypeptide binding]; other site 557598001606 [2Fe-2S] cluster binding site [ion binding]; other site 557598001607 NADH-quinone oxidoreductase, F subunit; Region: nuoF_fam; TIGR01959 557598001608 SLBB domain; Region: SLBB; pfam10531 557598001609 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 557598001610 NADH dehydrogenase subunit G; Validated; Region: PRK09129 557598001611 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 557598001612 catalytic loop [active] 557598001613 iron binding site [ion binding]; other site 557598001614 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 557598001615 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 557598001616 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; cl09929 557598001617 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 557598001618 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 557598001619 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 557598001620 4Fe-4S binding domain; Region: Fer4; pfam00037 557598001621 4Fe-4S binding domain; Region: Fer4; pfam00037 557598001622 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 557598001623 NADH dehydrogenase subunit J; Provisional; Region: PRK06433 557598001624 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 557598001625 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 557598001626 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 557598001627 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 557598001628 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 557598001629 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 557598001630 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 557598001631 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 557598001632 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 557598001633 FAD binding site [chemical binding]; other site 557598001634 hypothetical protein; Provisional; Region: PRK05208 557598001635 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 557598001636 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 557598001637 CTP synthetase; Validated; Region: pyrG; PRK05380 557598001638 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 557598001639 Catalytic site [active] 557598001640 active site 557598001641 UTP binding site [chemical binding]; other site 557598001642 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 557598001643 active site 557598001644 putative oxyanion hole; other site 557598001645 catalytic triad [active] 557598001646 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 557598001647 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 557598001648 enolase; Provisional; Region: eno; PRK00077 557598001649 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 557598001650 dimer interface [polypeptide binding]; other site 557598001651 metal binding site [ion binding]; metal-binding site 557598001652 substrate binding pocket [chemical binding]; other site 557598001653 cell division protein FtsB; Reviewed; Region: ftsB; PRK00888 557598001654 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 557598001655 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 557598001656 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557598001657 metal binding site [ion binding]; metal-binding site 557598001658 active site 557598001659 I-site; other site 557598001660 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 557598001661 Fe-S cluster binding site [ion binding]; other site 557598001662 active site 557598001663 ribosomal-protein-alanine N-acetyltransferase; Provisional; Region: rimI; PRK09491 557598001664 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 557598001665 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 557598001666 Glycoprotease family; Region: Peptidase_M22; pfam00814 557598001667 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 557598001668 EAL domain; Region: EAL; pfam00563 557598001669 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 557598001670 putative binding surface; other site 557598001671 active site 557598001672 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 557598001673 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 557598001674 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 557598001675 ATP binding site [chemical binding]; other site 557598001676 Mg2+ binding site [ion binding]; other site 557598001677 G-X-G motif; other site 557598001678 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 557598001679 chemotaxis regulator CheZ; Provisional; Region: PRK11166 557598001680 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 557598001681 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 557598001682 active site 557598001683 phosphorylation site [posttranslational modification] 557598001684 intermolecular recognition site; other site 557598001685 dimerization interface [polypeptide binding]; other site 557598001686 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; cd00588 557598001687 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 557598001688 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 557598001689 active site 557598001690 phosphorylation site [posttranslational modification] 557598001691 intermolecular recognition site; other site 557598001692 dimerization interface [polypeptide binding]; other site 557598001693 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 557598001694 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 557598001695 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 557598001696 active site 557598001697 phosphorylation site [posttranslational modification] 557598001698 intermolecular recognition site; other site 557598001699 dimerization interface [polypeptide binding]; other site 557598001700 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 557598001701 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 557598001702 phosphorylation site [posttranslational modification] 557598001703 dimer interface [polypeptide binding]; other site 557598001704 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 557598001705 ATP binding site [chemical binding]; other site 557598001706 Mg2+ binding site [ion binding]; other site 557598001707 G-X-G motif; other site 557598001708 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557598001709 dimer interface [polypeptide binding]; other site 557598001710 putative CheW interface [polypeptide binding]; other site 557598001711 Response regulator receiver domain; Region: Response_reg; pfam00072 557598001712 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 557598001713 active site 557598001714 phosphorylation site [posttranslational modification] 557598001715 intermolecular recognition site; other site 557598001716 dimerization interface [polypeptide binding]; other site 557598001717 chemotaxis protein CheA; Provisional; Region: PRK10547 557598001718 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 557598001719 putative binding surface; other site 557598001720 active site 557598001721 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 557598001722 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 557598001723 ATP binding site [chemical binding]; other site 557598001724 Mg2+ binding site [ion binding]; other site 557598001725 G-X-G motif; other site 557598001726 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 557598001727 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 557598001728 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 557598001729 PAS domain; Region: PAS_9; pfam13426 557598001730 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 557598001731 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557598001732 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557598001733 dimer interface [polypeptide binding]; other site 557598001734 putative CheW interface [polypeptide binding]; other site 557598001735 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 557598001736 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 557598001737 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 557598001738 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 557598001739 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 557598001740 active site 557598001741 phosphorylation site [posttranslational modification] 557598001742 intermolecular recognition site; other site 557598001743 dimerization interface [polypeptide binding]; other site 557598001744 CheB methylesterase; Region: CheB_methylest; pfam01339 557598001745 CheD chemotactic sensory transduction; Region: CheD; cl00810 557598001746 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 557598001747 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 557598001748 dimer interface [polypeptide binding]; other site 557598001749 active site 557598001750 acyl carrier protein; Provisional; Region: acpP; PRK00982 557598001751 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 557598001752 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 557598001753 NAD(P) binding site [chemical binding]; other site 557598001754 homotetramer interface [polypeptide binding]; other site 557598001755 homodimer interface [polypeptide binding]; other site 557598001756 active site 557598001757 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 557598001758 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 557598001759 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 557598001760 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 557598001761 dimer interface [polypeptide binding]; other site 557598001762 active site 557598001763 CoA binding pocket [chemical binding]; other site 557598001764 putative phosphate acyltransferase; Provisional; Region: PRK05331 557598001765 50S ribosomal protein L32; Validated; Region: rpmF; PRK01110 557598001766 Uncharacterized ACR, COG1399; Region: DUF177; cl00616 557598001767 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 557598001768 active site 557598001769 dimer interface [polypeptide binding]; other site 557598001770 Uncharacterized subfamily of the tetrapyrrole methylase family similar to ribosomal RNA small subunit methyltransferase I (RsmI); Region: RsmI_like; cd11649 557598001771 putative SAM binding site [chemical binding]; other site 557598001772 homodimer interface [polypeptide binding]; other site 557598001773 hypothetical protein; Validated; Region: PRK09070 557598001774 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 557598001775 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 557598001776 S-adenosylmethionine synthetase; Validated; Region: PRK05250 557598001777 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 557598001778 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 557598001779 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 557598001780 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 557598001781 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 557598001782 putative acyl-acceptor binding pocket; other site 557598001783 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 557598001784 putative acyl-acceptor binding pocket; other site 557598001785 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 557598001786 C-terminal domain interface [polypeptide binding]; other site 557598001787 GSH binding site (G-site) [chemical binding]; other site 557598001788 dimer interface [polypeptide binding]; other site 557598001789 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cl02776 557598001790 N-terminal domain interface [polypeptide binding]; other site 557598001791 dimer interface [polypeptide binding]; other site 557598001792 substrate binding pocket (H-site) [chemical binding]; other site 557598001793 Protein of unknown function (DUF2818); Region: DUF2818; pfam10993 557598001794 FlgN protein; Region: FlgN; pfam05130 557598001795 flagellar biosynthesis anti-sigma factor FlgM; Region: FlgM_jcvi; TIGR03824 557598001796 SAF-like; Region: SAF_2; pfam13144 557598001797 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 557598001798 Domains similar to fish antifreeze type III protein; Region: SAF; cl00555 557598001799 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 557598001800 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 557598001801 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557598001802 catalytic residue [active] 557598001803 Sortase and related acyltransferases [Cell envelope biogenesis, outer membrane]; Region: COG1247 557598001804 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 557598001805 Coenzyme A binding pocket [chemical binding]; other site 557598001806 homoserine dehydrogenase; Provisional; Region: PRK06349 557598001807 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 557598001808 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 557598001809 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 557598001810 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 557598001811 Ligand Binding Site [chemical binding]; other site 557598001812 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 557598001813 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 557598001814 catalytic residues [active] 557598001815 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 557598001816 S-adenosylmethionine binding site [chemical binding]; other site 557598001817 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 557598001818 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 557598001819 Walker A motif; other site 557598001820 ATP binding site [chemical binding]; other site 557598001821 Walker B motif; other site 557598001822 arginine finger; other site 557598001823 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 557598001824 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 557598001825 S-adenosylmethionine binding site [chemical binding]; other site 557598001826 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3536 557598001827 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 557598001828 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 557598001829 Dehydroquinase class II; Region: DHquinase_II; pfam01220 557598001830 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 557598001831 trimer interface [polypeptide binding]; other site 557598001832 active site 557598001833 dimer interface [polypeptide binding]; other site 557598001834 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 557598001835 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 557598001836 carboxyltransferase (CT) interaction site; other site 557598001837 biotinylation site [posttranslational modification]; other site 557598001838 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 557598001839 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 557598001840 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 557598001841 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 557598001842 Ribosomal protein L11 methyltransferase (PrmA); Region: PrmA; pfam06325 557598001843 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 557598001844 S-adenosylmethionine binding site [chemical binding]; other site 557598001845 MJ0042 family finger-like domain; Region: MJ0042_CXXC; TIGR02098 557598001846 Protein of unknown function (DUF3426); Region: DUF3426; pfam11906 557598001847 Nitrate and nitrite sensing; Region: NIT; pfam08376 557598001848 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 557598001849 dimerization interface [polypeptide binding]; other site 557598001850 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 557598001851 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557598001852 dimer interface [polypeptide binding]; other site 557598001853 putative CheW interface [polypeptide binding]; other site 557598001854 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 557598001855 putative active site [active] 557598001856 Ap4A binding site [chemical binding]; other site 557598001857 nudix motif; other site 557598001858 putative metal binding site [ion binding]; other site 557598001859 Predicted membrane protein (DUF2238); Region: DUF2238; pfam09997 557598001860 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 557598001861 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 557598001862 ATP binding site [chemical binding]; other site 557598001863 Mg2+ binding site [ion binding]; other site 557598001864 G-X-G motif; other site 557598001865 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 557598001866 anchoring element; other site 557598001867 dimer interface [polypeptide binding]; other site 557598001868 ATP binding site [chemical binding]; other site 557598001869 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 557598001870 active site 557598001871 metal binding site [ion binding]; metal-binding site 557598001872 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 557598001873 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 557598001874 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 557598001875 active site 557598001876 HIGH motif; other site 557598001877 dimer interface [polypeptide binding]; other site 557598001878 KMSKS motif; other site 557598001879 transcriptional regulator CysB-like protein; Reviewed; Region: PRK12684 557598001880 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 557598001881 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 557598001882 substrate binding site [chemical binding]; other site 557598001883 dimerization interface [polypeptide binding]; other site 557598001884 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes [Amino acid transport and metabolism / Coenzyme metabolism]; Region: CysH; COG0175 557598001885 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 557598001886 Active Sites [active] 557598001887 Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism]; Region: CysI; COG0155 557598001888 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 557598001889 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 557598001890 Bacterial protein of unknown function (DUF934); Region: DUF934; pfam06073 557598001891 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 557598001892 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 557598001893 ligand binding site [chemical binding]; other site 557598001894 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 557598001895 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 557598001896 active site 557598001897 Riboflavin kinase; Region: Flavokinase; smart00904 557598001898 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 557598001899 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 557598001900 active site 557598001901 HIGH motif; other site 557598001902 nucleotide binding site [chemical binding]; other site 557598001903 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 557598001904 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 557598001905 active site 557598001906 KMSKS motif; other site 557598001907 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 557598001908 tRNA binding surface [nucleotide binding]; other site 557598001909 anticodon binding site; other site 557598001910 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 557598001911 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 557598001912 lipoprotein signal peptidase; Provisional; Region: PRK14787 557598001913 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism]; Region: lytB; COG0761 557598001914 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 557598001915 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 557598001916 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557598001917 dimer interface [polypeptide binding]; other site 557598001918 putative CheW interface [polypeptide binding]; other site 557598001919 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 557598001920 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 557598001921 PAS domain; Region: PAS_9; pfam13426 557598001922 putative active site [active] 557598001923 heme pocket [chemical binding]; other site 557598001924 phosphoribosylglycinamide formyltransferase 2; Validated; Region: purT; PRK09288 557598001925 Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; Region: FDH_GDH_like; cl17240 557598001926 NAD binding site [chemical binding]; other site 557598001927 ATP-grasp domain; Region: ATP-grasp; pfam02222 557598001928 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 557598001929 apolar tunnel; other site 557598001930 heme binding site [chemical binding]; other site 557598001931 dimerization interface [polypeptide binding]; other site 557598001932 Dihydroneopterin aldolase (DHNA) and 7,8-dihydroneopterin triphosphate epimerase domain (DHNTPE); these enzymes have been designated folB and folX, respectively. Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and...; Region: DHNA_DHNTPE; cd00534 557598001933 homooctamer interface [polypeptide binding]; other site 557598001934 active site 557598001935 putative glycerol-3-phosphate acyltransferase PlsY; Provisional; Region: PRK00220 557598001936 Protein of unknown function (DUF330); Region: DUF330; cl01135 557598001937 mce related protein; Region: MCE; pfam02470 557598001938 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 557598001939 ABC transporter; Region: ABC_tran; pfam00005 557598001940 Q-loop/lid; other site 557598001941 ABC transporter signature motif; other site 557598001942 Walker B; other site 557598001943 D-loop; other site 557598001944 H-loop/switch region; other site 557598001945 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 557598001946 Permease; Region: Permease; pfam02405 557598001947 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 557598001948 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 557598001949 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 557598001950 ATP binding site [chemical binding]; other site 557598001951 putative Mg++ binding site [ion binding]; other site 557598001952 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 557598001953 nucleotide binding region [chemical binding]; other site 557598001954 ATP-binding site [chemical binding]; other site 557598001955 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 557598001956 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 557598001957 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 557598001958 Predicted metal-binding protein [General function prediction only]; Region: COG3019 557598001959 Putative multicopper oxidases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: SufI; COG2132 557598001960 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 557598001961 Multicopper oxidase; Region: Cu-oxidase; pfam00394 557598001962 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 557598001963 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional; Region: PRK11181 557598001964 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 557598001965 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 557598001966 PAS domain S-box; Region: sensory_box; TIGR00229 557598001967 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 557598001968 putative active site [active] 557598001969 heme pocket [chemical binding]; other site 557598001970 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 557598001971 PAS domain; Region: PAS_9; pfam13426 557598001972 putative active site [active] 557598001973 heme pocket [chemical binding]; other site 557598001974 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 557598001975 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557598001976 metal binding site [ion binding]; metal-binding site 557598001977 active site 557598001978 I-site; other site 557598001979 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 557598001980 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK13964 557598001981 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 557598001982 active site 557598001983 (T/H)XGH motif; other site 557598001984 hypothetical protein; Provisional; Region: PRK08999 557598001985 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 557598001986 active site 557598001987 8-oxo-dGMP binding site [chemical binding]; other site 557598001988 nudix motif; other site 557598001989 metal binding site [ion binding]; metal-binding site 557598001990 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 557598001991 active site 557598001992 thiamine phosphate binding site [chemical binding]; other site 557598001993 pyrophosphate binding site [ion binding]; other site 557598001994 Ferredoxin [Energy production and conversion]; Region: COG1146 557598001995 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 557598001996 Glutamyl- and glutaminyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]; Region: GlnS; COG0008 557598001997 glutamyl-Q tRNA(Asp) synthetase; Reviewed; Region: PRK05710 557598001998 active site 557598001999 HIGH motif; other site 557598002000 nucleotide binding site [chemical binding]; other site 557598002001 active site 557598002002 KMSKS motif; other site 557598002003 Putative SAM-dependent methyltransferase; Region: SAM_MT; cl17517 557598002004 Predicted membrane metal-binding protein [General function prediction only]; Region: ComEC; COG0658 557598002005 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 557598002006 Competence protein; Region: Competence; pfam03772 557598002007 Predicted hydrolase (metallo-beta-lactamase superfamily) [General function prediction only]; Region: ComEC; COG2333 557598002008 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 557598002009 Predicted permease [General function prediction only]; Region: COG2056 557598002010 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 557598002011 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 557598002012 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 557598002013 malate synthase A; Region: malate_syn_A; TIGR01344 557598002014 active site 557598002015 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557598002016 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 557598002017 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 557598002018 putative effector binding pocket; other site 557598002019 dimerization interface [polypeptide binding]; other site 557598002020 Uncharacterized conserved protein [Function unknown]; Region: HdeD; COG3247 557598002021 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 557598002022 PAS domain; Region: PAS_9; pfam13426 557598002023 putative active site [active] 557598002024 heme pocket [chemical binding]; other site 557598002025 PAS domain; Region: PAS; smart00091 557598002026 PAS fold; Region: PAS_7; pfam12860 557598002027 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 557598002028 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557598002029 metal binding site [ion binding]; metal-binding site 557598002030 active site 557598002031 I-site; other site 557598002032 oxidative damage protection protein; Provisional; Region: PRK05408 557598002033 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 557598002034 Polyphosphate kinase C-terminal domain; Region: PP_kinase_C; pfam13090 557598002035 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 557598002036 putative active site [active] 557598002037 catalytic site [active] 557598002038 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 557598002039 putative domain interface [polypeptide binding]; other site 557598002040 putative active site [active] 557598002041 catalytic site [active] 557598002042 Protein of unknown function (DUF456); Region: DUF456; pfam04306 557598002043 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 557598002044 Histone deacetylases and histone-like deacetylases, classII; Region: HDAC_classII_2; cd11599 557598002045 putative active site [active] 557598002046 Zn binding site [ion binding]; other site 557598002047 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 557598002048 oligomerisation interface [polypeptide binding]; other site 557598002049 mobile loop; other site 557598002050 roof hairpin; other site 557598002051 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 557598002052 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 557598002053 ring oligomerisation interface [polypeptide binding]; other site 557598002054 ATP/Mg binding site [chemical binding]; other site 557598002055 stacking interactions; other site 557598002056 hinge regions; other site 557598002057 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 557598002058 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 557598002059 trimer interface [polypeptide binding]; other site 557598002060 eyelet of channel; other site 557598002061 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 557598002062 Domain of unknown function DUF21; Region: DUF21; pfam01595 557598002063 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 557598002064 Transporter associated domain; Region: CorC_HlyC; smart01091 557598002065 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 557598002066 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 557598002067 Type IV leader peptidase family; Region: Peptidase_A24; pfam01478 557598002068 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 557598002069 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 557598002070 CoA-binding site [chemical binding]; other site 557598002071 Protein of unknown function (DUF1342); Region: DUF1342; cl01892 557598002072 Domain of unknown function (DUF329); Region: DUF329; pfam03884 557598002073 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 557598002074 The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; Region: PBP2_DppA_like; cd08493 557598002075 peptide binding site [polypeptide binding]; other site 557598002076 cytoplasmic glycerophosphodiester phosphodiesterase; Provisional; Region: ugpQ; PRK09454 557598002077 Glycerophosphodiester phosphodiesterase domain in Escherichia coli cytosolic glycerophosphodiester phosphodiesterase UgpQ and similar proteins; Region: GDPD_EcUgpQ_like; cd08562 557598002078 putative active site [active] 557598002079 catalytic site [active] 557598002080 putative metal binding site [ion binding]; other site 557598002081 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 557598002082 FAD binding domain; Region: FAD_binding_4; pfam01565 557598002083 NAD-dependent aldehyde dehydrogenases [Energy production and conversion]; Region: PutA; COG1012 557598002084 Mycobacterium tuberculosis succinate-semialdehyde dehydrogenase 1-like; Region: ALDH_SSADH1_GabD1; cd07100 557598002085 NAD(P) binding site [chemical binding]; other site 557598002086 catalytic residues [active] 557598002087 putative glutathione S-transferase; Provisional; Region: PRK10357 557598002088 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 557598002089 putative C-terminal domain interface [polypeptide binding]; other site 557598002090 putative GSH binding site (G-site) [chemical binding]; other site 557598002091 putative dimer interface [polypeptide binding]; other site 557598002092 C-terminal, alpha helical domain of an unknown subfamily 6 of Glutathione S-transferases; Region: GST_C_6; cd03205 557598002093 dimer interface [polypeptide binding]; other site 557598002094 N-terminal domain interface [polypeptide binding]; other site 557598002095 putative substrate binding pocket (H-site) [chemical binding]; other site 557598002096 Protein of unknown function (DUF541); Region: SIMPL; cl01077 557598002097 Uncharacterized conserved protein [Function unknown]; Region: COG2968 557598002098 PAS fold; Region: PAS_4; pfam08448 557598002099 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 557598002100 putative active site [active] 557598002101 heme pocket [chemical binding]; other site 557598002102 PAS domain S-box; Region: sensory_box; TIGR00229 557598002103 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 557598002104 putative active site [active] 557598002105 heme pocket [chemical binding]; other site 557598002106 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 557598002107 PAS domain; Region: PAS_9; pfam13426 557598002108 putative active site [active] 557598002109 heme pocket [chemical binding]; other site 557598002110 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 557598002111 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557598002112 metal binding site [ion binding]; metal-binding site 557598002113 active site 557598002114 I-site; other site 557598002115 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 557598002116 S-adenosyl-L-homocysteine hydrolase; Provisional; Region: PRK05476 557598002117 S-Adenosylhomocysteine Hydrolase, NAD-binding and catalytic domains; Region: SAHH; cd00401 557598002118 homotetramer interface [polypeptide binding]; other site 557598002119 ligand binding site [chemical binding]; other site 557598002120 catalytic site [active] 557598002121 NAD binding site [chemical binding]; other site 557598002122 carbon starvation protein A; Provisional; Region: PRK15015 557598002123 Carbon starvation protein CstA; Region: CstA; pfam02554 557598002124 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 557598002125 Protein of unknown function (DUF466); Region: DUF466; pfam04328 557598002126 succinyldiaminopimelate transaminase; Provisional; Region: PRK09147 557598002127 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 557598002128 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557598002129 homodimer interface [polypeptide binding]; other site 557598002130 catalytic residue [active] 557598002131 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 557598002132 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 557598002133 trimer interface [polypeptide binding]; other site 557598002134 active site 557598002135 substrate binding site [chemical binding]; other site 557598002136 CoA binding site [chemical binding]; other site 557598002137 Predicted ATPase [General function prediction only]; Region: COG1485 557598002138 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 557598002139 Walker B; other site 557598002140 D-loop; other site 557598002141 H-loop/switch region; other site 557598002142 Sporulation related domain; Region: SPOR; pfam05036 557598002143 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 557598002144 active site 557598002145 multimer interface [polypeptide binding]; other site 557598002146 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK11194 557598002147 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 557598002148 FeS/SAM binding site; other site 557598002149 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 557598002150 non-specific DNA binding site [nucleotide binding]; other site 557598002151 salt bridge; other site 557598002152 sequence-specific DNA binding site [nucleotide binding]; other site 557598002153 Domain of unknown function (DUF4115); Region: DUF4115; pfam13464 557598002154 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 557598002155 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 557598002156 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 557598002157 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 557598002158 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 557598002159 dimer interface [polypeptide binding]; other site 557598002160 motif 1; other site 557598002161 active site 557598002162 motif 2; other site 557598002163 motif 3; other site 557598002164 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 557598002165 anticodon binding site; other site 557598002166 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 557598002167 Uncharacterized protein conserved in bacteria (DUF2133); Region: DUF2133; pfam09976 557598002168 outer membrane assembly lipoprotein YfgL; Region: assembly_YfgL; TIGR03300 557598002169 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 557598002170 Trp docking motif [polypeptide binding]; other site 557598002171 active site 557598002172 ribosome-associated GTPase EngA; Region: GTPase_EngA; TIGR03594 557598002173 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 557598002174 Switch II region; other site 557598002175 G3 box; other site 557598002176 GTP/Mg2+ binding site [chemical binding]; other site 557598002177 G4 box; other site 557598002178 G5 box; other site 557598002179 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 557598002180 G1 box; other site 557598002181 GTP/Mg2+ binding site [chemical binding]; other site 557598002182 Switch I region; other site 557598002183 G2 box; other site 557598002184 G3 box; other site 557598002185 Switch II region; other site 557598002186 G4 box; other site 557598002187 G5 box; other site 557598002188 bacterial Hfq-like; Region: Hfq; cd01716 557598002189 hexamer interface [polypeptide binding]; other site 557598002190 Sm1 motif; other site 557598002191 RNA binding site [nucleotide binding]; other site 557598002192 Sm2 motif; other site 557598002193 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 557598002194 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 557598002195 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 557598002196 HflX GTPase family; Region: HflX; cd01878 557598002197 G1 box; other site 557598002198 GTP/Mg2+ binding site [chemical binding]; other site 557598002199 Switch I region; other site 557598002200 G2 box; other site 557598002201 G3 box; other site 557598002202 Switch II region; other site 557598002203 G4 box; other site 557598002204 G5 box; other site 557598002205 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 557598002206 HflK protein; Region: hflK; TIGR01933 557598002207 HflC protein; Region: hflC; TIGR01932 557598002208 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 557598002209 ATP phosphoribosyltransferase regulatory subunit; Provisional; Region: PRK12421 557598002210 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 557598002211 dimer interface [polypeptide binding]; other site 557598002212 motif 1; other site 557598002213 active site 557598002214 motif 2; other site 557598002215 motif 3; other site 557598002216 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 557598002217 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 557598002218 GDP-binding site [chemical binding]; other site 557598002219 ACT binding site; other site 557598002220 IMP binding site; other site 557598002221 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 557598002222 dihydrodipicolinate synthase; Region: dapA; TIGR00674 557598002223 dimer interface [polypeptide binding]; other site 557598002224 active site 557598002225 catalytic residue [active] 557598002226 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 557598002227 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 557598002228 Walker A/P-loop; other site 557598002229 ATP binding site [chemical binding]; other site 557598002230 Q-loop/lid; other site 557598002231 ABC transporter signature motif; other site 557598002232 Walker B; other site 557598002233 D-loop; other site 557598002234 H-loop/switch region; other site 557598002235 ABC transporter; Region: ABC_tran_2; pfam12848 557598002236 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 557598002237 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 557598002238 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 557598002239 NAD(P) binding site [chemical binding]; other site 557598002240 homotetramer interface [polypeptide binding]; other site 557598002241 homodimer interface [polypeptide binding]; other site 557598002242 active site 557598002243 HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain; Region: HAMP; smart00304 557598002244 dimerization interface [polypeptide binding]; other site 557598002245 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557598002246 dimer interface [polypeptide binding]; other site 557598002247 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 557598002248 putative CheW interface [polypeptide binding]; other site 557598002249 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 557598002250 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 557598002251 substrate binding site [chemical binding]; other site 557598002252 ligand binding site [chemical binding]; other site 557598002253 Predicted small secreted protein [Function unknown]; Region: COG5510 557598002254 isopropylmalate isomerase small subunit; Provisional; Region: leuD; PRK01641 557598002255 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 557598002256 substrate binding site [chemical binding]; other site 557598002257 GAF domain; Region: GAF; pfam01590 557598002258 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 557598002259 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 557598002260 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557598002261 metal binding site [ion binding]; metal-binding site 557598002262 active site 557598002263 I-site; other site 557598002264 gamma-glutamyl:cysteine ligase; Provisional; Region: PRK13516 557598002265 carboxylate-amine ligase, YbdK family; Region: gshA_cyan_rel; TIGR02050 557598002266 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 557598002267 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 557598002268 catalytic triad [active] 557598002269 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4394 557598002270 Uncharacterized protein conserved in bacteria (DUF2331); Region: DUF2331; pfam10093 557598002271 elongation factor P; Validated; Region: PRK00529 557598002272 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 557598002273 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 557598002274 RNA binding site [nucleotide binding]; other site 557598002275 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 557598002276 RNA binding site [nucleotide binding]; other site 557598002277 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 557598002278 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 557598002279 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557598002280 metal binding site [ion binding]; metal-binding site 557598002281 active site 557598002282 I-site; other site 557598002283 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 557598002284 Domain present in phytochromes and cGMP-specific phosphodiesterases; Region: GAF; smart00065 557598002285 Putative multicopper oxidases [Secondary metabolites biosynthesis, transport, and catabolism]; Region: SufI; COG2132 557598002286 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 557598002287 Multicopper oxidase; Region: Cu-oxidase; pfam00394 557598002288 Multicopper oxidase; Region: Cu-oxidase_2; pfam07731 557598002289 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 557598002290 Long-chain fatty acid CoA synthetases and Bubblegum-like very long-chain fatty acid CoA synthetases; Region: VL_LC_FACS_like; cd05907 557598002291 acyl-activating enzyme (AAE) consensus motif; other site 557598002292 putative AMP binding site [chemical binding]; other site 557598002293 putative active site [active] 557598002294 putative CoA binding site [chemical binding]; other site 557598002295 Cystathionine beta-lyases/cystathionine gamma-synthases [Amino acid transport and metabolism]; Region: MetC; COG0626 557598002296 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 557598002297 homodimer interface [polypeptide binding]; other site 557598002298 substrate-cofactor binding pocket; other site 557598002299 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557598002300 catalytic residue [active] 557598002301 coproporphyrinogen III oxidase; Provisional; Region: PRK05330 557598002302 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; pfam01218 557598002303 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 557598002304 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 557598002305 active site 557598002306 dimer interface [polypeptide binding]; other site 557598002307 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 557598002308 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 557598002309 active site 557598002310 FMN binding site [chemical binding]; other site 557598002311 substrate binding site [chemical binding]; other site 557598002312 3Fe-4S cluster binding site [ion binding]; other site 557598002313 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 557598002314 domain interface; other site 557598002315 glutamate synthase small subunit family protein, proteobacterial; Region: gltD_gamma_fam; TIGR01318 557598002316 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 557598002317 recombination associated protein; Reviewed; Region: rdgC; PRK00321 557598002318 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 557598002319 RNA/DNA hybrid binding site [nucleotide binding]; other site 557598002320 active site 557598002321 MUG-like Uracil-DNA glycosylase enzyme family; Region: UDG_MUG_like; cd10032 557598002322 putative active site [active] 557598002323 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 557598002324 PAS domain; Region: PAS_9; pfam13426 557598002325 putative active site [active] 557598002326 heme pocket [chemical binding]; other site 557598002327 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 557598002328 dimerization interface [polypeptide binding]; other site 557598002329 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 557598002330 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557598002331 dimer interface [polypeptide binding]; other site 557598002332 putative CheW interface [polypeptide binding]; other site 557598002333 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 557598002334 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 557598002335 catalytic residue [active] 557598002336 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 557598002337 ATP cone domain; Region: ATP-cone; pfam03477 557598002338 bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional; Region: ribD; PRK10786 557598002339 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 557598002340 catalytic motif [active] 557598002341 Zn binding site [ion binding]; other site 557598002342 RibD C-terminal domain; Region: RibD_C; cl17279 557598002343 Malate/L-lactate dehydrogenase; Region: Ldh_2; cl00900 557598002344 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557598002345 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 557598002346 The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold; Region: PBP2_CidR; cd08438 557598002347 putative dimerization interface [polypeptide binding]; other site 557598002348 LrgA family; Region: LrgA; cl00608 557598002349 Putative effector of murein hydrolase [Cell envelope biogenesis, outer membrane]; Region: LrgB; COG1346 557598002350 Flavin reductase like domain; Region: Flavin_Reduct; smart00903 557598002351 Barstar is an intracellular inhibitor of barnase, an extracellular ribonuclease of Bacillus amyloliquefaciens. Barstar binds tightly to the barnase active site and sterically blocks it, thus inhibiting its potentially lethal RNase activity inside the...; Region: Barstar_like; cl01048 557598002352 RNAase interaction site [polypeptide binding]; other site 557598002353 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 557598002354 active site 557598002355 Domain of unknown function DUF59; Region: DUF59; pfam01883 557598002356 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Mrp; COG0489 557598002357 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 557598002358 multidrug efflux system translocase MdfA; Provisional; Region: PRK15402 557598002359 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 557598002360 putative substrate translocation pore; other site 557598002361 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 557598002362 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 557598002363 active site 557598002364 HIGH motif; other site 557598002365 KMSKS motif; other site 557598002366 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 557598002367 tRNA binding surface [nucleotide binding]; other site 557598002368 anticodon binding site; other site 557598002369 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 557598002370 dimer interface [polypeptide binding]; other site 557598002371 putative tRNA-binding site [nucleotide binding]; other site 557598002372 HdeA/HdeB family; Region: HdeA; pfam06411 557598002373 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 557598002374 dimer interface [polypeptide binding]; other site 557598002375 motif 1; other site 557598002376 active site 557598002377 motif 2; other site 557598002378 motif 3; other site 557598002379 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 557598002380 D,D-heptose 1,7-bisphosphate phosphatase; Validated; Region: PRK08942 557598002381 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 557598002382 active site 557598002383 motif I; other site 557598002384 motif II; other site 557598002385 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 557598002386 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 557598002387 putative acyl-acceptor binding pocket; other site 557598002388 Protein of unknown function DUF45; Region: DUF45; pfam01863 557598002389 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 557598002390 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 557598002391 dimer interface [polypeptide binding]; other site 557598002392 active site 557598002393 metal binding site [ion binding]; metal-binding site 557598002394 glutathione binding site [chemical binding]; other site 557598002395 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 557598002396 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 557598002397 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 557598002398 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase; Region: mpl; TIGR01081 557598002399 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 557598002400 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 557598002401 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 557598002402 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 557598002403 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 557598002404 N-acetyl-D-glucosamine binding site [chemical binding]; other site 557598002405 catalytic residue [active] 557598002406 hydroxypyruvate isomerase; Region: OH-pyruv-isom; TIGR03234 557598002407 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 557598002408 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 557598002409 selenocysteinyl-tRNA-specific translation factor; Provisional; Region: PRK10512 557598002410 SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; Region: SelB; cd04171 557598002411 G1 box; other site 557598002412 putative GEF interaction site [polypeptide binding]; other site 557598002413 GTP/Mg2+ binding site [chemical binding]; other site 557598002414 Switch I region; other site 557598002415 G2 box; other site 557598002416 G3 box; other site 557598002417 Switch II region; other site 557598002418 G4 box; other site 557598002419 G5 box; other site 557598002420 selB_II: this subfamily represents the domain of elongation factor SelB, homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several...; Region: selB_II; cd03696 557598002421 This family represents the domain of elongation factor SelB, homologous to domain III of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements:...; Region: selB_III; cd04094 557598002422 Elongation factor SelB, winged helix; Region: SelB-wing_3; pfam09107 557598002423 selenocysteine synthase; Provisional; Region: PRK04311 557598002424 Selenocysteine synthase N terminal; Region: Se-cys_synth_N; pfam12390 557598002425 Selenocysteine synthase [seryl-tRNASer selenium transferase] [Amino acid transport and metabolism]; Region: SelA; COG1921 557598002426 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 557598002427 catalytic residue [active] 557598002428 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 557598002429 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 557598002430 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 557598002431 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 557598002432 ligand binding site [chemical binding]; other site 557598002433 Uncharacterized conserved protein [Function unknown]; Region: COG3791 557598002434 Glutathione-dependent formaldehyde-activating enzyme; Region: GFA; pfam04828 557598002435 Uncharacterized protein involved in formation of curli polymers [Cell envelope biogenesis, outer membrane]; Region: CsgG; COG1462 557598002436 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4259 557598002437 Putative bacterial lipoprotein (DUF799); Region: DUF799; cl01813 557598002438 GMP synthase; Reviewed; Region: guaA; PRK00074 557598002439 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 557598002440 AMP/PPi binding site [chemical binding]; other site 557598002441 candidate oxyanion hole; other site 557598002442 catalytic triad [active] 557598002443 potential glutamine specificity residues [chemical binding]; other site 557598002444 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 557598002445 ATP Binding subdomain [chemical binding]; other site 557598002446 Ligand Binding sites [chemical binding]; other site 557598002447 Dimerization subdomain; other site 557598002448 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 557598002449 SmpB-tmRNA interface; other site 557598002450 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 557598002451 putative coenzyme Q binding site [chemical binding]; other site 557598002452 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2914 557598002453 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 557598002454 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 557598002455 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 557598002456 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 557598002457 DNA binding residues [nucleotide binding] 557598002458 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 557598002459 FleN is a member of the Fer4_NifH superfamily. It shares the common function as an ATPase, with the ATP-binding domain at the N-terminus. In Pseudomonas aeruginosa, FleN gene is involved in regulating the number of flagella and chemotactic motility by...; Region: FleN-like; cd02038 557598002460 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK06995 557598002461 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 557598002462 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 557598002463 FHIPEP family; Region: FHIPEP; pfam00771 557598002464 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 557598002465 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257; cl15822 557598002466 thymidylate synthase; Reviewed; Region: thyA; PRK01827 557598002467 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 557598002468 dimerization interface [polypeptide binding]; other site 557598002469 active site 557598002470 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 557598002471 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 557598002472 folate binding site [chemical binding]; other site 557598002473 NADP+ binding site [chemical binding]; other site 557598002474 3-oxoadipate enol-lactonase; Region: protocat_pcaD; TIGR02427 557598002475 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 557598002476 enoyl-CoA hydratase; Provisional; Region: PRK05995 557598002477 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 557598002478 substrate binding site [chemical binding]; other site 557598002479 oxyanion hole (OAH) forming residues; other site 557598002480 trimer interface [polypeptide binding]; other site 557598002481 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 557598002482 substrate binding site [chemical binding]; other site 557598002483 dimerization interface [polypeptide binding]; other site 557598002484 active site 557598002485 calcium binding site [ion binding]; other site 557598002486 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 557598002487 Na2 binding site [ion binding]; other site 557598002488 putative substrate binding site 1 [chemical binding]; other site 557598002489 Na binding site 1 [ion binding]; other site 557598002490 putative substrate binding site 2 [chemical binding]; other site 557598002491 recombinase A; Provisional; Region: recA; PRK09354 557598002492 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 557598002493 hexamer interface [polypeptide binding]; other site 557598002494 Walker A motif; other site 557598002495 ATP binding site [chemical binding]; other site 557598002496 Walker B motif; other site 557598002497 recombination regulator RecX; Reviewed; Region: recX; PRK00117 557598002498 HemK family putative methylases; Region: hemK_fam; TIGR00536 557598002499 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 557598002500 S-adenosylmethionine binding site [chemical binding]; other site 557598002501 Lysine efflux permease [General function prediction only]; Region: COG1279 557598002502 chromosome replication initiation inhibitor protein; Validated; Region: PRK03635 557598002503 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 557598002504 The C-terminal substrate binding domain of LysR-type transcriptional regulator, ArgP (IciA), for arginine exporter (ArgO); contains the type 2 periplasmic binding fold; Region: PBP2_IciA_ArgP; cd08428 557598002505 putative dimerization interface [polypeptide binding]; other site 557598002506 enoyl-CoA hydratase; Provisional; Region: PRK09076 557598002507 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 557598002508 substrate binding site [chemical binding]; other site 557598002509 oxyanion hole (OAH) forming residues; other site 557598002510 trimer interface [polypeptide binding]; other site 557598002511 Family description; Region: DsbD_2; pfam13386 557598002512 formate dehydrogenase accessory protein FdhE; Provisional; Region: PRK03564 557598002513 formate dehydrogenase accessory protein FdhE; Region: FdhE; TIGR01562 557598002514 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; cl00859 557598002515 formate dehydrogenase, gamma subunit; Region: formate-DH-gamm; TIGR01583 557598002516 formate dehydrogenase, beta subunit, Fe-S containing; Region: FDH-beta; TIGR01582 557598002517 Formate dehydrogenase N, transmembrane; Region: Form-deh_trans; pfam09163 557598002518 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 557598002519 molybdopterin cofactor binding site; other site 557598002520 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 557598002521 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 557598002522 molybdopterin cofactor binding site; other site 557598002523 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 557598002524 formate dehydrogenase accessory protein; Reviewed; Region: PRK00724 557598002525 aspartate kinase; Reviewed; Region: PRK06635 557598002526 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 557598002527 putative nucleotide binding site [chemical binding]; other site 557598002528 putative catalytic residues [active] 557598002529 putative Mg ion binding site [ion binding]; other site 557598002530 putative aspartate binding site [chemical binding]; other site 557598002531 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 557598002532 putative allosteric regulatory site; other site 557598002533 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 557598002534 putative allosteric regulatory residue; other site 557598002535 Lecithin retinol acyltransferase; Region: LRAT; pfam04970 557598002536 YqaJ-like viral recombinase domain; Region: YqaJ; cl09232 557598002537 Protein of unknown function (DUF3768); Region: DUF3768; pfam12599 557598002538 phage/plasmid-like protein TIGR03299; Region: LGT_TIGR03299 557598002539 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 557598002540 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 557598002541 PAS domain; Region: PAS_9; pfam13426 557598002542 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 557598002543 GAF domain; Region: GAF; pfam01590 557598002544 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 557598002545 PAS domain; Region: PAS_9; pfam13426 557598002546 putative active site [active] 557598002547 heme pocket [chemical binding]; other site 557598002548 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 557598002549 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557598002550 metal binding site [ion binding]; metal-binding site 557598002551 active site 557598002552 I-site; other site 557598002553 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 557598002554 Integrase core domain; Region: rve_3; pfam13683 557598002555 Transposase; Region: HTH_Tnp_1; pfam01527 557598002556 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 557598002557 Transposase; Region: HTH_Tnp_1; cl17663 557598002558 Bacterial sugar transferase; Region: Bac_transf; pfam02397 557598002559 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 557598002560 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 557598002561 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 557598002562 anti sigma factor interaction site; other site 557598002563 regulatory phosphorylation site [posttranslational modification]; other site 557598002564 Response regulator receiver domain; Region: Response_reg; pfam00072 557598002565 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 557598002566 active site 557598002567 phosphorylation site [posttranslational modification] 557598002568 intermolecular recognition site; other site 557598002569 dimerization interface [polypeptide binding]; other site 557598002570 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 557598002571 PAS domain; Region: PAS_9; pfam13426 557598002572 putative active site [active] 557598002573 heme pocket [chemical binding]; other site 557598002574 Stage II sporulation protein E (SpoIIE); Region: SpoIIE; pfam07228 557598002575 Histidine kinase-like ATPase domain; Region: HATPase_c_2; pfam13581 557598002576 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 557598002577 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 557598002578 Substrate binding site; other site 557598002579 Mannose-6-phosphate isomerase; Region: MannoseP_isomer; pfam01050 557598002580 Carbohydrate Binding Module 6 (CBM6) and CBM35_like superfamily; Region: CBM6-CBM35-CBM36_like; cl14880 557598002581 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 557598002582 polysaccharide export protein EpsE; Region: EpsE; TIGR03028 557598002583 SLBB domain; Region: SLBB; pfam10531 557598002584 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 557598002585 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 557598002586 active site 557598002587 Acetyltransferase (isoleucine patch superfamily) [General function prediction only]; Region: WbbJ; COG0110 557598002588 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 557598002589 trimer interface [polypeptide binding]; other site 557598002590 active site 557598002591 substrate binding site [chemical binding]; other site 557598002592 CoA binding site [chemical binding]; other site 557598002593 colanic acid biosynthesis glycosyltransferase WcaL; Region: wcaL; TIGR04005 557598002594 This is a family of GT1 glycosyltransferases found specifically in certain bacteria. amsK in Erwinia amylovora, has been reported to be involved in the biosynthesis of amylovoran, a exopolysaccharide acting as a virulence factor; Region: GT1_amsK_like; cd03799 557598002595 putative ADP-binding pocket [chemical binding]; other site 557598002596 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 557598002597 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 557598002598 active site 557598002599 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 557598002600 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 557598002601 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 557598002602 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 557598002603 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 557598002604 The glycosyltransferase WecG/TagA superfamily contains Escherichia coli WecG, Bacillus subtilis TagA and related proteins. E. coli WecG is believed to be a UDP-N-acetyl-D-mannosaminuronic acid transferase, and is involved in enterobacterial common...; Region: Glyco_transf_WecG_TagA; cd06533 557598002605 polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; Region: pepcterm_ChnLen; TIGR03007 557598002606 exopolysaccharide/PEP-CTERM locus tyrosine autokinase; Region: pepcterm_TyrKin; TIGR03018 557598002607 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 557598002608 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 557598002609 EpsO protein participates in the methanolan synthesis; Region: EpsO_like; cd06438 557598002610 DXD motif; other site 557598002611 Serine acetyltransferase [Amino acid transport and metabolism]; Region: CysE; COG1045 557598002612 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 557598002613 trimer interface [polypeptide binding]; other site 557598002614 active site 557598002615 substrate binding site [chemical binding]; other site 557598002616 CoA binding site [chemical binding]; other site 557598002617 Glycosyl transferases group 1; Region: Glyco_trans_1_2; pfam13524 557598002618 PAS fold; Region: PAS_4; pfam08448 557598002619 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 557598002620 putative active site [active] 557598002621 heme pocket [chemical binding]; other site 557598002622 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 557598002623 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 557598002624 Walker A motif; other site 557598002625 ATP binding site [chemical binding]; other site 557598002626 Walker B motif; other site 557598002627 arginine finger; other site 557598002628 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 557598002629 N-Dimethylarginine dimethylaminohydrolase [Amino acid transport and metabolism]; Region: COG1834 557598002630 Amidinotransferase; Region: Amidinotransf; cl12043 557598002631 arginine-ornithine antiporter; Region: arg_ornith_anti; TIGR03810 557598002632 Acylphosphatase; Region: Acylphosphatase; pfam00708 557598002633 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypF; COG0068 557598002634 HypF finger; Region: zf-HYPF; pfam07503 557598002635 HypF finger; Region: zf-HYPF; pfam07503 557598002636 Telomere recombination; Region: Sua5_yciO_yrdC; pfam01300 557598002637 Protein of unknown function (DUF1615); Region: DUF1615; pfam07759 557598002638 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 557598002639 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 557598002640 catalytic residue [active] 557598002641 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 557598002642 classical (c) SDRs; Region: SDR_c; cd05233 557598002643 NAD(P) binding site [chemical binding]; other site 557598002644 active site 557598002645 Creatinine amidohydrolase; Region: Creatininase; pfam02633 557598002646 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 557598002647 catalytic nucleophile [active] 557598002648 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 557598002649 Solute carrier 5 family, sodium/glucose transporters and related proteins; solute-binding domain; Region: SLC5sbd; cd10322 557598002650 Na binding site [ion binding]; other site 557598002651 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 557598002652 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 557598002653 substrate binding pocket [chemical binding]; other site 557598002654 membrane-bound complex binding site; other site 557598002655 hinge residues; other site 557598002656 H-NS histone family; Region: Histone_HNS; pfam00816 557598002657 Domain in histone-like proteins of HNS family; Region: HNS; smart00528 557598002658 dihydroorotate dehydrogenase (subfamily 1) family protein; Region: pyrD_sub1_fam; TIGR01037 557598002659 Dihydroorotate dehydrogenase (DHOD) class 1A FMN-binding domain. 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...; Region: DHOD_1A_like; cd04741 557598002660 active site 557598002661 FMN binding site [chemical binding]; other site 557598002662 substrate binding site [chemical binding]; other site 557598002663 catalytic residues [active] 557598002664 homodimer interface [polypeptide binding]; other site 557598002665 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated; Region: PRK05724 557598002666 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 557598002667 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 557598002668 TilS substrate C-terminal domain; Region: TilS_C; pfam11734 557598002669 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 557598002670 YccA-like proteins; Region: YccA_like; cd10433 557598002671 SnoaL-like domain; Region: SnoaL_3; pfam13474 557598002672 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557598002673 metal binding site [ion binding]; metal-binding site 557598002674 active site 557598002675 I-site; other site 557598002676 trigger factor; Provisional; Region: tig; PRK01490 557598002677 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 557598002678 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 557598002679 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 557598002680 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 557598002681 oligomer interface [polypeptide binding]; other site 557598002682 active site residues [active] 557598002683 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 557598002684 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 557598002685 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 557598002686 Walker A motif; other site 557598002687 ATP binding site [chemical binding]; other site 557598002688 Walker B motif; other site 557598002689 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 557598002690 Uncharacterized protein conserved in bacteria (DUF2076); Region: DUF2076; pfam09849 557598002691 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in Deinococcus radiodurans DR2231 protein and its bacterial homologs; Region: NTP-PPase_DR2231_like; cd11530 557598002692 metal binding site [ion binding]; metal-binding site 557598002693 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 557598002694 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 557598002695 hinge; other site 557598002696 active site 557598002697 cytidylate kinase; Provisional; Region: cmk; PRK00023 557598002698 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 557598002699 CMP-binding site; other site 557598002700 The sites determining sugar specificity; other site 557598002701 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 557598002702 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 557598002703 RNA binding site [nucleotide binding]; other site 557598002704 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 557598002705 RNA binding site [nucleotide binding]; other site 557598002706 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 557598002707 RNA binding site [nucleotide binding]; other site 557598002708 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 557598002709 RNA binding site [nucleotide binding]; other site 557598002710 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 557598002711 RNA binding site [nucleotide binding]; other site 557598002712 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 557598002713 RNA binding site [nucleotide binding]; other site 557598002714 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 557598002715 IHF dimer interface [polypeptide binding]; other site 557598002716 IHF - DNA interface [nucleotide binding]; other site 557598002717 Protein of unknown function (DUF1049); Region: DUF1049; cl01539 557598002718 tetratricopeptide repeat protein; Provisional; Region: PRK11788 557598002719 Ras GTPase Activating Domain; Region: RasGAP; cl02569 557598002720 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 557598002721 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 557598002722 active site 557598002723 dimer interface [polypeptide binding]; other site 557598002724 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 557598002725 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 557598002726 putative ribose interaction site [chemical binding]; other site 557598002727 putative ADP binding site [chemical binding]; other site 557598002728 ADP-L-glycero-D-mannoheptose 6-epimerase (GME), extended (e) SDRs; Region: ADP_GME_SDR_e; cd05248 557598002729 ADP-L-glycero-D-manno-heptose-6-epimerase; Region: heptose_epim; TIGR02197 557598002730 NADP binding site [chemical binding]; other site 557598002731 homopentamer interface [polypeptide binding]; other site 557598002732 substrate binding site [chemical binding]; other site 557598002733 active site 557598002734 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 557598002735 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 557598002736 N-acetyl-D-glucosamine binding site [chemical binding]; other site 557598002737 catalytic residue [active] 557598002738 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 557598002739 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 557598002740 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 557598002741 hydroxyacylglutathione hydrolase; Region: GSH_gloB; TIGR03413 557598002742 Methyltransferase domain; Region: Methyltransf_11; pfam08241 557598002743 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 557598002744 RNA/DNA hybrid binding site [nucleotide binding]; other site 557598002745 active site 557598002746 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 557598002747 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 557598002748 active site 557598002749 catalytic site [active] 557598002750 substrate binding site [chemical binding]; other site 557598002751 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 557598002752 substrate binding site; other site 557598002753 dimer interface; other site 557598002754 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 557598002755 homotrimer interaction site [polypeptide binding]; other site 557598002756 zinc binding site [ion binding]; other site 557598002757 CDP-binding sites; other site 557598002758 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 557598002759 tetramer (dimer of dimers) interface [polypeptide binding]; other site 557598002760 active site 557598002761 dimer interface [polypeptide binding]; other site 557598002762 transcriptional regulator PhoU; Provisional; Region: PRK11115 557598002763 PhoU domain; Region: PhoU; pfam01895 557598002764 PhoU domain; Region: PhoU; pfam01895 557598002765 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 557598002766 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 557598002767 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 557598002768 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 557598002769 active site 557598002770 phosphorylation site [posttranslational modification] 557598002771 intermolecular recognition site; other site 557598002772 dimerization interface [polypeptide binding]; other site 557598002773 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; cl17355 557598002774 DNA binding site [nucleotide binding] 557598002775 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 557598002776 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 557598002777 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 557598002778 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 557598002779 dimer interface [polypeptide binding]; other site 557598002780 phosphorylation site [posttranslational modification] 557598002781 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 557598002782 ATP binding site [chemical binding]; other site 557598002783 Mg2+ binding site [ion binding]; other site 557598002784 G-X-G motif; other site 557598002785 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 557598002786 Ligand Binding Site [chemical binding]; other site 557598002787 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 557598002788 Ligand Binding Site [chemical binding]; other site 557598002789 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 557598002790 Excalibur calcium-binding domain; Region: Excalibur; pfam05901 557598002791 Archaea-specific editing domain of threonyl-tRNA synthetase; Region: tRNA-Thr_ED; pfam08915 557598002792 Ogr/Delta-like zinc finger; Region: Ogr_Delta; pfam04606 557598002793 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 557598002794 non-specific DNA binding site [nucleotide binding]; other site 557598002795 salt bridge; other site 557598002796 sequence-specific DNA binding site [nucleotide binding]; other site 557598002797 Bacteriophage replication gene A protein (GPA); Region: Phage_GPA; cl15276 557598002798 Domain of unknown function (DUF3596); Region: DUF3596; pfam12167 557598002799 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 557598002800 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 557598002801 active site 557598002802 DNA binding site [nucleotide binding] 557598002803 Int/Topo IB signature motif; other site 557598002804 phosphoglycolate phosphatase; Provisional; Region: PRK13222 557598002805 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 557598002806 motif II; other site 557598002807 Domain of unknown function (DUF4376); Region: DUF4376; pfam14301 557598002808 Integrase core domain; Region: rve; pfam00665 557598002809 Sodium Bile acid symporter family; Region: SBF; cl17470 557598002810 Arsenite efflux pump ACR3 and related permeases [Inorganic ion transport and metabolism]; Region: ACR3; COG0798 557598002811 Sodium Bile acid symporter family; Region: SBF; cl17470 557598002812 AIPR protein; Region: AIPR; pfam10592 557598002813 Replication protein; Region: Rep_1; cl02412 557598002814 Relaxase/Mobilisation nuclease domain; Region: Relaxase; pfam03432 557598002815 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cd00338 557598002816 catalytic residues [active] 557598002817 catalytic nucleophile [active] 557598002818 Recombinase; Region: Recombinase; pfam07508 557598002819 Arsenical resistance operon trans-acting repressor ArsD; Region: ArsD; pfam06953 557598002820 potential frameshift: common BLAST hit: gi|134293367|ref|YP_001117103.1| arsenite-activated ATPase ArsA 557598002821 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 557598002822 P loop; other site 557598002823 Nucleotide binding site [chemical binding]; other site 557598002824 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 557598002825 DTAP/Switch II; other site 557598002826 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 557598002827 P loop; other site 557598002828 Nucleotide binding site [chemical binding]; other site 557598002829 Switch I; other site 557598002830 potential frameshift: common BLAST hit: gi|94313018|ref|YP_586227.1| NADH:flavin oxidoreductase/NADH oxidase 557598002831 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 557598002832 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 557598002833 phosphate binding site [ion binding]; other site 557598002834 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 557598002835 S-adenosylmethionine binding site [chemical binding]; other site 557598002836 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 557598002837 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 557598002838 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 557598002839 DNA-binding site [nucleotide binding]; DNA binding site 557598002840 RNA-binding motif; other site 557598002841 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 557598002842 rRNA binding site [nucleotide binding]; other site 557598002843 predicted 30S ribosome binding site; other site 557598002844 D-amino acid dehydrogenase small subunit; Validated; Region: PRK00711 557598002845 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 557598002846 hydroxyglutarate oxidase; Provisional; Region: PRK11728 557598002847 chemotaxis methyltransferase CheR; Provisional; Region: PRK10611 557598002848 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 557598002849 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 557598002850 iron-sulfur cluster insertion protein ErpA; Provisional; Region: PRK13623 557598002851 N-acetyl-gamma-glutamyl-phosphate reductase; Validated; Region: argC; PRK00436 557598002852 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 557598002853 peroxidase; Provisional; Region: PRK15000 557598002854 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 557598002855 dimer interface [polypeptide binding]; other site 557598002856 decamer (pentamer of dimers) interface [polypeptide binding]; other site 557598002857 catalytic triad [active] 557598002858 peroxidatic and resolving cysteines [active] 557598002859 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 557598002860 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 557598002861 dimer interface [polypeptide binding]; other site 557598002862 conserved gate region; other site 557598002863 ABC-ATPase subunit interface; other site 557598002864 dipeptide transporter; Provisional; Region: PRK10913 557598002865 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 557598002866 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 557598002867 dimer interface [polypeptide binding]; other site 557598002868 conserved gate region; other site 557598002869 putative PBP binding loops; other site 557598002870 ABC-ATPase subunit interface; other site 557598002871 dipeptide transporter ATP-binding subunit; Provisional; Region: dppD; PRK11022 557598002872 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 557598002873 Walker A/P-loop; other site 557598002874 ATP binding site [chemical binding]; other site 557598002875 Q-loop/lid; other site 557598002876 ABC transporter signature motif; other site 557598002877 Walker B; other site 557598002878 D-loop; other site 557598002879 H-loop/switch region; other site 557598002880 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 557598002881 dipeptide transporter ATP-binding subunit; Provisional; Region: dppF; PRK11308 557598002882 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 557598002883 Walker A/P-loop; other site 557598002884 ATP binding site [chemical binding]; other site 557598002885 Q-loop/lid; other site 557598002886 ABC transporter signature motif; other site 557598002887 Walker B; other site 557598002888 D-loop; other site 557598002889 H-loop/switch region; other site 557598002890 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain; Region: oligo_HPY; TIGR01727 557598002891 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 557598002892 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 557598002893 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 557598002894 FeS/SAM binding site; other site 557598002895 TRAM domain; Region: TRAM; cl01282 557598002896 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5394 557598002897 PHB/PHA accumulation regulator DNA-binding domain; Region: PHB_acc_N; pfam07879 557598002898 PHB accumulation regulatory domain; Region: PHB_acc; pfam05233 557598002899 PHB accumulation regulatory domain; Region: PHB_acc; pfam05233 557598002900 Phasin protein; Region: Phasin_2; pfam09361 557598002901 Predicted carboxypeptidase [Amino acid transport and metabolism]; Region: COG2866 557598002902 Peptidase M14-like domain of ATP/GTP binding proteins and cytosolic carboxypeptidases; uncharacterized bacterial subgroup; Region: M14_Nna1_like_1; cd06234 557598002903 putative active site [active] 557598002904 Zn binding site [ion binding]; other site 557598002905 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 557598002906 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 557598002907 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557598002908 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 557598002909 metal binding site [ion binding]; metal-binding site 557598002910 active site 557598002911 I-site; other site 557598002912 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 557598002913 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 557598002914 DNA-binding site [nucleotide binding]; DNA binding site 557598002915 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 557598002916 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557598002917 homodimer interface [polypeptide binding]; other site 557598002918 catalytic residue [active] 557598002919 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 557598002920 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 557598002921 S-adenosylmethionine binding site [chemical binding]; other site 557598002922 N-ethylammeline chlorohydrolase; Provisional; Region: PRK09045 557598002923 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 557598002924 active site 557598002925 putative substrate binding pocket [chemical binding]; other site 557598002926 Protein of unknown function (DUF2442); Region: DUF2442; pfam10387 557598002927 Predicted membrane protein, hemolysin III homolog [General function prediction only]; Region: COG1272 557598002928 channel protein, hemolysin III family; Region: hlyIII; TIGR01065 557598002929 bifunctional tRNA (mnm(5)s(2)U34)-methyltransferase/FAD-dependent cmnm(5)s(2)U34 oxidoreductase; Reviewed; Region: mnmC; PRK01747 557598002930 Uncharacterized conserved protein [Function unknown]; Region: COG4121 557598002931 polyphosphate kinase 2, PA0141 family; Region: PPK2_P_aer; TIGR03707 557598002932 H-NS histone family; Region: Histone_HNS; pfam00816 557598002933 Domain in histone-like proteins of HNS family; Region: HNS; smart00528 557598002934 excinuclease ABC subunit B; Provisional; Region: PRK05298 557598002935 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 557598002936 ATP binding site [chemical binding]; other site 557598002937 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 557598002938 nucleotide binding region [chemical binding]; other site 557598002939 ATP-binding site [chemical binding]; other site 557598002940 Ultra-violet resistance protein B; Region: UvrB; pfam12344 557598002941 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 557598002942 FAD binding domain; Region: FAD_binding_4; pfam01565 557598002943 DNA polymerase III, subunit gamma and tau; Region: dnaX_nterm; TIGR02397 557598002944 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 557598002945 Walker A motif; other site 557598002946 ATP binding site [chemical binding]; other site 557598002947 Walker B motif; other site 557598002948 arginine finger; other site 557598002949 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 557598002950 hypothetical protein; Validated; Region: PRK00153 557598002951 recombination protein RecR; Reviewed; Region: recR; PRK00076 557598002952 RecR protein; Region: RecR; pfam02132 557598002953 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 557598002954 putative active site [active] 557598002955 putative metal-binding site [ion binding]; other site 557598002956 tetramer interface [polypeptide binding]; other site 557598002957 ParA-like protein; Provisional; Region: PHA02518 557598002958 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 557598002959 P-loop; other site 557598002960 Magnesium ion binding site [ion binding]; other site 557598002961 Na+/phosphate symporter [Inorganic ion transport and metabolism]; Region: NptA; COG1283 557598002962 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 557598002963 CHAD domain; Region: CHAD; pfam05235 557598002964 Ion transport protein; Region: Ion_trans; pfam00520 557598002965 Ion channel; Region: Ion_trans_2; pfam07885 557598002966 zinc-ribbon domain; Region: zf-ribbon_3; pfam13248 557598002967 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 557598002968 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 557598002969 dimer interface [polypeptide binding]; other site 557598002970 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557598002971 catalytic residue [active] 557598002972 lipoyl synthase; Provisional; Region: PRK05481 557598002973 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 557598002974 FeS/SAM binding site; other site 557598002975 lipoate-protein ligase B; Provisional; Region: PRK14342 557598002976 Protein of unknown function (DUF493); Region: DUF493; pfam04359 557598002977 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 557598002978 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 557598002979 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; smart00936 557598002980 threonine dehydratase; Reviewed; Region: PRK09224 557598002981 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 557598002982 tetramer interface [polypeptide binding]; other site 557598002983 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557598002984 catalytic residue [active] 557598002985 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_1; cd04906 557598002986 putative Ile/Val binding site [chemical binding]; other site 557598002987 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_2; cd04907 557598002988 putative Ile/Val binding site [chemical binding]; other site 557598002989 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 557598002990 D-galactonate transporter; Region: 2A0114; TIGR00893 557598002991 putative substrate translocation pore; other site 557598002992 membrane protein FdrA; Validated; Region: PRK06091 557598002993 CoA binding domain; Region: CoA_binding; pfam02629 557598002994 CoA-ligase; Region: Ligase_CoA; pfam00549 557598002995 Protein of unknown function (DUF1116); Region: DUF1116; pfam06545 557598002996 Protein of unknown function (DUF2877); Region: DUF2877; pfam11392 557598002997 DNA-binding transcriptional activator AllS; Provisional; Region: PRK10094 557598002998 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 557598002999 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 557598003000 dimerization interface [polypeptide binding]; other site 557598003001 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 557598003002 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 557598003003 Tripartite ATP-independent periplasmic transporters, DctQ component; Region: DctQ; pfam04290 557598003004 DctM-like transporters; Region: DctM; pfam06808 557598003005 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; COG1593 557598003006 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 557598003007 CoA-transferase family III; Region: CoA_transf_3; pfam02515 557598003008 acetyl-CoA acetyltransferase; Provisional; Region: PRK08131 557598003009 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 557598003010 dimer interface [polypeptide binding]; other site 557598003011 active site 557598003012 3-hydroxy-acyl-CoA dehydrogenase; Validated; Region: PRK08268 557598003013 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 557598003014 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 557598003015 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 557598003016 enoyl-CoA hydratase; Provisional; Region: PRK08138 557598003017 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 557598003018 substrate binding site [chemical binding]; other site 557598003019 oxyanion hole (OAH) forming residues; other site 557598003020 trimer interface [polypeptide binding]; other site 557598003021 helix_turn_helix isocitrate lyase regulation; Region: HTH_ICLR; smart00346 557598003022 Transcriptional regulator [Transcription]; Region: IclR; COG1414 557598003023 Bacterial transcriptional regulator; Region: IclR; pfam01614 557598003024 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 557598003025 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 557598003026 active site 557598003027 benzoate transport; Region: 2A0115; TIGR00895 557598003028 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 557598003029 putative substrate translocation pore; other site 557598003030 Predicted protease with the C-terminal PDZ domain [General function prediction only]; Region: COG3975 557598003031 M61 glycyl aminopeptidase; Region: Peptidase_M61; pfam05299 557598003032 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 557598003033 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 557598003034 Low-spin heme binding site [chemical binding]; other site 557598003035 Putative water exit pathway; other site 557598003036 Binuclear center (active site) [active] 557598003037 Putative proton exit pathway; other site 557598003038 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 557598003039 cbb3-type cytochrome c oxidase subunit II; Provisional; Region: PRK14487 557598003040 Cbb3-type cytochrome oxidase component FixQ; Region: FixQ; pfam05545 557598003041 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 557598003042 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 557598003043 Cytochrome c; Region: Cytochrom_C; pfam00034 557598003044 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 557598003045 4Fe-4S binding domain; Region: Fer4_5; pfam12801 557598003046 4Fe-4S binding domain; Region: Fer4; pfam00037 557598003047 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 557598003048 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3198 557598003049 FixH; Region: FixH; pfam05751 557598003050 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 557598003051 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 557598003052 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 557598003053 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 557598003054 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 557598003055 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 557598003056 active site 557598003057 HIGH motif; other site 557598003058 KMSK motif region; other site 557598003059 Anticodon-binding domain of arginyl tRNA synthetases; Region: Anticodon_Ia_Arg; cd07956 557598003060 tRNA binding surface [nucleotide binding]; other site 557598003061 anticodon binding site; other site 557598003062 Protein of unknown function (DUF461); Region: DUF461; pfam04314 557598003063 Merozoite surface antigen 2c; Region: MSA-2c; pfam12238 557598003064 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 557598003065 Thiopurine S-methyltransferase (TPMT); Region: TPMT; pfam05724 557598003066 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 557598003067 S-adenosylmethionine binding site [chemical binding]; other site 557598003068 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5339 557598003069 Bacterial protein of unknown function (DUF945); Region: DUF945; pfam06097 557598003070 DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]; Region: DnaQ; COG0847 557598003071 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 557598003072 active site 557598003073 catalytic site [active] 557598003074 substrate binding site [chemical binding]; other site 557598003075 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]; Region: COG2905 557598003076 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 557598003077 ligand binding site [chemical binding]; other site 557598003078 flexible hinge region; other site 557598003079 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the bacterial CAP_ED (cAMP receptor protein effector domain) family of transcription factors and the DUF294 domain. Members of CAP_ED, include CAP...; Region: CBS_pair_CAP-ED_DUF294_assoc_bac; cd04589 557598003080 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 557598003081 metal binding triad; other site 557598003082 Benzoate membrane transport protein; Region: BenE; pfam03594 557598003083 benzoate transporter; Region: benE; TIGR00843 557598003084 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 557598003085 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 557598003086 ATP binding site [chemical binding]; other site 557598003087 Mg2+ binding site [ion binding]; other site 557598003088 G-X-G motif; other site 557598003089 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 557598003090 ATP binding site [chemical binding]; other site 557598003091 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 557598003092 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 557598003093 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 557598003094 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 557598003095 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 557598003096 Protein export membrane protein; Region: SecD_SecF; pfam02355 557598003097 PAS domain S-box; Region: sensory_box; TIGR00229 557598003098 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 557598003099 putative active site [active] 557598003100 heme pocket [chemical binding]; other site 557598003101 PAS fold; Region: PAS_7; pfam12860 557598003102 PAS fold; Region: PAS_3; pfam08447 557598003103 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 557598003104 heme pocket [chemical binding]; other site 557598003105 putative active site [active] 557598003106 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 557598003107 dimer interface [polypeptide binding]; other site 557598003108 phosphorylation site [posttranslational modification] 557598003109 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 557598003110 ATP binding site [chemical binding]; other site 557598003111 Mg2+ binding site [ion binding]; other site 557598003112 G-X-G motif; other site 557598003113 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 557598003114 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 557598003115 active site 557598003116 phosphorylation site [posttranslational modification] 557598003117 intermolecular recognition site; other site 557598003118 dimerization interface [polypeptide binding]; other site 557598003119 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 557598003120 Response regulator receiver domain; Region: Response_reg; pfam00072 557598003121 active site 557598003122 phosphorylation site [posttranslational modification] 557598003123 intermolecular recognition site; other site 557598003124 dimerization interface [polypeptide binding]; other site 557598003125 FOG: HPt domain [Signal transduction mechanisms]; Region: ArcB; COG2198 557598003126 formyltetrahydrofolate deformylase; Reviewed; Region: purU; PRK06027 557598003127 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 557598003128 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 557598003129 putative active site [active] 557598003130 putative substrate binding site [chemical binding]; other site 557598003131 putative cosubstrate binding site; other site 557598003132 catalytic site [active] 557598003133 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK10792 557598003134 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 557598003135 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 557598003136 homodimer interface [polypeptide binding]; other site 557598003137 NADP binding site [chemical binding]; other site 557598003138 substrate binding site [chemical binding]; other site 557598003139 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 557598003140 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557598003141 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 557598003142 dimer interface [polypeptide binding]; other site 557598003143 putative CheW interface [polypeptide binding]; other site 557598003144 Transposase DDE domain; Region: DDE_Tnp_1_5; pfam13737 557598003145 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 557598003146 potential frameshift: common BLAST hit: gi|171058644|ref|YP_001790993.1| integrase catalytic region 557598003147 Integrase core domain; Region: rve_2; pfam13333 557598003148 Integrase core domain; Region: rve; pfam00665 557598003149 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 557598003150 Transposase; Region: HTH_Tnp_1; cl17663 557598003151 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 557598003152 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 557598003153 trimer interface [polypeptide binding]; other site 557598003154 eyelet of channel; other site 557598003155 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 557598003156 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557598003157 active site 557598003158 I-site; other site 557598003159 metal binding site [ion binding]; metal-binding site 557598003160 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 557598003161 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 557598003162 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 557598003163 PAS domain; Region: PAS_9; pfam13426 557598003164 putative active site [active] 557598003165 heme pocket [chemical binding]; other site 557598003166 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 557598003167 Periplasmic binding protein domain; Region: Peripla_BP_4; pfam13407 557598003168 ligand binding site [chemical binding]; other site 557598003169 Orn/Lys/Arg decarboxylase, N-terminal domain; Region: OKR_DC_1_N; pfam03709 557598003170 Arginine/lysine/ornithine decarboxylases [Amino acid transport and metabolism]; Region: LdcC; COG1982 557598003171 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 557598003172 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 557598003173 catalytic residue [active] 557598003174 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 557598003175 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 557598003176 alpha-gamma subunit interface [polypeptide binding]; other site 557598003177 beta-gamma subunit interface [polypeptide binding]; other site 557598003178 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 557598003179 gamma-beta subunit interface [polypeptide binding]; other site 557598003180 alpha-beta subunit interface [polypeptide binding]; other site 557598003181 urease subunit alpha; Reviewed; Region: ureC; PRK13207 557598003182 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 557598003183 subunit interactions [polypeptide binding]; other site 557598003184 active site 557598003185 flap region; other site 557598003186 Integral membrane protein possibly involved in chromosome condensation [Cell division and chromosome partitioning]; Region: CrcB; COG0239 557598003187 camphor resistance protein CrcB; Provisional; Region: ccrB; PRK01636 557598003188 urease accessory protein UreE; Provisional; Region: ureE; PRK14711 557598003189 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 557598003190 dimer interface [polypeptide binding]; other site 557598003191 catalytic residues [active] 557598003192 Urease accessory protein UreF [Posttranslational modification, protein turnover, chaperones]; Region: UreF; COG0830 557598003193 UreF; Region: UreF; pfam01730 557598003194 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 557598003195 UreD urease accessory protein; Region: UreD; cl00530 557598003196 Urea transporter; Region: UT; cl01829 557598003197 cobalt transport protein CbiM; Validated; Region: PRK06265 557598003198 Cobalt uptake substrate-specific transmembrane region; Region: CbiM; pfam01891 557598003199 PDGLE domain; Region: PDGLE; pfam13190 557598003200 HdeA/HdeB family; Region: HdeA; cl05752 557598003201 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 557598003202 threonine/serine transporter TdcC; Provisional; Region: PRK13629; cl17672 557598003203 Domain of unknown function (DUF4072); Region: DUF4072; pfam13284 557598003204 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 557598003205 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 557598003206 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 557598003207 motif II; other site 557598003208 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 557598003209 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 557598003210 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 557598003211 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 557598003212 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 557598003213 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 557598003214 Walker A motif; other site 557598003215 ATP binding site [chemical binding]; other site 557598003216 Walker B motif; other site 557598003217 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 557598003218 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 557598003219 putative secretion ATPase, PEP-CTERM locus subfamily; Region: pepcterm_ATPase; TIGR03015 557598003220 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 557598003221 Walker A motif; other site 557598003222 ATP binding site [chemical binding]; other site 557598003223 Walker B motif; other site 557598003224 arginine finger; other site 557598003225 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 557598003226 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 557598003227 Walker A/P-loop; other site 557598003228 ATP binding site [chemical binding]; other site 557598003229 Q-loop/lid; other site 557598003230 ABC transporter signature motif; other site 557598003231 Walker B; other site 557598003232 D-loop; other site 557598003233 H-loop/switch region; other site 557598003234 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 557598003235 Permease; Region: Permease; pfam02405 557598003236 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 557598003237 mce related protein; Region: MCE; pfam02470 557598003238 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; pfam05494 557598003239 Sulphate Transporter and Anti-Sigma factor antagonist domain found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors; Region: STAS; cl00604 557598003240 VacJ like lipoprotein; Region: VacJ; cl01073 557598003241 Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]; Region: COG0436 557598003242 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 557598003243 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557598003244 homodimer interface [polypeptide binding]; other site 557598003245 catalytic residue [active] 557598003246 Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: SppA; COG0616 557598003247 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 557598003248 tandem repeat interface [polypeptide binding]; other site 557598003249 oligomer interface [polypeptide binding]; other site 557598003250 active site residues [active] 557598003251 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 557598003252 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 557598003253 motif II; other site 557598003254 23S rRNA pseudouridylate synthase C; Provisional; Region: PRK11025 557598003255 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 557598003256 RNA binding surface [nucleotide binding]; other site 557598003257 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 557598003258 active site 557598003259 Ribonucleases G and E [Translation, ribosomal structure and biogenesis]; Region: CafA; COG1530 557598003260 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 557598003261 homodimer interface [polypeptide binding]; other site 557598003262 oligonucleotide binding site [chemical binding]; other site 557598003263 CRISPR/Cas system-associated protein Csy1; Region: Csy1_I-F; cd09735 557598003264 CRISPR/Cas system-associated RAMP superfamily protein Csy2; Region: Csy2_I-F; cd09736 557598003265 CRISPR/Cas system-associated RAMP superfamily protein Csy3; Region: Csy3_I-F; cd09737 557598003266 CRISPR/Cas system-associated RAMP superfamily protein Cas6f; Region: Cas6_I-F; cl09835 557598003267 CRISPR/Cas system-associated RAMP superfamily protein Cas6f; Region: Cas6_I-F; cd09739 557598003268 ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: ModA; COG0725 557598003269 ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: Sbp; COG1613 557598003270 CRISPR/Cas system-associated protein Cas1; Region: Cas1_I-II-III; cl00656 557598003271 cobalt ABC transporter, permease protein CbiQ; Region: CbiQ_TIGR; TIGR02454 557598003272 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 557598003273 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 557598003274 Walker A/P-loop; other site 557598003275 ATP binding site [chemical binding]; other site 557598003276 Q-loop/lid; other site 557598003277 ABC transporter signature motif; other site 557598003278 Walker B; other site 557598003279 D-loop; other site 557598003280 H-loop/switch region; other site 557598003281 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 557598003282 ClC chloride channel EriC. This domain is found in the EriC chloride transporters that mediate the extreme acid resistance response in eubacteria and archaea. This response allows bacteria to survive in the acidic environments by decarboxylation-linked...; Region: EriC; cd01031 557598003283 Cl- selectivity filter; other site 557598003284 Cl- binding residues [ion binding]; other site 557598003285 pore gating glutamate residue; other site 557598003286 dimer interface [polypeptide binding]; other site 557598003287 H+/Cl- coupling transport residue; other site 557598003288 TonB-dependent copper receptor; Region: TonB-copper; TIGR01778 557598003289 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 557598003290 N-terminal plug; other site 557598003291 ligand-binding site [chemical binding]; other site 557598003292 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 557598003293 Peptidase family M23; Region: Peptidase_M23; pfam01551 557598003294 Methyltransferase domain; Region: Methyltransf_32; pfam13679 557598003295 Methyltransferase domain; Region: Methyltransf_31; pfam13847 557598003296 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557598003297 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 557598003298 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 557598003299 putative effector binding pocket; other site 557598003300 dimerization interface [polypeptide binding]; other site 557598003301 Predicted membrane protein [Function unknown]; Region: COG2259 557598003302 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 557598003303 putative active site [active] 557598003304 metal binding site [ion binding]; metal-binding site 557598003305 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 557598003306 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 557598003307 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 557598003308 ABC transporter; Region: ABC_tran_2; pfam12848 557598003309 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 557598003310 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 557598003311 active site 557598003312 DNA binding site [nucleotide binding] 557598003313 Int/Topo IB signature motif; other site 557598003314 selenophosphate synthetase; Provisional; Region: PRK00943 557598003315 Selenophosphate synthetase (SelD) catalyzes the conversion of selenium to selenophosphate which is required by a number of bacterial, archaeal and eukaryotic organisms for synthesis of Secys-tRNA, the precursor of selenocysteine in selenoenzymes. The...; Region: SelD; cd02195 557598003316 dimerization interface [polypeptide binding]; other site 557598003317 putative ATP binding site [chemical binding]; other site 557598003318 tRNA 2-selenouridine synthase; Provisional; Region: PRK11784 557598003319 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 557598003320 active site residue [active] 557598003321 amino acid transporter; Region: 2A0306; TIGR00909 557598003322 Amino acid permease; Region: AA_permease_2; pfam13520 557598003323 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4174 557598003324 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 557598003325 dimer interface [polypeptide binding]; other site 557598003326 conserved gate region; other site 557598003327 ABC-ATPase subunit interface; other site 557598003328 Protein of unknown function, DUF484; Region: DUF484; cl17449 557598003329 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 557598003330 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557598003331 metal binding site [ion binding]; metal-binding site 557598003332 active site 557598003333 I-site; other site 557598003334 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 557598003335 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4239 557598003336 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 557598003337 dimer interface [polypeptide binding]; other site 557598003338 conserved gate region; other site 557598003339 putative PBP binding loops; other site 557598003340 ABC-ATPase subunit interface; other site 557598003341 ABC-type uncharacterized transport system, duplicated ATPase component [General function prediction only]; Region: COG4172 557598003342 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 557598003343 Walker A/P-loop; other site 557598003344 ATP binding site [chemical binding]; other site 557598003345 Q-loop/lid; other site 557598003346 ABC transporter signature motif; other site 557598003347 Walker B; other site 557598003348 D-loop; other site 557598003349 H-loop/switch region; other site 557598003350 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 557598003351 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 557598003352 Walker A/P-loop; other site 557598003353 ATP binding site [chemical binding]; other site 557598003354 Q-loop/lid; other site 557598003355 ABC transporter signature motif; other site 557598003356 Walker B; other site 557598003357 D-loop; other site 557598003358 H-loop/switch region; other site 557598003359 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 557598003360 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 557598003361 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 557598003362 generic binding surface II; other site 557598003363 generic binding surface I; other site 557598003364 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 557598003365 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 557598003366 Uncharacterized conserved protein [Function unknown]; Region: COG2835 557598003367 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 557598003368 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 557598003369 Ligand binding site; other site 557598003370 oligomer interface; other site 557598003371 adenylate kinase; Reviewed; Region: adk; PRK00279 557598003372 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 557598003373 AMP-binding site [chemical binding]; other site 557598003374 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 557598003375 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 557598003376 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 557598003377 PrkA family serine protein kinase; Provisional; Region: PRK15455 557598003378 AAA ATPase domain; Region: AAA_16; pfam13191 557598003379 PrkA serine protein kinase C-terminal domain; Region: PrkA; pfam06798 557598003380 hypothetical protein; Provisional; Region: PRK05325 557598003381 SpoVR family protein; Provisional; Region: PRK11767 557598003382 Uncharacterized conserved protein [Function unknown]; Region: SpoVR; COG2719 557598003383 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 557598003384 NAD(P) binding site [chemical binding]; other site 557598003385 homotetramer interface [polypeptide binding]; other site 557598003386 homodimer interface [polypeptide binding]; other site 557598003387 active site 557598003388 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 557598003389 poly(R)-hydroxyalkanoic acid synthase, class III, PhaC subunit; Region: PHA_synth_III_C; TIGR01836 557598003390 putative acyltransferase; Provisional; Region: PRK05790 557598003391 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 557598003392 dimer interface [polypeptide binding]; other site 557598003393 active site 557598003394 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 557598003395 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 557598003396 HIGH motif; other site 557598003397 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 557598003398 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 557598003399 active site 557598003400 KMSKS motif; other site 557598003401 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 557598003402 tRNA binding surface [nucleotide binding]; other site 557598003403 anticodon binding site; other site 557598003404 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 557598003405 Uncharacterized conserved protein [Function unknown]; Region: COG3287 557598003406 FIST N domain; Region: FIST; pfam08495 557598003407 FIST C domain; Region: FIST_C; pfam10442 557598003408 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 557598003409 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557598003410 metal binding site [ion binding]; metal-binding site 557598003411 active site 557598003412 I-site; other site 557598003413 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 557598003414 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557598003415 dimer interface [polypeptide binding]; other site 557598003416 putative CheW interface [polypeptide binding]; other site 557598003417 EAL-domain associated signalling protein domain; Region: YkuI_C; pfam10388 557598003418 GPR1/FUN34/yaaH family; Region: Grp1_Fun34_YaaH; cl00685 557598003419 7-cyano-7-deazaguanine reductase; Provisional; Region: PRK13258 557598003420 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 557598003421 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 557598003422 FeS/SAM binding site; other site 557598003423 6-pyruvoyl tetrahydropterin synthase; Region: PTPS; pfam01242 557598003424 active site 557598003425 6-pyruvoyl tetrahydropterin synthase; Region: PTPS; pfam01242 557598003426 active site 557598003427 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 557598003428 Ligand Binding Site [chemical binding]; other site 557598003429 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 557598003430 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; cl00290 557598003431 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 557598003432 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557598003433 metal binding site [ion binding]; metal-binding site 557598003434 active site 557598003435 I-site; other site 557598003436 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 557598003437 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 557598003438 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 557598003439 active site 557598003440 phosphorylation site [posttranslational modification] 557598003441 intermolecular recognition site; other site 557598003442 dimerization interface [polypeptide binding]; other site 557598003443 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; cl17355 557598003444 DNA binding site [nucleotide binding] 557598003445 7TMR-DISM extracellular 2; Region: 7TMR-DISMED2; pfam07696 557598003446 7TM diverse intracellular signalling; Region: 7TMR-DISM_7TM; pfam07695 557598003447 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 557598003448 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 557598003449 dimer interface [polypeptide binding]; other site 557598003450 phosphorylation site [posttranslational modification] 557598003451 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 557598003452 ATP binding site [chemical binding]; other site 557598003453 Mg2+ binding site [ion binding]; other site 557598003454 G-X-G motif; other site 557598003455 Autotransporter beta-domain; Region: Autotransporter; pfam03797 557598003456 Agmatinase-like family includes proclavaminic acid amidinohydrolase; Region: Agmatinase_PAH; cd11592 557598003457 agmatinase; Region: agmatinase; TIGR01230 557598003458 oligomer interface [polypeptide binding]; other site 557598003459 putative active site [active] 557598003460 Mn binding site [ion binding]; other site 557598003461 Domain of unknown function (DUF4376); Region: DUF4376; pfam14301 557598003462 Phage Tail Collar Domain; Region: Collar; pfam07484 557598003463 Uncharacterized protein conserved in bacteria (DUF2313); Region: DUF2313; cl01542 557598003464 Uncharacterized homolog of phage Mu protein gp47 [Function unknown]; Region: XkdT; COG3299 557598003465 Phage protein GP46; Region: GP46; cl01814 557598003466 Bacteriophage Mu Gp45 protein; Region: Phage_Mu_Gp45; cl15410 557598003467 phage baseplate assembly protein V; Region: phage_P2_V; TIGR01644 557598003468 Phage late control gene D protein (GPD); Region: Phage_GPD; pfam05954 557598003469 DNA circulation protein N-terminus; Region: DNA_circ_N; pfam07157 557598003470 Predicted chitinase [General function prediction only]; Region: COG3179 557598003471 catalytic residue [active] 557598003472 Mu-like prophage tail sheath protein gpL [General function prediction only]; Region: COG4386 557598003473 Phage tail sheath protein; Region: Phage_sheath_1; pfam04984 557598003474 Domain of unknown function (DUF1834); Region: DUF1834; cl02087 557598003475 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 557598003476 amidase catalytic site [active] 557598003477 Zn binding residues [ion binding]; other site 557598003478 substrate binding site [chemical binding]; other site 557598003479 Mor transcription activator family; Region: Mor; cl02360 557598003480 Protein of unknown function (DUF3164); Region: DUF3164; pfam11363 557598003481 AAA domain; Region: AAA_22; pfam13401 557598003482 Mu DNA-binding domain; Region: HTH_Tnp_Mu_1; pfam02316 557598003483 Integrase core domain; Region: rve; pfam00665 557598003484 Mu transposase, C-terminal; Region: Mu-transpos_C; pfam09299 557598003485 Winged helix-turn-helix DNA-binding; Region: HTH_35; cl17423 557598003486 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 557598003487 non-specific DNA binding site [nucleotide binding]; other site 557598003488 sequence-specific DNA binding site [nucleotide binding]; other site 557598003489 salt bridge; other site 557598003490 Predicted transcriptional regulator [Transcription]; Region: COG2932 557598003491 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 557598003492 Catalytic site [active] 557598003493 Phage P2 GpU; Region: Phage_P2_GpU; pfam06995 557598003494 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 557598003495 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 557598003496 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 557598003497 potential frameshift: common BLAST hit: gi|171058644|ref|YP_001790993.1| integrase catalytic region 557598003498 Integrase core domain; Region: rve_2; pfam13333 557598003499 Integrase core domain; Region: rve; pfam00665 557598003500 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 557598003501 Transposase; Region: HTH_Tnp_1; cl17663 557598003502 potential frameshift: common BLAST hit: gi|194288968|ref|YP_002004875.1| type I restriction-modification deoxyribonuclease, R subunit 557598003503 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 557598003504 potential frameshift: common BLAST hit: gi|15676962|ref|NP_274113.1| bacteriophage transposase 557598003505 Mu DNA-binding domain; Region: HTH_Tnp_Mu_1; pfam02316 557598003506 RIP metalloprotease RseP; Region: TIGR00054 557598003507 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 557598003508 NMT1-like family; Region: NMT1_2; pfam13379 557598003509 ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]; Region: TauC; COG0600 557598003510 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 557598003511 putative PBP binding loops; other site 557598003512 dimer interface [polypeptide binding]; other site 557598003513 ABC-ATPase subunit interface; other site 557598003514 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 557598003515 ATP-binding cassette domain of the nitrate and sulfonate transporters; Region: ABC_NrtD_SsuB_transporters; cd03293 557598003516 Walker A/P-loop; other site 557598003517 ATP binding site [chemical binding]; other site 557598003518 Q-loop/lid; other site 557598003519 ABC transporter signature motif; other site 557598003520 Walker B; other site 557598003521 D-loop; other site 557598003522 H-loop/switch region; other site 557598003523 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]; Region: COG4191 557598003524 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 557598003525 dimer interface [polypeptide binding]; other site 557598003526 phosphorylation site [posttranslational modification] 557598003527 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 557598003528 ATP binding site [chemical binding]; other site 557598003529 Mg2+ binding site [ion binding]; other site 557598003530 G-X-G motif; other site 557598003531 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 557598003532 putative substrate binding pocket [chemical binding]; other site 557598003533 trimer interface [polypeptide binding]; other site 557598003534 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 557598003535 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 557598003536 active site 557598003537 phosphorylation site [posttranslational modification] 557598003538 intermolecular recognition site; other site 557598003539 dimerization interface [polypeptide binding]; other site 557598003540 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 557598003541 Walker A motif; other site 557598003542 ATP binding site [chemical binding]; other site 557598003543 Walker B motif; other site 557598003544 arginine finger; other site 557598003545 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 557598003546 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 557598003547 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 557598003548 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 557598003549 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 557598003550 ABC-ATPase subunit interface; other site 557598003551 dimer interface [polypeptide binding]; other site 557598003552 putative PBP binding regions; other site 557598003553 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 557598003554 intersubunit interface [polypeptide binding]; other site 557598003555 Putative heme degradation protein [Inorganic ion transport and metabolism]; Region: HemS; COG3720 557598003556 Haemin-degrading HemS.ChuX domain; Region: HemS; pfam05171 557598003557 Haemin-degrading HemS.ChuX domain; Region: HemS; pfam05171 557598003558 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 557598003559 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 557598003560 N-terminal plug; other site 557598003561 ligand-binding site [chemical binding]; other site 557598003562 Hemin uptake protein hemP; Region: hemP; pfam10636 557598003563 putative heme utilization radical SAM enzyme HutW; Region: rSAM_HutW; TIGR04107 557598003564 Haem utilisation ChuX/HutX; Region: ChuX_HutX; cl01509 557598003565 NADH(P)-binding; Region: NAD_binding_10; pfam13460 557598003566 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557598003567 NAD(P) binding site [chemical binding]; other site 557598003568 active site 557598003569 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 557598003570 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 557598003571 substrate binding site [chemical binding]; other site 557598003572 hexamer interface [polypeptide binding]; other site 557598003573 metal binding site [ion binding]; metal-binding site 557598003574 Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; Region: CE4_SF; cl15692 557598003575 exonuclease V subunit alpha; Provisional; Region: recD; PRK10875 557598003576 AAA domain; Region: AAA_30; pfam13604 557598003577 Family description; Region: UvrD_C_2; pfam13538 557598003578 Part of AAA domain; Region: AAA_19; pfam13245 557598003579 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 557598003580 UvrD-like helicase C-terminal domain; Region: UvrD_C; pfam13361 557598003581 Family description; Region: UvrD_C_2; pfam13538 557598003582 exodeoxyribonuclease V, gamma subunit; Region: recC; TIGR01450 557598003583 exonuclease V subunit gamma; Provisional; Region: recC; PRK11069 557598003584 exonuclease V subunit gamma; Provisional; Region: recC; PRK11069 557598003585 Transglycosylase SLT domain; Region: SLT_2; pfam13406 557598003586 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 557598003587 N-acetyl-D-glucosamine binding site [chemical binding]; other site 557598003588 catalytic residue [active] 557598003589 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 557598003590 Winged helix-turn-helix transcription repressor, HrcA DNA-binding; Region: HrcA_DNA-bdg; pfam03444 557598003591 Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]; Region: CinA; COG1058 557598003592 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 557598003593 putative MPT binding site; other site 557598003594 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 557598003595 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 557598003596 Walker A/P-loop; other site 557598003597 ATP binding site [chemical binding]; other site 557598003598 Q-loop/lid; other site 557598003599 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 557598003600 ABC transporter signature motif; other site 557598003601 Walker B; other site 557598003602 D-loop; other site 557598003603 H-loop/switch region; other site 557598003604 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK04539 557598003605 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK02231 557598003606 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 557598003607 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557598003608 dimer interface [polypeptide binding]; other site 557598003609 putative CheW interface [polypeptide binding]; other site 557598003610 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 557598003611 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 557598003612 FeS/SAM binding site; other site 557598003613 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 557598003614 inner membrane protein; Provisional; Region: PRK10995 557598003615 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Add; COG1816 557598003616 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 557598003617 active site 557598003618 purine riboside binding site [chemical binding]; other site 557598003619 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 557598003620 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 557598003621 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 557598003622 protein binding site [polypeptide binding]; other site 557598003623 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 557598003624 protein binding site [polypeptide binding]; other site 557598003625 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 557598003626 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 557598003627 minor groove reading motif; other site 557598003628 helix-hairpin-helix signature motif; other site 557598003629 substrate binding pocket [chemical binding]; other site 557598003630 active site 557598003631 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; pfam10576 557598003632 electron transport complex RsxE subunit; Provisional; Region: PRK12405 557598003633 FMN-binding domain; Region: FMN_bind; cl01081 557598003634 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; cl00779 557598003635 electron transport complex, RnfABCDGE type, C subunit; Region: rnfC; TIGR01945 557598003636 SLBB domain; Region: SLBB; pfam10531 557598003637 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 557598003638 electron transport complex protein RnfB; Provisional; Region: PRK05113 557598003639 Putative Fe-S cluster; Region: FeS; pfam04060 557598003640 4Fe-4S binding domain; Region: Fer4; pfam00037 557598003641 electron transport complex protein RsxA; Provisional; Region: PRK05151 557598003642 acetyl-CoA synthetase; Provisional; Region: PRK00174 557598003643 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 557598003644 active site 557598003645 CoA binding site [chemical binding]; other site 557598003646 acyl-activating enzyme (AAE) consensus motif; other site 557598003647 AMP binding site [chemical binding]; other site 557598003648 acetate binding site [chemical binding]; other site 557598003649 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 557598003650 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u4; cd11480 557598003651 Na binding site [ion binding]; other site 557598003652 Protein of unknown function, DUF485; Region: DUF485; pfam04341 557598003653 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557598003654 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 557598003655 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 557598003656 dimerization interface [polypeptide binding]; other site 557598003657 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 557598003658 putative active site [active] 557598003659 putative metal binding site [ion binding]; other site 557598003660 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 557598003661 substrate binding site [chemical binding]; other site 557598003662 peptidyl-prolyl cis-trans isomerase A (rotamase A); Provisional; Region: PRK10903 557598003663 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 557598003664 substrate binding site [chemical binding]; other site 557598003665 Protein of unknown function, DUF486; Region: DUF486; cl01236 557598003666 AsmA family; Region: AsmA; pfam05170 557598003667 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cl14632 557598003668 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 557598003669 competence protein ComEA helix-hairpin-helix repeat region; Region: TIGR00426 557598003670 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl14786 557598003671 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 557598003672 Nitrogen regulatory protein P-II; Region: P-II; smart00938 557598003673 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 557598003674 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 557598003675 dimerization interface [polypeptide binding]; other site 557598003676 ATP binding site [chemical binding]; other site 557598003677 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 557598003678 dimerization interface [polypeptide binding]; other site 557598003679 ATP binding site [chemical binding]; other site 557598003680 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 557598003681 putative active site [active] 557598003682 catalytic triad [active] 557598003683 Domain of unknown function (DUF1857); Region: DUF1857; pfam08982 557598003684 hydrophobic ligand binding site; other site 557598003685 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 557598003686 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 557598003687 heme binding site [chemical binding]; other site 557598003688 ferroxidase pore; other site 557598003689 ferroxidase diiron center [ion binding]; other site 557598003690 Bacterioferritin-associated ferredoxin [Inorganic ion transport and metabolism]; Region: Bfd; COG2906 557598003691 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]; Region: COG1875 557598003692 PIN domain of bacterial Smg6-like homologs with PhoH-like ATPase domains; Region: PIN_PhoHL-ATPase; cd09883 557598003693 putative active site [active] 557598003694 PhoH-like protein; Region: PhoH; pfam02562 557598003695 3-isopropylmalate dehydrogenase; Provisional; Region: PRK00772 557598003696 tartrate dehydrogenase; Region: TTC; TIGR02089 557598003697 aspartate-semialdehyde dehydrogenase; Reviewed; Region: PRK06598 557598003698 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 557598003699 aspartate-semialdehyde dehydrogenase; Reviewed; Region: PRK05671 557598003700 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 557598003701 FimV C-terminal domain; Region: FimV_Cterm; TIGR03504 557598003702 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 557598003703 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 557598003704 dimerization interface 3.5A [polypeptide binding]; other site 557598003705 active site 557598003706 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 557598003707 active site 557598003708 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 557598003709 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 557598003710 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557598003711 catalytic residue [active] 557598003712 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 557598003713 substrate binding site [chemical binding]; other site 557598003714 active site 557598003715 catalytic residues [active] 557598003716 heterodimer interface [polypeptide binding]; other site 557598003717 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 557598003718 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 557598003719 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 557598003720 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_C39_likeD; cd02421 557598003721 type I secretion system ATPase, LssB family; Region: type_I_sec_LssB; TIGR03375 557598003722 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 557598003723 ATP-binding cassette domain of bacteriocin exporters, subfamily C; Region: ABCC_bacteriocin_exporters; cd03245 557598003724 Walker A/P-loop; other site 557598003725 ATP binding site [chemical binding]; other site 557598003726 Q-loop/lid; other site 557598003727 ABC transporter signature motif; other site 557598003728 Walker B; other site 557598003729 D-loop; other site 557598003730 H-loop/switch region; other site 557598003731 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 557598003732 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 557598003733 HlyD family secretion protein; Region: HlyD_3; pfam13437 557598003734 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 557598003735 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 557598003736 DNA binding residues [nucleotide binding] 557598003737 dimerization interface [polypeptide binding]; other site 557598003738 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 557598003739 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u4; cd11480 557598003740 Na binding site [ion binding]; other site 557598003741 Protein of unknown function, DUF485; Region: DUF485; pfam04341 557598003742 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 557598003743 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 557598003744 dimer interface [polypeptide binding]; other site 557598003745 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557598003746 catalytic residue [active] 557598003747 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 557598003748 Clade 3 of the heme-binding enzyme catalase; Region: catalase_clade_3; cd08156 557598003749 tetramer interface [polypeptide binding]; other site 557598003750 heme binding pocket [chemical binding]; other site 557598003751 NADPH binding site [chemical binding]; other site 557598003752 Predicted phosphohydrolase (DHH superfamily) [General function prediction only]; Region: COG2404 557598003753 putative ABC transporter ATP-binding protein; Provisional; Region: PRK10636 557598003754 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 557598003755 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 557598003756 Walker A/P-loop; other site 557598003757 ATP binding site [chemical binding]; other site 557598003758 Q-loop/lid; other site 557598003759 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 557598003760 ABC transporter signature motif; other site 557598003761 Walker B; other site 557598003762 D-loop; other site 557598003763 ABC transporter; Region: ABC_tran_2; pfam12848 557598003764 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 557598003765 NAD synthetase; Provisional; Region: PRK13981 557598003766 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 557598003767 multimer interface [polypeptide binding]; other site 557598003768 active site 557598003769 catalytic triad [active] 557598003770 protein interface 1 [polypeptide binding]; other site 557598003771 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 557598003772 homodimer interface [polypeptide binding]; other site 557598003773 NAD binding pocket [chemical binding]; other site 557598003774 ATP binding pocket [chemical binding]; other site 557598003775 Mg binding site [ion binding]; other site 557598003776 active-site loop [active] 557598003777 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 557598003778 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 557598003779 Periplasmic protein involved in polysaccharide export, contains SLBB domain of b-grasp fold [Cell wall/membrane/envelope biogenesis]; Region: Wza; COG1596 557598003780 Polysaccharide biosynthesis/export protein; Region: Poly_export; pfam02563 557598003781 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 557598003782 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 557598003783 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 557598003784 catalytic site [active] 557598003785 Serine carboxypeptidase; Region: Peptidase_S10; cl08270 557598003786 Bacteriophage abortive infection AbiH; Region: AbiH; pfam14253 557598003787 P22_AR N-terminal domain; Region: P22_AR_N; pfam10547 557598003788 Integrase core domain; Region: rve_3; pfam13683 557598003789 Transposase; Region: HTH_Tnp_1; pfam01527 557598003790 Phage tail sheath protein FI [General function prediction only]; Region: COG3497 557598003791 YcaO domain protein; Region: TIGR03549 557598003792 OsmC-like protein; Region: OsmC; pfam02566 557598003793 YcaO-like family; Region: YcaO; pfam02624 557598003794 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 557598003795 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 557598003796 putative membrane fusion protein; Region: TIGR02828 557598003797 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 557598003798 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 557598003799 multidrug efflux system subunit MdtC; Provisional; Region: PRK10614 557598003800 Protein export membrane protein; Region: SecD_SecF; cl14618 557598003801 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 557598003802 Protein of unknown function (DUF2029); Region: DUF2029; pfam09594 557598003803 uncharacterized YdjC-like family proteins from bacteria; Region: YdjC_like_3; cd10807 557598003804 putative active site [active] 557598003805 YdjC motif; other site 557598003806 Mg binding site [ion binding]; other site 557598003807 putative homodimer interface [polypeptide binding]; other site 557598003808 potential protein location (hypothetical protein) that overlaps protein (cellobiose phosphorylase) 557598003809 GtrA-like protein; Region: GtrA; pfam04138 557598003810 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 557598003811 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 557598003812 Ligand binding site; other site 557598003813 Putative Catalytic site; other site 557598003814 DXD motif; other site 557598003815 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 557598003816 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl17364 557598003817 magnesium-transporting ATPase MgtA; Provisional; Region: PRK10517 557598003818 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; pfam00690 557598003819 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 557598003820 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 557598003821 Soluble P-type ATPase [General function prediction only]; Region: COG4087 557598003822 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 557598003823 catalase/hydroperoxidase HPI(I); Provisional; Region: PRK15061 557598003824 N-terminal catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_1; cd00649 557598003825 dimer interface [polypeptide binding]; other site 557598003826 active site 557598003827 heme binding site [chemical binding]; other site 557598003828 C-terminal non-catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_2; cd08200 557598003829 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; pfam09346 557598003830 Protein of unknown function (DUF1116); Region: DUF1116; pfam06545 557598003831 membrane protein FdrA; Validated; Region: PRK06091 557598003832 CoA binding domain; Region: CoA_binding; pfam02629 557598003833 CoA-ligase; Region: Ligase_CoA; pfam00549 557598003834 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 557598003835 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 557598003836 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 557598003837 putative DNA-binding transcriptional regulator; Provisional; Region: PRK11074 557598003838 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 557598003839 dimerization interface [polypeptide binding]; other site 557598003840 Isochorismatase family; Region: Isochorismatase; pfam00857 557598003841 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 557598003842 catalytic triad [active] 557598003843 conserved cis-peptide bond; other site 557598003844 Protein of unknown function (DUF2877); Region: DUF2877; pfam11392 557598003845 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 557598003846 BAAT / Acyl-CoA thioester hydrolase C terminal; Region: BAAT_C; pfam08840 557598003847 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 557598003848 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557598003849 NAD(P) binding site [chemical binding]; other site 557598003850 active site 557598003851 Uncharacterized protein conserved in bacteria (DUF2256); Region: DUF2256; pfam10013 557598003852 SnoaL-like domain; Region: SnoaL_2; pfam12680 557598003853 short chain dehydrogenase; Provisional; Region: PRK08251 557598003854 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557598003855 NAD(P) binding site [chemical binding]; other site 557598003856 active site 557598003857 Protein of unknown function (DUF3833); Region: DUF3833; pfam12915 557598003858 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 557598003859 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 557598003860 S-adenosylmethionine binding site [chemical binding]; other site 557598003861 Protein of unknown function (DUF1365); Region: DUF1365; pfam07103 557598003862 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 557598003863 Flavin containing amine oxidoreductase; Region: Amino_oxidase; pfam01593 557598003864 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 557598003865 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 557598003866 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 557598003867 Ricin-type beta-trefoil lectin domain; Region: Ricin_B_lectin; pfam00652 557598003868 Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly specific...; Region: RICIN; cd00161 557598003869 putative sugar binding sites [chemical binding]; other site 557598003870 Q-X-W motif; other site 557598003871 Winged helix DNA-binding domain; Region: HTH_27; pfam13463 557598003872 Predicted membrane protein [Function unknown]; Region: COG1289 557598003873 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 557598003874 Glucosamine-6-phosphate isomerases/6-phosphogluconolactonase; Region: Glucosamine_iso; pfam01182 557598003875 active site 557598003876 aspartate aminotransferase; Provisional; Region: PRK05764 557598003877 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 557598003878 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557598003879 homodimer interface [polypeptide binding]; other site 557598003880 catalytic residue [active] 557598003881 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 557598003882 Cytochrome C' Region: Cytochrom_C_2; pfam01322 557598003883 Predicted membrane protein [Function unknown]; Region: COG3671 557598003884 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cl17326 557598003885 metal binding site 2 [ion binding]; metal-binding site 557598003886 putative DNA binding helix; other site 557598003887 metal binding site 1 [ion binding]; metal-binding site 557598003888 dimer interface [polypeptide binding]; other site 557598003889 structural Zn2+ binding site [ion binding]; other site 557598003890 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 557598003891 CobW/HypB/UreG, nucleotide-binding domain; Region: cobW; pfam02492 557598003892 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; smart00833 557598003893 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 557598003894 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 557598003895 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 557598003896 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 557598003897 ABC-ATPase subunit interface; other site 557598003898 dimer interface [polypeptide binding]; other site 557598003899 putative PBP binding regions; other site 557598003900 Metal binding protein PsaA. These proteins have been shown to function as initial receptors in ABC transport of Mn2+ and as surface adhesins in some eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins that...; Region: PsaA; cd01137 557598003901 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 557598003902 metal binding site [ion binding]; metal-binding site 557598003903 Predicted permeases [General function prediction only]; Region: RarD; COG2962 557598003904 EamA-like transporter family; Region: EamA; pfam00892 557598003905 Lecithin retinol acyltransferase; Region: LRAT; pfam04970 557598003906 Lecithin retinol acyltransferase; Region: LRAT; pfam04970 557598003907 lysophospholipase L2; Provisional; Region: PRK10749 557598003908 YqaJ-like viral recombinase domain; Region: YqaJ; pfam09588 557598003909 Protein of unknown function (DUF3768); Region: DUF3768; pfam12599 557598003910 Domain of unknown function (DUF932); Region: DUF932; cl12129 557598003911 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 557598003912 active site 557598003913 phosphorylation site [posttranslational modification] 557598003914 intermolecular recognition site; other site 557598003915 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; cd00588 557598003916 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 557598003917 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 557598003918 active site 557598003919 phosphorylation site [posttranslational modification] 557598003920 intermolecular recognition site; other site 557598003921 dimerization interface [polypeptide binding]; other site 557598003922 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 557598003923 Tar ligand binding domain homologue; Region: TarH; pfam02203 557598003924 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557598003925 dimer interface [polypeptide binding]; other site 557598003926 putative CheW interface [polypeptide binding]; other site 557598003927 Transposase DDE domain; Region: DDE_Tnp_1_5; pfam13737 557598003928 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 557598003929 C4-dicarboxylate transporters of the Tellurite-resistance/Dicarboxylate Transporter (TDT) family; Region: TDT_C4-dicarb_trans; cd09325 557598003930 Tellurite resistance protein and related permeases [Inorganic ion transport and metabolism]; Region: TehA; COG1275 557598003931 gating phenylalanine in ion channel; other site 557598003932 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 557598003933 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 557598003934 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 557598003935 putative dimerization interface [polypeptide binding]; other site 557598003936 methionine sulfoxide reductase B; Provisional; Region: PRK00222 557598003937 SelR domain; Region: SelR; pfam01641 557598003938 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 557598003939 diiron binding motif [ion binding]; other site 557598003940 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 557598003941 dimer interface [polypeptide binding]; other site 557598003942 substrate binding site [chemical binding]; other site 557598003943 metal binding sites [ion binding]; metal-binding site 557598003944 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 557598003945 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557598003946 dimer interface [polypeptide binding]; other site 557598003947 putative CheW interface [polypeptide binding]; other site 557598003948 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 557598003949 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 557598003950 putative substrate translocation pore; other site 557598003951 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 557598003952 efflux pump membrane protein (multidrug resistance protein A); Region: 8a0101; TIGR00998 557598003953 HlyD family secretion protein; Region: HlyD_3; pfam13437 557598003954 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 557598003955 MarR family; Region: MarR_2; cl17246 557598003956 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 557598003957 Putative metal-binding domain of cation transport ATPase; Region: ATPase-cat_bd; pfam12156 557598003958 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 557598003959 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 557598003960 metal-binding site [ion binding] 557598003961 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 557598003962 haloacid dehalogenase-like hydrolase; Region: HAD; pfam12710 557598003963 Soluble P-type ATPase [General function prediction only]; Region: COG4087 557598003964 GTPase RsgA; Reviewed; Region: PRK00098 557598003965 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 557598003966 RNA binding site [nucleotide binding]; other site 557598003967 homodimer interface [polypeptide binding]; other site 557598003968 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 557598003969 GTPase/Zn-binding domain interface [polypeptide binding]; other site 557598003970 GTP/Mg2+ binding site [chemical binding]; other site 557598003971 G4 box; other site 557598003972 G5 box; other site 557598003973 G1 box; other site 557598003974 Switch I region; other site 557598003975 G2 box; other site 557598003976 G3 box; other site 557598003977 Switch II region; other site 557598003978 Pterin 4 alpha carbinolamine dehydratase; Region: Pterin_4a; pfam01329 557598003979 aromatic arch; other site 557598003980 DCoH dimer interaction site [polypeptide binding]; other site 557598003981 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 557598003982 DCoH tetramer interaction site [polypeptide binding]; other site 557598003983 substrate binding site [chemical binding]; other site 557598003984 Peptidase family M48; Region: Peptidase_M48; pfam01435 557598003985 Multiple antibiotic transporter [Intracellular trafficking and secretion]; Region: MarC; COG2095 557598003986 multidrug efflux system protein MdtI; Provisional; Region: PRK10650 557598003987 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 557598003988 Protein of unknown function (DUF1289); Region: DUF1289; pfam06945 557598003989 Cysteine-rich CWC; Region: Cys_rich_CWC; pfam14375 557598003990 Predicted permeases [General function prediction only]; Region: COG0679 557598003991 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 557598003992 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 557598003993 putative active site [active] 557598003994 putative PHP Thumb interface [polypeptide binding]; other site 557598003995 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 557598003996 generic binding surface I; other site 557598003997 generic binding surface II; other site 557598003998 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 557598003999 Malic enzyme, N-terminal domain; Region: malic; pfam00390 557598004000 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 557598004001 putative NAD(P) binding site [chemical binding]; other site 557598004002 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 557598004003 TRAP transporter, DctM subunit; Region: dctM; TIGR00786 557598004004 DctM-like transporters; Region: DctM; pfam06808 557598004005 TRAP-type C4-dicarboxylate transport system, small permease component [Carbohydrate transport and metabolism]; Region: DctM; COG3090 557598004006 TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: DctP; COG1638 557598004007 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 557598004008 PAS domain S-box; Region: sensory_box; TIGR00229 557598004009 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 557598004010 putative active site [active] 557598004011 heme pocket [chemical binding]; other site 557598004012 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 557598004013 dimer interface [polypeptide binding]; other site 557598004014 phosphorylation site [posttranslational modification] 557598004015 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 557598004016 ATP binding site [chemical binding]; other site 557598004017 Mg2+ binding site [ion binding]; other site 557598004018 G-X-G motif; other site 557598004019 poly(A) polymerase; Region: pcnB; TIGR01942 557598004020 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 557598004021 active site 557598004022 NTP binding site [chemical binding]; other site 557598004023 metal binding triad [ion binding]; metal-binding site 557598004024 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 557598004025 Polymerase A arginine-rich C-terminus; Region: PolyA_pol_arg_C; pfam12626 557598004026 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 557598004027 catalytic center binding site [active] 557598004028 ATP binding site [chemical binding]; other site 557598004029 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 557598004030 oligomerization interface [polypeptide binding]; other site 557598004031 active site 557598004032 metal binding site [ion binding]; metal-binding site 557598004033 pantoate--beta-alanine ligase; Region: panC; TIGR00018 557598004034 Pantoate-beta-alanine ligase; Region: PanC; cd00560 557598004035 active site 557598004036 ATP-binding site [chemical binding]; other site 557598004037 pantoate-binding site; other site 557598004038 HXXH motif; other site 557598004039 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 557598004040 tetramerization interface [polypeptide binding]; other site 557598004041 active site 557598004042 FinO bacterial conjugation repressor domain; the basic protein FinO is part of the the two component FinOP system which is responsible for repressing bacterial conjugation; the FinOP system represses the transfer (tra) operon of the F-plasmid which...; Region: FinO_conjug_rep; cl15270 557598004043 putative transporter; Provisional; Region: PRK11660 557598004044 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 557598004045 Sulfate transporter family; Region: Sulfate_transp; pfam00916 557598004046 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 557598004047 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 557598004048 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 557598004049 active site 557598004050 HIGH motif; other site 557598004051 nucleotide binding site [chemical binding]; other site 557598004052 catalytic core domain of glutaminyl-tRNA synthetase; Region: GlnRS_core; cd00807 557598004053 KMSKS motif; other site 557598004054 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 557598004055 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 557598004056 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 557598004057 active site 557598004058 HIGH motif; other site 557598004059 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 557598004060 KMSKS motif; other site 557598004061 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 557598004062 tRNA binding surface [nucleotide binding]; other site 557598004063 anticodon binding site; other site 557598004064 50S ribosomal protein L31; Reviewed; Region: rpmE; PRK00019 557598004065 Cytochrome C' Region: Cytochrom_C_2; pfam01322 557598004066 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 557598004067 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 557598004068 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 557598004069 Walker A/P-loop; other site 557598004070 ATP binding site [chemical binding]; other site 557598004071 Q-loop/lid; other site 557598004072 ABC transporter signature motif; other site 557598004073 Walker B; other site 557598004074 D-loop; other site 557598004075 H-loop/switch region; other site 557598004076 PII uridylyl-transferase; Provisional; Region: PRK03059 557598004077 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 557598004078 metal binding triad; other site 557598004079 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 557598004080 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 557598004081 Zn2+ binding site [ion binding]; other site 557598004082 Mg2+ binding site [ion binding]; other site 557598004083 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 557598004084 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 557598004085 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 557598004086 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 557598004087 Predicted permeases [General function prediction only]; Region: COG0795 557598004088 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 557598004089 multifunctional aminopeptidase A; Provisional; Region: PRK00913 557598004090 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 557598004091 interface (dimer of trimers) [polypeptide binding]; other site 557598004092 Substrate-binding/catalytic site; other site 557598004093 Zn-binding sites [ion binding]; other site 557598004094 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; pfam04364 557598004095 Cobalamin adenosyltransferase; Region: Cob_adeno_trans; pfam01923 557598004096 Staphylococcal nuclease homologues; Region: SNc; smart00318 557598004097 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cl00140 557598004098 Catalytic site; other site 557598004099 hypothetical protein; Provisional; Region: PRK09936 557598004100 bacteriophage N4 receptor, outer membrane subunit; Provisional; Region: PRK09782 557598004101 Bacteriophage N adsorption protein A C-term; Region: NfrA_C; pfam13283 557598004102 UDP-N-acetylglucosamine 2-epimerase; Region: wecB; TIGR00236 557598004103 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 557598004104 active site 557598004105 homodimer interface [polypeptide binding]; other site 557598004106 bacteriophage N4 adsorption protein B; Provisional; Region: nfrB; PRK11234 557598004107 active site 557598004108 Glycosyl transferase family group 2; Region: Glyco_trans_2_3; pfam13632 557598004109 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 557598004110 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1666 557598004111 Proteins similar to Escherichia coli YajQ; Region: YajQ_like; cd11740 557598004112 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 557598004113 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 557598004114 Protein export membrane protein; Region: SecD_SecF; cl14618 557598004115 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 557598004116 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 557598004117 HlyD family secretion protein; Region: HlyD_3; pfam13437 557598004118 hemin importer ATP-binding subunit; Provisional; Region: hmuV; PRK13548 557598004119 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 557598004120 Walker A/P-loop; other site 557598004121 ATP binding site [chemical binding]; other site 557598004122 Q-loop/lid; other site 557598004123 ABC transporter signature motif; other site 557598004124 Walker B; other site 557598004125 D-loop; other site 557598004126 H-loop/switch region; other site 557598004127 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 557598004128 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 557598004129 ABC-ATPase subunit interface; other site 557598004130 dimer interface [polypeptide binding]; other site 557598004131 putative PBP binding regions; other site 557598004132 dihydrodipicolinate reductase; Provisional; Region: PRK00048 557598004133 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 557598004134 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 557598004135 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 557598004136 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 557598004137 ferric uptake regulator; Provisional; Region: fur; PRK09462 557598004138 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 557598004139 metal binding site 2 [ion binding]; metal-binding site 557598004140 putative DNA binding helix; other site 557598004141 metal binding site 1 [ion binding]; metal-binding site 557598004142 dimer interface [polypeptide binding]; other site 557598004143 structural Zn2+ binding site [ion binding]; other site 557598004144 leucyl/phenylalanyl-tRNA--protein transferase; Reviewed; Region: aat; PRK00301 557598004145 arginyl-tRNA-protein transferase; Provisional; Region: PRK01305 557598004146 Arginine-tRNA-protein transferase, N terminus; Region: ATE_N; pfam04376 557598004147 Arginine-tRNA-protein transferase, C terminus; Region: ATE_C; pfam04377 557598004148 Protein of unknown function (DUF2628); Region: DUF2628; pfam10947 557598004149 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 557598004150 S-adenosylmethionine binding site [chemical binding]; other site 557598004151 This CD includes bacterial (Agrobacterium tumefaciens and Caulobacter crescentus ProX, and Clostridium sticklandii PrdX) and eukaryotic (Plasmodium falciparum N-terminal ProRS editing domain) sequences. The C. sticklandii PrdX protein, a homolog of the...; Region: PrdX_deacylase; cd04335 557598004152 putative deacylase active site [active] 557598004153 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 557598004154 electron transport complex RsxE subunit; Provisional; Region: PRK12405 557598004155 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; pfam03116 557598004156 electron transport complex, RnfABCDGE type, C subunit; Region: rnfC; TIGR01945 557598004157 SLBB domain; Region: SLBB; pfam10531 557598004158 4Fe-4S binding domain; Region: Fer4_6; pfam12837 557598004159 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 557598004160 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit [Energy production and conversion]; Region: PorG; COG1014 557598004161 4Fe-4S binding domain; Region: Fer4_6; pfam12837 557598004162 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, beta subunit [Energy production and conversion]; Region: PorB; COG1013 557598004163 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 557598004164 TPP-binding site [chemical binding]; other site 557598004165 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, alpha subunit [Energy production and conversion]; Region: PorA; COG0674 557598004166 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 557598004167 dimer interface [polypeptide binding]; other site 557598004168 PYR/PP interface [polypeptide binding]; other site 557598004169 TPP binding site [chemical binding]; other site 557598004170 substrate binding site [chemical binding]; other site 557598004171 electron transport complex, RnfABCDGE type, B subunit; Region: rnfB; TIGR01944 557598004172 Putative Fe-S cluster; Region: FeS; cl17515 557598004173 4Fe-4S binding domain; Region: Fer4; pfam00037 557598004174 arginine decarboxylase; Provisional; Region: PRK05354 557598004175 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase; Region: PLPDE_III_ADC; cd06830 557598004176 dimer interface [polypeptide binding]; other site 557598004177 active site 557598004178 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 557598004179 catalytic residues [active] 557598004180 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 557598004181 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 557598004182 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 557598004183 ligand binding site [chemical binding]; other site 557598004184 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 557598004185 active site 557598004186 ribulose/triose binding site [chemical binding]; other site 557598004187 phosphate binding site [ion binding]; other site 557598004188 substrate (anthranilate) binding pocket [chemical binding]; other site 557598004189 product (indole) binding pocket [chemical binding]; other site 557598004190 Predicted hydrolase of the alpha/beta-hydrolase fold [General function prediction only]; Region: COG0429 557598004191 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 557598004192 MPT binding site; other site 557598004193 trimer interface [polypeptide binding]; other site 557598004194 hypothetical protein; Provisional; Region: PRK05255 557598004195 Fe-S oxidoreductases [Energy production and conversion]; Region: COG0731 557598004196 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 557598004197 FeS/SAM binding site; other site 557598004198 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 557598004199 Ligand Binding Site [chemical binding]; other site 557598004200 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 557598004201 active site 557598004202 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 557598004203 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 557598004204 Walker A motif; other site 557598004205 ATP binding site [chemical binding]; other site 557598004206 Walker B motif; other site 557598004207 arginine finger; other site 557598004208 RNA polymerase sigma factor RpoE; Region: RpoE_Sigma70; TIGR02939 557598004209 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 557598004210 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 557598004211 DNA binding residues [nucleotide binding] 557598004212 Anti sigma-E protein RseA, N-terminal domain; Region: RseA_N; pfam03872 557598004213 Positive regulator of sigma(E), RseC/MucC; Region: RseC_MucC; pfam04246 557598004214 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 557598004215 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 557598004216 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 557598004217 protein binding site [polypeptide binding]; other site 557598004218 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 557598004219 protein binding site [polypeptide binding]; other site 557598004220 Glutaredoxin-like domain (DUF836); Region: DUF836; pfam05768 557598004221 GTP-binding protein LepA; Provisional; Region: PRK05433 557598004222 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 557598004223 G1 box; other site 557598004224 putative GEF interaction site [polypeptide binding]; other site 557598004225 GTP/Mg2+ binding site [chemical binding]; other site 557598004226 Switch I region; other site 557598004227 G2 box; other site 557598004228 G3 box; other site 557598004229 Switch II region; other site 557598004230 G4 box; other site 557598004231 G5 box; other site 557598004232 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 557598004233 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 557598004234 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 557598004235 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 557598004236 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 557598004237 Catalytic site [active] 557598004238 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 557598004239 ribonuclease III; Reviewed; Region: rnc; PRK00102 557598004240 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 557598004241 dimerization interface [polypeptide binding]; other site 557598004242 active site 557598004243 metal binding site [ion binding]; metal-binding site 557598004244 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 557598004245 dsRNA binding site [nucleotide binding]; other site 557598004246 GTPase Era; Reviewed; Region: era; PRK00089 557598004247 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 557598004248 G1 box; other site 557598004249 GTP/Mg2+ binding site [chemical binding]; other site 557598004250 Switch I region; other site 557598004251 G2 box; other site 557598004252 Switch II region; other site 557598004253 G3 box; other site 557598004254 G4 box; other site 557598004255 G5 box; other site 557598004256 KH domain; Region: KH_2; pfam07650 557598004257 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 557598004258 Recombination protein O N terminal; Region: RecO_N; pfam11967 557598004259 Recombination protein O C terminal; Region: RecO_C; pfam02565 557598004260 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 557598004261 active site 557598004262 hydrophilic channel; other site 557598004263 dimerization interface [polypeptide binding]; other site 557598004264 catalytic residues [active] 557598004265 active site lid [active] 557598004266 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 557598004267 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 557598004268 ligand binding domain of Tar- and Tsr-related chemoreceptors; Region: Tar_Tsr_LBD; cl00144 557598004269 HAMP domain; Region: HAMP; pfam00672 557598004270 dimerization interface [polypeptide binding]; other site 557598004271 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557598004272 dimer interface [polypeptide binding]; other site 557598004273 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 557598004274 putative CheW interface [polypeptide binding]; other site 557598004275 putative DNA-binding transcriptional regulator; Provisional; Region: PRK10837 557598004276 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 557598004277 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 557598004278 putative dimerization interface [polypeptide binding]; other site 557598004279 ribonuclease activity regulator protein RraA; Provisional; Region: PRK09372 557598004280 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 557598004281 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 557598004282 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 557598004283 Domain of Unknown Function (DUF748); Region: DUF748; pfam05359 557598004284 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 557598004285 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 557598004286 active site 557598004287 dimerization interface [polypeptide binding]; other site 557598004288 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 557598004289 DNA binding residues [nucleotide binding] 557598004290 dimerization interface [polypeptide binding]; other site 557598004291 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 557598004292 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 557598004293 dimer interface [polypeptide binding]; other site 557598004294 phosphorylation site [posttranslational modification] 557598004295 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 557598004296 ATP binding site [chemical binding]; other site 557598004297 Mg2+ binding site [ion binding]; other site 557598004298 G-X-G motif; other site 557598004299 tetrathionate reductase subunit A; Provisional; Region: PRK14991 557598004300 The MopB_Tetrathionate-Ra CD contains tetrathionate reductase, subunit A, (TtrA) and other related proteins. The Salmonella enterica tetrathionate reductase catalyses the reduction of trithionate but not sulfur or thiosulfate. Members of this CD belong...; Region: MopB_Tetrathionate-Ra; cd02758 557598004301 putative [Fe4-S4] binding site [ion binding]; other site 557598004302 putative molybdopterin cofactor binding site [chemical binding]; other site 557598004303 This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of tetrathionate reductase, subunit A, (TtrA); respiratory arsenate As(V) reductase, catalytic subunit (ArrA); and other related proteins; Region: MopB_CT_Tetrathionate_Arsenate-R; cd02780 557598004304 putative molybdopterin cofactor binding site; other site 557598004305 tetrathionate reductase subunit C; Provisional; Region: PRK14992 557598004306 tetrathionate reductase subunit C; Provisional; Region: PRK14992 557598004307 tetrathionate reductase subunit B; Provisional; Region: PRK14993 557598004308 4Fe-4S binding domain; Region: Fer4; pfam00037 557598004309 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 557598004310 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 557598004311 dimer interface [polypeptide binding]; other site 557598004312 ssDNA binding site [nucleotide binding]; other site 557598004313 tetramer (dimer of dimers) interface [polypeptide binding]; other site 557598004314 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 557598004315 Smr domain; Region: Smr; pfam01713 557598004316 thioredoxin reductase; Provisional; Region: PRK10262 557598004317 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 557598004318 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 557598004319 acylglycerophosphoethanolamine acyltransferase; Provisional; Region: PRK06814 557598004320 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 557598004321 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 557598004322 motif 1; other site 557598004323 active site 557598004324 motif 2; other site 557598004325 motif 3; other site 557598004326 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 557598004327 DHHA1 domain; Region: DHHA1; pfam02272 557598004328 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs; Region: NDUFA9_like_SDR_a; cd05271 557598004329 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 557598004330 putative NAD(P) binding site [chemical binding]; other site 557598004331 active site 557598004332 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 557598004333 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 557598004334 N-acetyl-D-glucosamine binding site [chemical binding]; other site 557598004335 catalytic residue [active] 557598004336 Cation transport protein; Region: TrkH; cl17365 557598004337 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 557598004338 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 557598004339 TrkA-N domain; Region: TrkA_N; pfam02254 557598004340 TrkA-C domain; Region: TrkA_C; pfam02080 557598004341 TrkA-N domain; Region: TrkA_N; pfam02254 557598004342 TrkA-C domain; Region: TrkA_C; pfam02080 557598004343 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 557598004344 catalytic triad [active] 557598004345 dimer interface [polypeptide binding]; other site 557598004346 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 557598004347 dihydrolipoamide dehydrogenase; Validated; Region: PRK06292 557598004348 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 557598004349 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 557598004350 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 557598004351 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 557598004352 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 557598004353 active site 557598004354 metal binding site [ion binding]; metal-binding site 557598004355 substrate binding site [chemical binding]; other site 557598004356 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 557598004357 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 557598004358 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 557598004359 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 557598004360 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 557598004361 glutamine binding [chemical binding]; other site 557598004362 catalytic triad [active] 557598004363 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 557598004364 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 557598004365 dimer interface [polypeptide binding]; other site 557598004366 ssDNA binding site [nucleotide binding]; other site 557598004367 tetramer (dimer of dimers) interface [polypeptide binding]; other site 557598004368 YqaJ-like viral recombinase domain; Region: YqaJ; pfam09588 557598004369 RecT family; Region: RecT; cl04285 557598004370 aminotransferase; Validated; Region: PRK07777 557598004371 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 557598004372 non-specific DNA binding site [nucleotide binding]; other site 557598004373 salt bridge; other site 557598004374 sequence-specific DNA binding site [nucleotide binding]; other site 557598004375 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 557598004376 Catalytic site [active] 557598004377 replicative DNA helicase; Region: DnaB; TIGR00665 557598004378 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 557598004379 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 557598004380 Walker A motif; other site 557598004381 ATP binding site [chemical binding]; other site 557598004382 Walker B motif; other site 557598004383 NinB protein; Region: NinB; pfam05772 557598004384 Protein of unknown function (DUF968); Region: DUF968; pfam06147 557598004385 Protein of unknown function (DUF1364); Region: DUF1364; pfam07102 557598004386 hypothetical protein; Region: PHA00675 557598004387 Terminase small subunit; Region: Terminase_2; pfam03592 557598004388 potential frameshift: common BLAST hit: gi|215487825|ref|YP_002330256.1| terminase, large subunit 557598004389 hypothetical protein; Region: PHA00675 557598004390 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 557598004391 HsdM N-terminal domain; Region: HsdM_N; pfam12161 557598004392 Methyltransferase domain; Region: Methyltransf_26; pfam13659 557598004393 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 557598004394 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 557598004395 Protein of unknown function DUF91; Region: DUF91; cl00709 557598004396 Uncharacterized conserved protein [Function unknown]; Region: COG3586 557598004397 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 557598004398 active site 557598004399 NTP binding site [chemical binding]; other site 557598004400 metal binding triad [ion binding]; metal-binding site 557598004401 antibiotic binding site [chemical binding]; other site 557598004402 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 557598004403 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 557598004404 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 557598004405 ATP binding site [chemical binding]; other site 557598004406 putative Mg++ binding site [ion binding]; other site 557598004407 Superfamily II helicase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG5519 557598004408 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4643 557598004409 Toprim domain; Region: Toprim_3; pfam13362 557598004410 P22_AR N-terminal domain; Region: P22_AR_N; pfam10547 557598004411 Phage regulatory protein Rha (Phage_pRha); Region: Phage_pRha; pfam09669 557598004412 Helix-turn-helix domain; Region: HTH_39; pfam14090 557598004413 Prophage CP4-57 regulatory protein (AlpA); Region: Phage_AlpA; cl17523 557598004414 integrase; Provisional; Region: PRK09692 557598004415 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 557598004416 active site 557598004417 Int/Topo IB signature motif; other site 557598004418 acyl-CoA synthetase; Validated; Region: PRK08316 557598004419 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 557598004420 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 557598004421 Coenzyme A binding pocket [chemical binding]; other site 557598004422 hypothetical protein; Region: PHA00671 557598004423 hypothetical protein; Region: PHA00670 557598004424 Bacteriophage head to tail connecting protein; Region: Head-tail_con; pfam12236 557598004425 Uncharacterized protein conserved in bacteria, putative virulence factor [Function unknown]; Region: SrfC; COG4458 557598004426 putative protease; Region: PHA00666 557598004427 major capsid protein; Region: PHA00665 557598004428 hypothetical protein; Region: PHA00664 557598004429 hypothetical protein; Region: PHA00662 557598004430 hypothetical protein; Region: PHA00661 557598004431 Predicted transcriptional regulator [Transcription]; Region: COG2944 557598004432 Plasmid maintenance system antidote protein [General function prediction only]; Region: VapI; COG3093 557598004433 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 557598004434 sequence-specific DNA binding site [nucleotide binding]; other site 557598004435 salt bridge; other site 557598004436 Plasmid maintenance system killer protein; Region: Plasmid_killer; pfam05015 557598004437 hypothetical protein; Region: PHA00660 557598004438 Glycosyl hydrolase 108; Region: Glyco_hydro_108; pfam05838 557598004439 crystallin beta/gamma motif-containing protein; Region: PHA00657 557598004440 crystallin beta/gamma motif-containing protein; Region: PHA00657 557598004441 hypothetical protein; Provisional; Region: PHA02515 557598004442 Domain of unknown function (DUF4376); Region: DUF4376; pfam14301 557598004443 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 557598004444 catalytic residues [active] 557598004445 Domain of unknown function (DUF4297); Region: DUF4297; pfam14130 557598004446 Domain of unknown function (DUF1837); Region: DUF1837; pfam08878 557598004447 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 557598004448 ATP binding site [chemical binding]; other site 557598004449 putative Mg++ binding site [ion binding]; other site 557598004450 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 557598004451 nucleotide binding region [chemical binding]; other site 557598004452 ATP-binding site [chemical binding]; other site 557598004453 Phage regulatory protein Rha (Phage_pRha); Region: Phage_pRha; pfam09669 557598004454 integrase; Provisional; Region: PRK09692 557598004455 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 557598004456 active site 557598004457 Int/Topo IB signature motif; other site 557598004458 O-succinylbenzoic acid--CoA ligase; Reviewed; Region: PRK07445 557598004459 potassium-transporting ATPase subunit A; Provisional; Region: PRK05482 557598004460 potassium-transporting ATPase subunit B; Provisional; Region: PRK01122 557598004461 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 557598004462 potassium-transporting ATPase subunit C; Reviewed; Region: PRK00315 557598004463 Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]; Region: KdpD; COG2205 557598004464 Osmosensitive K+ channel His kinase sensor domain; Region: KdpD; pfam02702 557598004465 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 557598004466 Ligand Binding Site [chemical binding]; other site 557598004467 Domain of unknown function (DUF4118); Region: DUF4118; pfam13493 557598004468 GAF domain; Region: GAF_3; pfam13492 557598004469 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 557598004470 dimer interface [polypeptide binding]; other site 557598004471 phosphorylation site [posttranslational modification] 557598004472 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 557598004473 ATP binding site [chemical binding]; other site 557598004474 Mg2+ binding site [ion binding]; other site 557598004475 G-X-G motif; other site 557598004476 DNA-binding transcriptional activator KdpE; Provisional; Region: PRK10529 557598004477 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 557598004478 active site 557598004479 phosphorylation site [posttranslational modification] 557598004480 intermolecular recognition site; other site 557598004481 dimerization interface [polypeptide binding]; other site 557598004482 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 557598004483 DNA binding site [nucleotide binding] 557598004484 SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]; Region: LexA; COG1974 557598004485 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 557598004486 Catalytic site [active] 557598004487 phosphonate metabolism protein PhnM; Provisional; Region: PRK15446 557598004488 PhnM is believed to be a subunit of the membrane associated C-P lyase complex. C-P lyase is thought to catalyze the direct cleavage of inactivated C-P bonds to yield inorganic phosphate and the corresponding hydrocarbons. It is responsible for cleavage...; Region: PhnM; cd01306 557598004489 active site 557598004490 phosphonate C-P lyase system protein PhnL; Region: CP_lyasePhnL; TIGR02324 557598004491 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 557598004492 Walker A/P-loop; other site 557598004493 ATP binding site [chemical binding]; other site 557598004494 Q-loop/lid; other site 557598004495 ABC transporter signature motif; other site 557598004496 Walker B; other site 557598004497 D-loop; other site 557598004498 H-loop/switch region; other site 557598004499 phosphonate C-P lyase system protein PhnK; Provisional; Region: phnK; PRK11701 557598004500 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 557598004501 Walker A/P-loop; other site 557598004502 ATP binding site [chemical binding]; other site 557598004503 Q-loop/lid; other site 557598004504 ABC transporter signature motif; other site 557598004505 Walker B; other site 557598004506 D-loop; other site 557598004507 H-loop/switch region; other site 557598004508 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 557598004509 Phosphonate metabolism protein PhnJ; Region: PhnJ; pfam06007 557598004510 Bacterial phosphonate metabolism protein (PhnI); Region: PhnI; pfam05861 557598004511 Bacterial phosphonate metabolism protein (PhnH); Region: PhnH; pfam05845 557598004512 Phosphonate metabolism protein PhnG; Region: PhnG; cl01454 557598004513 phosphonates metabolism transcriptional regulator PhnF; Region: C_P_lyase_phnF; TIGR02325 557598004514 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 557598004515 DNA-binding site [nucleotide binding]; DNA binding site 557598004516 UTRA domain; Region: UTRA; pfam07702 557598004517 Protein of unknown function (DUF1045); Region: DUF1045; cl15435 557598004518 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 557598004519 active site 557598004520 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 557598004521 putative 2-aminoethylphosphonate ABC transporter, ATP-binding protein; Region: PhnT2; TIGR03265 557598004522 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 557598004523 Walker A/P-loop; other site 557598004524 ATP binding site [chemical binding]; other site 557598004525 Q-loop/lid; other site 557598004526 ABC transporter signature motif; other site 557598004527 Walker B; other site 557598004528 D-loop; other site 557598004529 H-loop/switch region; other site 557598004530 TOBE domain; Region: TOBE_2; pfam08402 557598004531 putative 2-aminoethylphosphonate ABC transporter, permease protein; Region: PhnU2; TIGR03262 557598004532 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 557598004533 dimer interface [polypeptide binding]; other site 557598004534 conserved gate region; other site 557598004535 putative PBP binding loops; other site 557598004536 ABC-ATPase subunit interface; other site 557598004537 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 557598004538 dimer interface [polypeptide binding]; other site 557598004539 conserved gate region; other site 557598004540 putative PBP binding loops; other site 557598004541 ABC-ATPase subunit interface; other site 557598004542 ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent; Region: NrdJ_Z; TIGR02504 557598004543 Class II ribonucleotide reductase, dimeric form; Region: RNR_II_dimer; cd02888 557598004544 active site 557598004545 dimer interface [polypeptide binding]; other site 557598004546 effector binding site; other site 557598004547 xanthine permease; Region: pbuX; TIGR03173 557598004548 Protein of unknown function (DUF1255); Region: DUF1255; pfam06865 557598004549 Uncharacterized small membrane protein [Function unknown]; Region: COG2363 557598004550 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 557598004551 HAMP domain; Region: HAMP; pfam00672 557598004552 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557598004553 dimer interface [polypeptide binding]; other site 557598004554 putative CheW interface [polypeptide binding]; other site 557598004555 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 557598004556 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 557598004557 dimerization domain [polypeptide binding]; other site 557598004558 dimer interface [polypeptide binding]; other site 557598004559 catalytic residues [active] 557598004560 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 557598004561 Major Facilitator Superfamily; Region: MFS_1; pfam07690 557598004562 putative substrate translocation pore; other site 557598004563 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 557598004564 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 557598004565 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 557598004566 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 557598004567 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 557598004568 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cd06587 557598004569 active site 557598004570 metal binding site [ion binding]; metal-binding site 557598004571 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 557598004572 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 557598004573 Long-chain fatty acid transport protein [Lipid metabolism]; Region: FadL; COG2067 557598004574 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism]; Region: FadB; COG1250 557598004575 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 557598004576 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 557598004577 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; cl09929 557598004578 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 557598004579 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 557598004580 substrate binding site [chemical binding]; other site 557598004581 oxyanion hole (OAH) forming residues; other site 557598004582 acetyl-CoA acetyltransferase; Provisional; Region: PRK09052 557598004583 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 557598004584 dimer interface [polypeptide binding]; other site 557598004585 active site 557598004586 OsmC-like protein; Region: OsmC; pfam02566 557598004587 3-deoxy-7-phosphoheptulonate synthase; Reviewed; Region: PRK08673 557598004588 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase [Cell envelope biogenesis, outer membrane]; Region: KdsA; cl17225 557598004589 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 557598004590 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 557598004591 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 557598004592 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 557598004593 dimer interface [polypeptide binding]; other site 557598004594 conserved gate region; other site 557598004595 putative PBP binding loops; other site 557598004596 ABC-ATPase subunit interface; other site 557598004597 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 557598004598 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 557598004599 substrate binding pocket [chemical binding]; other site 557598004600 membrane-bound complex binding site; other site 557598004601 hinge residues; other site 557598004602 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 557598004603 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557598004604 dimer interface [polypeptide binding]; other site 557598004605 putative CheW interface [polypeptide binding]; other site 557598004606 potential frameshift: common BLAST hit: gi|209397184|ref|YP_002273588.1| phage integrase family protein 557598004607 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 557598004608 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 557598004609 active site 557598004610 DNA binding site [nucleotide binding] 557598004611 Int/Topo IB signature motif; other site 557598004612 Sulfite oxidase and related enzymes [General function prediction only]; Region: COG2041 557598004613 bacterial subgroup of the sulfite oxidase (SO) family of molybdopterin binding domains. This domain is found in a variety of oxidoreductases. Common features of all known members of this family, like sulfite oxidase and nitrite reductase, are that they...; Region: bact_SO_family_Moco; cd02108 557598004614 Moco binding site; other site 557598004615 metal coordination site [ion binding]; other site 557598004616 Bacteriophage lysis protein; Region: Phage_lysis; pfam03245 557598004617 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 557598004618 catalytic residues [active] 557598004619 Domain of unknown function (DUF4376); Region: DUF4376; pfam14301 557598004620 Phage Tail Collar Domain; Region: Collar; pfam07484 557598004621 Domain of unknown function (DUF4376); Region: DUF4376; pfam14301 557598004622 Phage tail protein (Tail_P2_I); Region: Tail_P2_I; cl01817 557598004623 Baseplate J-like protein; Region: Baseplate_J; cl01294 557598004624 Gene 25-like lysozyme; Region: GPW_gp25; cl01403 557598004625 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 557598004626 Phage Tail Protein X; Region: Phage_tail_X; cl02088 557598004627 Phage P2 GpU; Region: Phage_P2_GpU; cl01391 557598004628 phage tail tape measure protein, TP901 family, core region; Region: tape_meas_TP901; TIGR01760 557598004629 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; cl00220 557598004630 KilA-N domain; Region: KilA-N; pfam04383 557598004631 Phage tail tube protein FII; Region: Phage_tube; cl01390 557598004632 Phage tail sheath protein; Region: Phage_sheath_1; cl01389 557598004633 Gp37 protein; Region: Gp37; pfam09646 557598004634 Phage major capsid protein E; Region: Phage_cap_E; pfam03864 557598004635 Bacteriophage lambda head decoration protein D; Region: HDPD; pfam02924 557598004636 Signal peptide peptidase A (SppA) 36K type, a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_36K_type; cd07022 557598004637 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 557598004638 tandem repeat interface [polypeptide binding]; other site 557598004639 oligomer interface [polypeptide binding]; other site 557598004640 active site residues [active] 557598004641 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; cd02205 557598004642 Phage-related baseplate assembly protein; Region: Phage_base_V; cl17812 557598004643 Phage portal protein, lambda family; Region: Phage_portal_2; pfam05136 557598004644 phage portal protein, lambda family; Region: portal_lambda; TIGR01539 557598004645 gpW; Region: gpW; pfam02831 557598004646 Phage terminase large subunit (GpA); Region: Terminase_GpA; pfam05876 557598004647 Phage DNA packaging protein Nu1; Region: Phage_Nu1; cl01720 557598004648 Prophage antirepressor [Transcription]; Region: COG3617 557598004649 BRO family, N-terminal domain; Region: Bro-N; smart01040 557598004650 Predicted membrane protein (DUF2238); Region: DUF2238; cl01464 557598004651 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 557598004652 non-specific DNA binding site [nucleotide binding]; other site 557598004653 salt bridge; other site 557598004654 sequence-specific DNA binding site [nucleotide binding]; other site 557598004655 conjugal transfer protein TraL; Provisional; Region: PRK13886 557598004656 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 557598004657 active site 557598004658 catalytic site [active] 557598004659 substrate binding site [chemical binding]; other site 557598004660 Pyocin activator protein PrtN; Region: PyocinActivator; pfam11112 557598004661 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 557598004662 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 557598004663 active site 557598004664 DNA binding site [nucleotide binding] 557598004665 Int/Topo IB signature motif; other site 557598004666 Restriction endonuclease; Region: Mrr_cat; pfam04471 557598004667 tRNA-dihydrouridine synthase A; Provisional; Region: PRK11815 557598004668 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 557598004669 FMN binding site [chemical binding]; other site 557598004670 active site 557598004671 catalytic residues [active] 557598004672 substrate binding site [chemical binding]; other site 557598004673 Phage antirepressor protein KilAC domain; Region: ANT; cl01462 557598004674 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 557598004675 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 557598004676 BCCT family transporter; Region: BCCT; pfam02028 557598004677 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 557598004678 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 557598004679 catalytic residues [active] 557598004680 transcription termination factor Rho; Provisional; Region: rho; PRK09376 557598004681 Rho termination factor, N-terminal domain; Region: Rho_N; smart00959 557598004682 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 557598004683 RNA binding site [nucleotide binding]; other site 557598004684 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 557598004685 multimer interface [polypeptide binding]; other site 557598004686 Walker A motif; other site 557598004687 ATP binding site [chemical binding]; other site 557598004688 Walker B motif; other site 557598004689 UPF0126 domain; Region: UPF0126; pfam03458 557598004690 Predicted membrane protein [Function unknown]; Region: COG2860 557598004691 UPF0126 domain; Region: UPF0126; pfam03458 557598004692 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 557598004693 putative active site [active] 557598004694 putative CoA binding site [chemical binding]; other site 557598004695 nudix motif; other site 557598004696 metal binding site [ion binding]; metal-binding site 557598004697 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 557598004698 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 557598004699 Active Sites [active] 557598004700 sulfate adenylyltransferase subunit 1; Provisional; Region: cysN; PRK05124 557598004701 CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex; Region: CysN_ATPS; cd04166 557598004702 CysD dimerization site [polypeptide binding]; other site 557598004703 G1 box; other site 557598004704 putative GEF interaction site [polypeptide binding]; other site 557598004705 GTP/Mg2+ binding site [chemical binding]; other site 557598004706 Switch I region; other site 557598004707 G2 box; other site 557598004708 G3 box; other site 557598004709 Switch II region; other site 557598004710 G4 box; other site 557598004711 G5 box; other site 557598004712 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 557598004713 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 557598004714 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 557598004715 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 557598004716 ATP binding site [chemical binding]; other site 557598004717 Mg++ binding site [ion binding]; other site 557598004718 motif III; other site 557598004719 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 557598004720 nucleotide binding region [chemical binding]; other site 557598004721 peptidyl-prolyl cis-trans isomerase, EpsD family; Region: cis_trans_EpsD; TIGR02925 557598004722 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 557598004723 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 557598004724 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 557598004725 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 557598004726 YciI-like protein; Reviewed; Region: PRK11370 557598004727 intracellular septation protein A; Reviewed; Region: PRK00259 557598004728 META domain; Region: META; cl01245 557598004729 META domain; Region: META; pfam03724 557598004730 Domain of unknown function (DUF4377); Region: DUF4377; pfam14302 557598004731 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 557598004732 PAS domain; Region: PAS_9; pfam13426 557598004733 putative active site [active] 557598004734 heme pocket [chemical binding]; other site 557598004735 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 557598004736 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557598004737 dimer interface [polypeptide binding]; other site 557598004738 putative CheW interface [polypeptide binding]; other site 557598004739 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 557598004740 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 557598004741 putative catalytic site [active] 557598004742 putative metal binding site [ion binding]; other site 557598004743 putative phosphate binding site [ion binding]; other site 557598004744 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins; Region: PLDc_CLS_1; cd09110 557598004745 putative active site [active] 557598004746 catalytic site [active] 557598004747 Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins; Region: PLDc_ybhO_like_2; cd09159 557598004748 putative active site [active] 557598004749 catalytic site [active] 557598004750 hypothetical protein; Provisional; Region: PRK11820 557598004751 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 557598004752 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 557598004753 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 557598004754 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 557598004755 substrate binding site [chemical binding]; other site 557598004756 dimer interface [polypeptide binding]; other site 557598004757 ATP binding site [chemical binding]; other site 557598004758 D-ribose pyranase; Provisional; Region: PRK11797 557598004759 ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]; Region: MglA; COG1129 557598004760 First domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_I; cd03216 557598004761 Walker A/P-loop; other site 557598004762 ATP binding site [chemical binding]; other site 557598004763 Q-loop/lid; other site 557598004764 ABC transporter signature motif; other site 557598004765 Walker B; other site 557598004766 D-loop; other site 557598004767 H-loop/switch region; other site 557598004768 Second domain of the ATP-binding cassette component of monosaccharide transport system; Region: ABC_Carb_Monos_II; cd03215 557598004769 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 557598004770 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 557598004771 TM-ABC transporter signature motif; other site 557598004772 D-ribose transporter subunit RbsB; Provisional; Region: PRK10653 557598004773 Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs; Region: PBP1_ribose_binding; cd06323 557598004774 ligand binding site [chemical binding]; other site 557598004775 dimerization interface [polypeptide binding]; other site 557598004776 Protein of unknown function (DUF3149); Region: DUF3149; pfam11346 557598004777 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 557598004778 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 557598004779 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 557598004780 Esterase/lipase [General function prediction only]; Region: COG1647 557598004781 K+ potassium transporter; Region: K_trans; pfam02705 557598004782 Cache domain; Region: Cache_1; pfam02743 557598004783 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 557598004784 dimerization interface [polypeptide binding]; other site 557598004785 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557598004786 dimer interface [polypeptide binding]; other site 557598004787 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 557598004788 putative CheW interface [polypeptide binding]; other site 557598004789 Isochorismatase family; Region: Isochorismatase; pfam00857 557598004790 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; cl00220 557598004791 catalytic triad [active] 557598004792 conserved cis-peptide bond; other site 557598004793 EamA-like transporter family; Region: EamA; pfam00892 557598004794 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 557598004795 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 557598004796 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 557598004797 conserved cys residue [active] 557598004798 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557598004799 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 557598004800 multiple promoter invertase; Provisional; Region: mpi; PRK13413 557598004801 catalytic residues [active] 557598004802 catalytic nucleophile [active] 557598004803 Presynaptic Site I dimer interface [polypeptide binding]; other site 557598004804 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 557598004805 Synaptic Flat tetramer interface [polypeptide binding]; other site 557598004806 Synaptic Site I dimer interface [polypeptide binding]; other site 557598004807 DNA binding site [nucleotide binding] 557598004808 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 557598004809 DNA-binding interface [nucleotide binding]; DNA binding site 557598004810 Superfamily II helicase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG5519 557598004811 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 557598004812 active site 557598004813 metal binding site [ion binding]; metal-binding site 557598004814 interdomain interaction site; other site 557598004815 Domain of unknown function (DUF927); Region: DUF927; cl12098 557598004816 KilA-N domain; Region: KilA-N; pfam04383 557598004817 Helix-turn-helix domain; Region: HTH_17; pfam12728 557598004818 integrase; Provisional; Region: PRK09692 557598004819 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 557598004820 active site 557598004821 Int/Topo IB signature motif; other site 557598004822 replicative DNA helicase; Region: DnaB; TIGR00665 557598004823 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 557598004824 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 557598004825 Walker A motif; other site 557598004826 ATP binding site [chemical binding]; other site 557598004827 Walker B motif; other site 557598004828 DNA binding loops [nucleotide binding] 557598004829 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 557598004830 dimer interface [polypeptide binding]; other site 557598004831 [2Fe-2S] cluster binding site [ion binding]; other site 557598004832 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 557598004833 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 557598004834 peptidase PmbA; Provisional; Region: PRK11040 557598004835 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 557598004836 endonuclease III; Region: ENDO3c; smart00478 557598004837 minor groove reading motif; other site 557598004838 helix-hairpin-helix signature motif; other site 557598004839 substrate binding pocket [chemical binding]; other site 557598004840 active site 557598004841 Disulfide bond formation protein DsbB; Region: DsbB; pfam02600 557598004842 Xaa-His dipeptidase; Region: aa-his-dipept; TIGR01893 557598004843 M20 Peptidase D has specificity for beta-alanyl-L-histidine dipeptide; Region: M20_pepD; cd03890 557598004844 metal binding site [ion binding]; metal-binding site 557598004845 dimer interface [polypeptide binding]; other site 557598004846 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dam; COG0338 557598004847 Mu-like prophage protein Com; Region: Mu-like_Com; cl11540 557598004848 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 557598004849 catalytic residues [active] 557598004850 Domain of unknown function (DUF4376); Region: DUF4376; pfam14301 557598004851 Bacteriophage lambda tail assembly protein I; Region: Lambda_tail_I; cl01945 557598004852 Putative phage tail protein; Region: Phage-tail_3; pfam13550 557598004853 Domain of unknown function (DUF1833); Region: DUF1833; pfam08875 557598004854 Phage-related minor tail protein [Function unknown]; Region: COG5281 557598004855 Prophage tail length tape measure protein; Region: TMP_2; pfam06791 557598004856 Lambda phage tail tape-measure protein (Tape_meas_lam_C); Region: Tape_meas_lam_C; pfam09718 557598004857 Cytotoxic translational repressor of toxin-antitoxin stability system [Translation, ribosomal structure and biogenesis / Cell division and chromosome partitioning]; Region: RelE; COG2026 557598004858 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 557598004859 Phage related hypothetical protein (DUF1799); Region: DUF1799; pfam08809 557598004860 Domain of unknown function (DUF1789); Region: DUF1789; pfam08748 557598004861 Phage tail protein; Region: Phage_tail_3; pfam08813 557598004862 Protein of unknown function (DUF3168); Region: DUF3168; pfam11367 557598004863 Bacteriophage protein of unknown function (DUF646); Region: DUF646; pfam04883 557598004864 Bacteriophage head-tail adaptor [General function prediction only]; Region: COG5614 557598004865 Head-Tail Connector Protein gp6 of Bacteriophage HK97 and similar proteins; Region: gp6; cd08054 557598004866 oligomerization interface [polypeptide binding]; other site 557598004867 phage major capsid protein, HK97 family; Region: major_cap_HK97; TIGR01554 557598004868 Phage capsid family; Region: Phage_capsid; pfam05065 557598004869 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_1; cd07016 557598004870 oligomer interface [polypeptide binding]; other site 557598004871 Clp protease; Region: CLP_protease; pfam00574 557598004872 active site residues [active] 557598004873 Phage-related protein [Function unknown]; Region: COG4695 557598004874 Phage portal protein; Region: Phage_portal; pfam04860 557598004875 Phage terminase-like protein, large subunit [General function prediction only]; Region: COG4626 557598004876 Restriction endonuclease [Defense mechanisms]; Region: McrA; COG1403 557598004877 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 557598004878 active site 557598004879 BRO family, N-terminal domain; Region: Bro-N; smart01040 557598004880 ORF11CD3 domain; Region: ORF11CD3; pfam10549 557598004881 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 557598004882 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 557598004883 Prophage antirepressor [Transcription]; Region: COG3617 557598004884 BRO family, N-terminal domain; Region: Bro-N; smart01040 557598004885 Endodeoxyribonuclease RusA; Region: RusA; pfam05866 557598004886 Protein of unknown function (DUF1376); Region: DUF1376; pfam07120 557598004887 Phage regulatory protein CII (CP76); Region: Phage_CP76; pfam06892 557598004888 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 557598004889 Predicted GTPase [General function prediction only]; Region: ThdF; COG0486 557598004890 Domain in histone-like proteins of HNS family; Region: HNS; smart00528 557598004891 H-NS histone family; Region: Histone_HNS; pfam00816 557598004892 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 557598004893 AAA domain; Region: AAA_23; pfam13476 557598004894 Walker A/P-loop; other site 557598004895 ATP binding site [chemical binding]; other site 557598004896 integrase; Provisional; Region: int; PHA02601 557598004897 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 557598004898 active site 557598004899 DNA binding site [nucleotide binding] 557598004900 Int/Topo IB signature motif; other site 557598004901 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 557598004902 dimer interface [polypeptide binding]; other site 557598004903 putative radical transfer pathway; other site 557598004904 diiron center [ion binding]; other site 557598004905 tyrosyl radical; other site 557598004906 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK07207 557598004907 ATP cone domain; Region: ATP-cone; pfam03477 557598004908 ATP cone domain; Region: ATP-cone; pfam03477 557598004909 Class I ribonucleotide reductase; Region: RNR_I; cd01679 557598004910 active site 557598004911 dimer interface [polypeptide binding]; other site 557598004912 catalytic residues [active] 557598004913 effector binding site; other site 557598004914 R2 peptide binding site; other site 557598004915 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 557598004916 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; cd00625 557598004917 transmembrane helices; other site 557598004918 Phosphoenolpyruvate:glucose-phosphotransferase regulator; Region: MtfA; pfam06167 557598004919 glycerate dehydrogenase; Provisional; Region: PRK06487 557598004920 Putative D-isomer specific 2-hydroxyacid dehydrogenases; Region: 2-Hacid_dh_4; cd12162 557598004921 putative ligand binding site [chemical binding]; other site 557598004922 putative NAD binding site [chemical binding]; other site 557598004923 catalytic site [active] 557598004924 Uroporphyrin-III C-methyltransferase (S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT); Region: SUMT; cd11642 557598004925 active site 557598004926 SAM binding site [chemical binding]; other site 557598004927 homodimer interface [polypeptide binding]; other site 557598004928 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 557598004929 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 557598004930 active site 557598004931 phosphorylation site [posttranslational modification] 557598004932 intermolecular recognition site; other site 557598004933 dimerization interface [polypeptide binding]; other site 557598004934 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 557598004935 DNA binding site [nucleotide binding] 557598004936 sensor protein QseC; Provisional; Region: PRK10337 557598004937 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 557598004938 dimer interface [polypeptide binding]; other site 557598004939 phosphorylation site [posttranslational modification] 557598004940 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 557598004941 ATP binding site [chemical binding]; other site 557598004942 Mg2+ binding site [ion binding]; other site 557598004943 G-X-G motif; other site 557598004944 Putative effector of murein hydrolase [Cell envelope biogenesis, outer membrane]; Region: LrgB; COG1346 557598004945 LrgA family; Region: LrgA; pfam03788 557598004946 hypothetical protein; Provisional; Region: PRK01842 557598004947 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 557598004948 active site 557598004949 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 557598004950 trimer interface [polypeptide binding]; other site 557598004951 eyelet of channel; other site 557598004952 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 557598004953 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 557598004954 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 557598004955 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 557598004956 nudix motif; other site 557598004957 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 557598004958 ABC1 family; Region: ABC1; cl17513 557598004959 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family 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: APH_ChoK_like; cd05120 557598004960 active site 557598004961 ATP binding site [chemical binding]; other site 557598004962 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 557598004963 NlpC/P60 family; Region: NLPC_P60; pfam00877 557598004964 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 557598004965 lipoprotein releasing system, ATP-binding protein; Region: LolD_lipo_ex; TIGR02211 557598004966 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 557598004967 Walker A/P-loop; other site 557598004968 ATP binding site [chemical binding]; other site 557598004969 Q-loop/lid; other site 557598004970 ABC transporter signature motif; other site 557598004971 Walker B; other site 557598004972 D-loop; other site 557598004973 H-loop/switch region; other site 557598004974 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 557598004975 Mechanosensitive ion channel; Region: MS_channel; pfam00924 557598004976 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 557598004977 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 557598004978 active site 557598004979 phosphorylation site [posttranslational modification] 557598004980 intermolecular recognition site; other site 557598004981 dimerization interface [polypeptide binding]; other site 557598004982 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 557598004983 DNA binding residues [nucleotide binding] 557598004984 dimerization interface [polypeptide binding]; other site 557598004985 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 557598004986 nudix motif; other site 557598004987 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 557598004988 active site 557598004989 DNA polymerase IV; Validated; Region: PRK02406 557598004990 DNA binding site [nucleotide binding] 557598004991 nicotinate-nucleotide pyrophosphorylase; Provisional; Region: PRK06978 557598004992 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 557598004993 dimerization interface [polypeptide binding]; other site 557598004994 active site 557598004995 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 557598004996 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 557598004997 dimerization interface [polypeptide binding]; other site 557598004998 DPS ferroxidase diiron center [ion binding]; other site 557598004999 ion pore; other site 557598005000 DNA gyrase subunit A; Validated; Region: PRK05560 557598005001 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 557598005002 CAP-like domain; other site 557598005003 active site 557598005004 primary dimer interface [polypeptide binding]; other site 557598005005 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 557598005006 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 557598005007 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 557598005008 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 557598005009 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 557598005010 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 557598005011 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 557598005012 CoenzymeA binding site [chemical binding]; other site 557598005013 subunit interaction site [polypeptide binding]; other site 557598005014 PHB binding site; other site 557598005015 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 557598005016 CoenzymeA binding site [chemical binding]; other site 557598005017 subunit interaction site [polypeptide binding]; other site 557598005018 PHB binding site; other site 557598005019 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 557598005020 homodimer interface [polypeptide binding]; other site 557598005021 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 557598005022 substrate-cofactor binding pocket; other site 557598005023 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557598005024 catalytic residue [active] 557598005025 Chorismate mutase type II; Region: CM_2; cl00693 557598005026 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 557598005027 Prephenate dehydratase; Region: PDT; pfam00800 557598005028 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 557598005029 putative L-Phe binding site [chemical binding]; other site 557598005030 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 557598005031 histidinol-phosphate aminotransferase; Validated; Region: PRK02731 557598005032 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 557598005033 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557598005034 homodimer interface [polypeptide binding]; other site 557598005035 catalytic residue [active] 557598005036 anthranilate synthase component I; Provisional; Region: PRK13565 557598005037 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 557598005038 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 557598005039 phosphoglycolate phosphatase; Provisional; Region: PRK13222 557598005040 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 557598005041 active site 557598005042 motif I; other site 557598005043 motif II; other site 557598005044 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 557598005045 putative active site [active] 557598005046 putative catalytic site [active] 557598005047 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 557598005048 beta-hexosaminidase; Provisional; Region: PRK05337 557598005049 Bacterial protein of unknown function (DUF883); Region: DUF883; pfam05957 557598005050 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 557598005051 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 557598005052 active site 557598005053 HIGH motif; other site 557598005054 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 557598005055 active site 557598005056 KMSKS motif; other site 557598005057 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 557598005058 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 557598005059 23S rRNA m(5)U1939 methyltransferase; Reviewed; Region: rumA; PRK13168 557598005060 TRAM domain; Region: TRAM; cl01282 557598005061 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 557598005062 S-adenosylmethionine binding site [chemical binding]; other site 557598005063 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK08690 557598005064 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 557598005065 NAD binding site [chemical binding]; other site 557598005066 homotetramer interface [polypeptide binding]; other site 557598005067 homodimer interface [polypeptide binding]; other site 557598005068 substrate binding site [chemical binding]; other site 557598005069 active site 557598005070 Protein of unknown function, DUF484; Region: DUF484; cl17449 557598005071 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 557598005072 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 557598005073 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 557598005074 enoyl-CoA hydratase; Provisional; Region: PRK06142 557598005075 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 557598005076 substrate binding site [chemical binding]; other site 557598005077 oxyanion hole (OAH) forming residues; other site 557598005078 trimer interface [polypeptide binding]; other site 557598005079 Protein of unknown function (DUF3579); Region: DUF3579; pfam12112 557598005080 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 557598005081 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 557598005082 Serine hydrolase; Region: Ser_hydrolase; cl17834 557598005083 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 557598005084 catalytic site [active] 557598005085 leucine-responsive transcriptional regulator; Provisional; Region: PRK11169 557598005086 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 557598005087 putative DNA binding site [nucleotide binding]; other site 557598005088 dimerization interface [polypeptide binding]; other site 557598005089 putative Zn2+ binding site [ion binding]; other site 557598005090 AsnC family; Region: AsnC_trans_reg; pfam01037 557598005091 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed; Region: PRK11905 557598005092 Proline dehydrogenase [Amino acid transport and metabolism]; Region: PutA; COG0506 557598005093 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 557598005094 Glutamate binding site [chemical binding]; other site 557598005095 NAD binding site [chemical binding]; other site 557598005096 catalytic residues [active] 557598005097 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 557598005098 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 557598005099 dimerization interface [polypeptide binding]; other site 557598005100 ligand binding site [chemical binding]; other site 557598005101 Cupin; Region: Cupin_6; pfam12852 557598005102 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 557598005103 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 557598005104 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 557598005105 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557598005106 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 557598005107 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 557598005108 substrate binding pocket [chemical binding]; other site 557598005109 dimerization interface [polypeptide binding]; other site 557598005110 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 557598005111 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 557598005112 monofunctional biosynthetic peptidoglycan transglycosylase; Provisional; Region: mtgA; PRK00056 557598005113 Transglycosylase; Region: Transgly; cl17702 557598005114 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 557598005115 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 557598005116 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 557598005117 shikimate binding site; other site 557598005118 NAD(P) binding site [chemical binding]; other site 557598005119 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 557598005120 active site residue [active] 557598005121 glutamine synthetase; Provisional; Region: glnA; PRK09469 557598005122 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 557598005123 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 557598005124 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 557598005125 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 557598005126 ring oligomerisation interface [polypeptide binding]; other site 557598005127 ATP/Mg binding site [chemical binding]; other site 557598005128 stacking interactions; other site 557598005129 hinge regions; other site 557598005130 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 557598005131 oligomerisation interface [polypeptide binding]; other site 557598005132 mobile loop; other site 557598005133 roof hairpin; other site 557598005134 Uncharacterized protein conserved in bacteria (DUF2147); Region: DUF2147; pfam09917 557598005135 C4-dicarboxylate transporter DctA; Reviewed; Region: PRK01663 557598005136 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 557598005137 Protein of unknown function (DUF465); Region: DUF465; cl01070 557598005138 37-kD nucleoid-associated bacterial protein; Region: NA37; pfam04245 557598005139 glutamate dehydrogenase; Provisional; Region: PRK09414 557598005140 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 557598005141 NAD(P) binding domain of glutamate dehydrogenase, subgroup 2; Region: NAD_bind_2_Glu_DH; cd05313 557598005142 NAD(P) binding site [chemical binding]; other site 557598005143 Bacterial NAD-glutamate dehydrogenase; Region: Bac_GDH; pfam05088 557598005144 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Region: ELFV_dehydrog; smart00839 557598005145 lysine-arginine-ornithine-binding periplasmic protein; Region: 3A0103s03R; TIGR01096 557598005146 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 557598005147 substrate binding pocket [chemical binding]; other site 557598005148 membrane-bound complex binding site; other site 557598005149 hinge residues; other site 557598005150 Protein of unknown function (DUF2776); Region: DUF2776; pfam10951 557598005151 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; cl00859 557598005152 lipoprotein; Provisional; Region: PRK10540 557598005153 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 557598005154 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 557598005155 S-adenosylmethionine binding site [chemical binding]; other site 557598005156 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 557598005157 MgtE intracellular N domain; Region: MgtE_N; smart00924 557598005158 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain in the magnesium transporter, MgtE. MgtE and its homologs are found in eubacteria, archaebacteria, and eukaryota. Members of this family transport Mg2+ or other...; Region: CBS_pair_Mg_transporter; cd04606 557598005159 Divalent cation transporter; Region: MgtE; pfam01769 557598005160 Predicted ferric reductase [Inorganic ion transport and metabolism]; Region: COG4097 557598005161 Ferric reductase like transmembrane component; Region: Ferric_reduct; pfam01794 557598005162 NAD(P) binding domain of ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) domain, which varies in orientation with respect to the NAD(P)...; Region: FNR_like_3; cd06198 557598005163 FAD binding pocket [chemical binding]; other site 557598005164 FAD binding motif [chemical binding]; other site 557598005165 phosphate binding motif [ion binding]; other site 557598005166 beta-alpha-beta structure motif; other site 557598005167 NAD binding pocket [chemical binding]; other site 557598005168 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 557598005169 homotrimer interaction site [polypeptide binding]; other site 557598005170 putative active site [active] 557598005171 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 557598005172 homotrimer interaction site [polypeptide binding]; other site 557598005173 putative active site [active] 557598005174 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 557598005175 homotrimer interaction site [polypeptide binding]; other site 557598005176 putative active site [active] 557598005177 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 557598005178 homotrimer interaction site [polypeptide binding]; other site 557598005179 putative active site [active] 557598005180 hypothetical protein; Provisional; Region: PRK09945 557598005181 Pertactin-like passenger domains (virulence factors) of autotransporter proteins of the type V secretion system. Autotransporters are proteins used by Gram-negative bacteria to transport proteins across their outer membranes. The C-terminal (beta) domain...; Region: PL_Passenger_AT; cd00253 557598005182 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 557598005183 Autotransporter beta-domain; Region: Autotransporter; smart00869 557598005184 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 557598005185 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 557598005186 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 557598005187 dimer interface [polypeptide binding]; other site 557598005188 phosphorylation site [posttranslational modification] 557598005189 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 557598005190 ATP binding site [chemical binding]; other site 557598005191 Mg2+ binding site [ion binding]; other site 557598005192 G-X-G motif; other site 557598005193 nitrogen regulation protein NR(I); Region: ntrC; TIGR01818 557598005194 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 557598005195 active site 557598005196 phosphorylation site [posttranslational modification] 557598005197 intermolecular recognition site; other site 557598005198 dimerization interface [polypeptide binding]; other site 557598005199 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 557598005200 Walker A motif; other site 557598005201 ATP binding site [chemical binding]; other site 557598005202 Walker B motif; other site 557598005203 arginine finger; other site 557598005204 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 557598005205 hypothetical protein; Reviewed; Region: PRK00024 557598005206 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 557598005207 MPN+ (JAMM) motif; other site 557598005208 Zinc-binding site [ion binding]; other site 557598005209 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 557598005210 Flavoprotein; Region: Flavoprotein; pfam02441 557598005211 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 557598005212 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 557598005213 trimer interface [polypeptide binding]; other site 557598005214 active site 557598005215 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 557598005216 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 557598005217 Walker A/P-loop; other site 557598005218 ATP binding site [chemical binding]; other site 557598005219 Q-loop/lid; other site 557598005220 ABC transporter signature motif; other site 557598005221 Walker B; other site 557598005222 D-loop; other site 557598005223 H-loop/switch region; other site 557598005224 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 557598005225 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 557598005226 Walker A/P-loop; other site 557598005227 ATP binding site [chemical binding]; other site 557598005228 Q-loop/lid; other site 557598005229 ABC transporter signature motif; other site 557598005230 Walker B; other site 557598005231 D-loop; other site 557598005232 H-loop/switch region; other site 557598005233 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 557598005234 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 557598005235 TM-ABC transporter signature motif; other site 557598005236 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 557598005237 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 557598005238 TM-ABC transporter signature motif; other site 557598005239 Arginine/ornithine N-succinyltransferase beta subunit [Amino acid transport and metabolism]; Region: AstA; COG3138 557598005240 Arginine N-succinyltransferase beta subunit; Region: AstA; cl11440 557598005241 Arginine/ornithine N-succinyltransferase beta subunit [Amino acid transport and metabolism]; Region: AstA; COG3138 557598005242 Arginine N-succinyltransferase beta subunit; Region: AstA; pfam04958 557598005243 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein; Reviewed; Region: argD; PRK05093 557598005244 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 557598005245 inhibitor-cofactor binding pocket; inhibition site 557598005246 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557598005247 catalytic residue [active] 557598005248 glucose-6-phosphate 1-dehydrogenase; Provisional; Region: PRK12853 557598005249 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 557598005250 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 557598005251 Predicted 6-phosphogluconate dehydrogenase [Carbohydrate transport and metabolism]; Region: Gnd; COG1023 557598005252 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 557598005253 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 557598005254 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 557598005255 catalytic loop [active] 557598005256 iron binding site [ion binding]; other site 557598005257 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 557598005258 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 557598005259 RNase E interface [polypeptide binding]; other site 557598005260 trimer interface [polypeptide binding]; other site 557598005261 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 557598005262 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 557598005263 RNase E interface [polypeptide binding]; other site 557598005264 trimer interface [polypeptide binding]; other site 557598005265 active site 557598005266 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 557598005267 putative nucleic acid binding region [nucleotide binding]; other site 557598005268 G-X-X-G motif; other site 557598005269 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 557598005270 RNA binding site [nucleotide binding]; other site 557598005271 domain interface; other site 557598005272 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 557598005273 16S/18S rRNA binding site [nucleotide binding]; other site 557598005274 S13e-L30e interaction site [polypeptide binding]; other site 557598005275 25S rRNA binding site [nucleotide binding]; other site 557598005276 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK05033 557598005277 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 557598005278 RNA binding site [nucleotide binding]; other site 557598005279 active site 557598005280 Pseudouridine synthase II TruB, C-terminal; Region: TruB-C_2; pfam09157 557598005281 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 557598005282 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 557598005283 Bacterial translation initiation factor IF-2 associated region; Region: IF2_assoc; pfam08364 557598005284 translation initiation factor IF-2; Region: IF-2; TIGR00487 557598005285 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 557598005286 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 557598005287 G1 box; other site 557598005288 putative GEF interaction site [polypeptide binding]; other site 557598005289 GTP/Mg2+ binding site [chemical binding]; other site 557598005290 Switch I region; other site 557598005291 G2 box; other site 557598005292 G3 box; other site 557598005293 Switch II region; other site 557598005294 G4 box; other site 557598005295 G5 box; other site 557598005296 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 557598005297 Translation-initiation factor 2; Region: IF-2; pfam11987 557598005298 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 557598005299 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 557598005300 NusA N-terminal domain; Region: NusA_N; pfam08529 557598005301 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 557598005302 RNA binding site [nucleotide binding]; other site 557598005303 homodimer interface [polypeptide binding]; other site 557598005304 NusA-like KH domain; Region: KH_5; pfam13184 557598005305 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 557598005306 G-X-X-G motif; other site 557598005307 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 557598005308 ribosome maturation protein RimP; Reviewed; Region: PRK00092 557598005309 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 557598005310 putative oligomer interface [polypeptide binding]; other site 557598005311 putative RNA binding site [nucleotide binding]; other site 557598005312 Long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07059 557598005313 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 557598005314 acyl-activating enzyme (AAE) consensus motif; other site 557598005315 putative AMP binding site [chemical binding]; other site 557598005316 putative active site [active] 557598005317 putative CoA binding site [chemical binding]; other site 557598005318 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 557598005319 ArsC family; Region: ArsC; pfam03960 557598005320 putative catalytic residues [active] 557598005321 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 557598005322 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 557598005323 metal binding site [ion binding]; metal-binding site 557598005324 dimer interface [polypeptide binding]; other site 557598005325 MarC family integral membrane protein; Region: MarC; cl00919 557598005326 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]; Region: COG4977 557598005327 AraC transcriptional regulators having an N-terminal Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GATase1_AraC_ArgR_like; cd03136 557598005328 conserved cys residue [active] 557598005329 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557598005330 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557598005331 Protein of unknown function (DUF861); Region: Cupin_3; cl17594 557598005332 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 557598005333 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 557598005334 nucleophile elbow; other site 557598005335 Surface antigen; Region: Bac_surface_Ag; pfam01103 557598005336 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 557598005337 active site 557598005338 dimerization interface [polypeptide binding]; other site 557598005339 coproporphyrinogen III oxidase; Provisional; Region: PRK08898 557598005340 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 557598005341 FeS/SAM binding site; other site 557598005342 HemN C-terminal domain; Region: HemN_C; pfam06969 557598005343 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 557598005344 homotrimer interaction site [polypeptide binding]; other site 557598005345 putative active site [active] 557598005346 Mechanosensitive ion channel; Region: MS_channel; pfam00924 557598005347 Uncharacterized oxidoreductases, Fe-dependent alcohol dehydrogenase family [Energy production and conversion]; Region: COG1979 557598005348 Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process; Region: BDH; cd08187 557598005349 dimer interface [polypeptide binding]; other site 557598005350 active site 557598005351 metal binding site [ion binding]; metal-binding site 557598005352 Protein of unknown function (DUF904); Region: DUF904; pfam06005 557598005353 Uncharacterized conserved protein [Function unknown]; Region: COG2308 557598005354 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2307 557598005355 A predicted alpha-helical domain with a conserved ER motif; Region: Alpha-E; pfam04168 557598005356 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 557598005357 Bacterial transglutaminase-like N-terminal region; Region: Bact_transglu_N; pfam08379 557598005358 Predicted proteasome-type protease [Posttranslational modification, protein turnover, chaperones]; Region: COG3484 557598005359 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 557598005360 active site 557598005361 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 557598005362 putative FMN binding site [chemical binding]; other site 557598005363 Domain of unknown function found in archaea, bacteria, and plants; Region: DUF296; cd11378 557598005364 trimer interface [polypeptide binding]; other site 557598005365 putative Zn binding site [ion binding]; other site 557598005366 Cobalt transport protein; Region: CbiQ; cl00463 557598005367 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 557598005368 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 557598005369 Walker A/P-loop; other site 557598005370 ATP binding site [chemical binding]; other site 557598005371 Q-loop/lid; other site 557598005372 ABC transporter signature motif; other site 557598005373 Walker B; other site 557598005374 D-loop; other site 557598005375 H-loop/switch region; other site 557598005376 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 557598005377 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 557598005378 Walker A/P-loop; other site 557598005379 ATP binding site [chemical binding]; other site 557598005380 Q-loop/lid; other site 557598005381 ABC transporter signature motif; other site 557598005382 Walker B; other site 557598005383 D-loop; other site 557598005384 H-loop/switch region; other site 557598005385 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK05286 557598005386 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 557598005387 quinone interaction residues [chemical binding]; other site 557598005388 active site 557598005389 catalytic residues [active] 557598005390 FMN binding site [chemical binding]; other site 557598005391 substrate binding site [chemical binding]; other site 557598005392 Glycine zipper 2TM domain; Region: Rick_17kDa_Anti; cl10470 557598005393 Protein of unknown function (DUF2788); Region: DUF2788; pfam10981 557598005394 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 557598005395 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 557598005396 dimerization interface [polypeptide binding]; other site 557598005397 ligand binding site [chemical binding]; other site 557598005398 Calcineurin-like phosphoesterase superfamily domain; Region: Metallophos_2; pfam12850 557598005399 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 557598005400 active site 557598005401 metal binding site [ion binding]; metal-binding site 557598005402 Domain of unknown function (DUF1854); Region: DUF1854; pfam08909 557598005403 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 557598005404 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 557598005405 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 557598005406 Walker A/P-loop; other site 557598005407 ATP binding site [chemical binding]; other site 557598005408 Q-loop/lid; other site 557598005409 ABC transporter signature motif; other site 557598005410 Walker B; other site 557598005411 D-loop; other site 557598005412 H-loop/switch region; other site 557598005413 cyanophycin synthetase; Provisional; Region: PRK14016 557598005414 ATP-grasp domain; Region: ATP-grasp_4; pfam13535 557598005415 cyanophycin synthetase; Provisional; Region: PRK14016 557598005416 ATP-grasp domain; Region: ATP-grasp_4; pfam13535 557598005417 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 557598005418 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 557598005419 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 557598005420 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 557598005421 putative active site [active] 557598005422 heme pocket [chemical binding]; other site 557598005423 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 557598005424 Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); Region: PAC; smart00086 557598005425 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 557598005426 putative active site [active] 557598005427 heme pocket [chemical binding]; other site 557598005428 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 557598005429 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557598005430 metal binding site [ion binding]; metal-binding site 557598005431 active site 557598005432 I-site; other site 557598005433 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 557598005434 Cation efflux family; Region: Cation_efflux; pfam01545 557598005435 putative metal dependent hydrolase; Provisional; Region: PRK11598 557598005436 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 557598005437 Sulfatase; Region: Sulfatase; pfam00884 557598005438 Predicted membrane protein [Function unknown]; Region: COG2261 557598005439 Histone deacetylase class IIa; Region: HDAC_classII_APAH; cd10001 557598005440 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 557598005441 active site 557598005442 Zn binding site [ion binding]; other site 557598005443 Polysaccharide biosynthesis protein; Region: Polysacc_synt; cl10513 557598005444 NfeD-like C-terminal, partner-binding; Region: NfeD; cl00686 557598005445 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 557598005446 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 557598005447 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 557598005448 zinc binding site [ion binding]; other site 557598005449 putative ligand binding site [chemical binding]; other site 557598005450 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 557598005451 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 557598005452 TM-ABC transporter signature motif; other site 557598005453 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: PhnK; COG1101 557598005454 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 557598005455 Walker A/P-loop; other site 557598005456 ATP binding site [chemical binding]; other site 557598005457 Q-loop/lid; other site 557598005458 ABC transporter signature motif; other site 557598005459 Walker B; other site 557598005460 D-loop; other site 557598005461 H-loop/switch region; other site 557598005462 Domain of unknown function (DUF4376); Region: DUF4376; pfam14301 557598005463 Uncharacterized protein conserved in bacteria (DUF2313); Region: DUF2313; cl01542 557598005464 Uncharacterized homolog of phage Mu protein gp47 [Function unknown]; Region: XkdT; COG3299 557598005465 Phage protein GP46; Region: GP46; cl01814 557598005466 Mu DNA-binding domain; Region: HTH_Tnp_Mu_1; pfam02316 557598005467 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 557598005468 non-specific DNA binding site [nucleotide binding]; other site 557598005469 Predicted transcriptional regulator [Transcription]; Region: COG2932 557598005470 salt bridge; other site 557598005471 sequence-specific DNA binding site [nucleotide binding]; other site 557598005472 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 557598005473 Catalytic site [active] 557598005474 Phage regulatory protein Rha (Phage_pRha); Region: Phage_pRha; pfam09669 557598005475 Methyltransferase domain; Region: Methyltransf_23; pfam13489 557598005476 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 557598005477 S-adenosylmethionine binding site [chemical binding]; other site 557598005478 Transposase DDE domain; Region: DDE_Tnp_1_5; pfam13737 557598005479 Transposase DDE domain; Region: DDE_Tnp_1_5; pfam13737 557598005480 Bacteriophage lysis protein; Region: Phage_lysis; pfam03245 557598005481 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 557598005482 Domain of unknown function (DUF4376); Region: DUF4376; pfam14301 557598005483 hypothetical protein; Provisional; Region: PHA02515 557598005484 hypothetical protein; Provisional; Region: PHA02515 557598005485 Mor transcription activator family; Region: Mor; cl02360 557598005486 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 557598005487 Methyltransferase domain; Region: Methyltransf_26; pfam13659 557598005488 potential frameshift: common BLAST hit: gi|94310245|ref|YP_583455.1| integrase catalytic subunit 557598005489 Integrase core domain; Region: rve_3; cl15866 557598005490 Integrase core domain; Region: rve; pfam00665 557598005491 Transposase DDE domain; Region: DDE_Tnp_1_5; pfam13737 557598005492 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 557598005493 pyridoxamine-phosphate oxidase; Region: pdxH; TIGR00558 557598005494 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 557598005495 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 557598005496 putative cation:proton antiport protein; Provisional; Region: PRK10669 557598005497 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 557598005498 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 557598005499 TrkA-N domain; Region: TrkA_N; pfam02254 557598005500 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 557598005501 putative active site [active] 557598005502 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 557598005503 HAD-superfamily hydrolase, subfamily IIIA; Region: HAD-SF-IIIA; TIGR01662 557598005504 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 557598005505 active site 557598005506 motif I; other site 557598005507 motif II; other site 557598005508 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3117; cl01200 557598005509 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 557598005510 OstA-like protein; Region: OstA; cl00844 557598005511 lipopolysaccharide transport periplasmic protein LptA; Region: outer_YhbN_LptA; TIGR03002 557598005512 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 557598005513 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 557598005514 Walker A/P-loop; other site 557598005515 ATP binding site [chemical binding]; other site 557598005516 Q-loop/lid; other site 557598005517 ABC transporter signature motif; other site 557598005518 Walker B; other site 557598005519 D-loop; other site 557598005520 H-loop/switch region; other site 557598005521 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 557598005522 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 557598005523 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 557598005524 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 557598005525 30S subunit binding site; other site 557598005526 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 557598005527 active site 557598005528 phosphorylation site [posttranslational modification] 557598005529 HPr kinase/phosphorylase; Provisional; Region: PRK05428 557598005530 HPr Serine kinase N terminus; Region: Hpr_kinase_N; pfam02603 557598005531 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 557598005532 Hpr binding site; other site 557598005533 active site 557598005534 homohexamer subunit interaction site [polypeptide binding]; other site 557598005535 glmZ(sRNA)-inactivating NTPase; Provisional; Region: PRK05416 557598005536 AAA domain; Region: AAA_18; pfam13238 557598005537 NGN-insert domain found between N-terminal domain (D1) and C-terminal KOW domain (DIII) repeats of some N-Utilization Substance G (NusG) N-terminal (NGN); Region: NGN-insert_like; cd09910 557598005538 Heptaprenyl diphosphate synthase component I; Region: Hpre_diP_synt_I; pfam07456 557598005539 aromatic acid decarboxylase; Validated; Region: PRK05920 557598005540 Flavoprotein; Region: Flavoprotein; pfam02441 557598005541 Uncharacterized conserved protein [Function unknown]; Region: COG0062 557598005542 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 557598005543 putative ATP binding site [chemical binding]; other site 557598005544 putative substrate binding site [chemical binding]; other site 557598005545 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 557598005546 RNA binding surface [nucleotide binding]; other site 557598005547 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 557598005548 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 557598005549 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557598005550 dimer interface [polypeptide binding]; other site 557598005551 putative CheW interface [polypeptide binding]; other site 557598005552 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 557598005553 Cobalt uptake substrate-specific transmembrane region; Region: CbiM; pfam01891 557598005554 Predicted membrane protein [Function unknown]; Region: COG3235 557598005555 DNA repair protein RadA; Provisional; Region: PRK11823 557598005556 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 557598005557 Walker A motif/ATP binding site; other site 557598005558 ATP binding site [chemical binding]; other site 557598005559 Walker B motif; other site 557598005560 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 557598005561 short chain dehydrogenase; Provisional; Region: PRK08703 557598005562 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557598005563 NAD(P) binding site [chemical binding]; other site 557598005564 active site 557598005565 squalene-associated FAD-dependent desaturase; Region: HpnE; TIGR03467 557598005566 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 557598005567 catalytic residues [active] 557598005568 substrate binding pocket [chemical binding]; other site 557598005569 substrate-Mg2+ binding site; other site 557598005570 aspartate-rich region 1; other site 557598005571 aspartate-rich region 2; other site 557598005572 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 557598005573 active site lid residues [active] 557598005574 substrate binding pocket [chemical binding]; other site 557598005575 catalytic residues [active] 557598005576 substrate-Mg2+ binding site; other site 557598005577 aspartate-rich region 1; other site 557598005578 aspartate-rich region 2; other site 557598005579 ADP-ribosylglycohydrolase; Region: ADP_ribosyl_GH; pfam03747 557598005580 DL-methionine transporter ATP-binding subunit; Provisional; Region: metN; PRK11153 557598005581 ATP-binding cassette domain of methionine transporter; Region: ABC_MetN_methionine_transporter; cd03258 557598005582 Walker A/P-loop; other site 557598005583 ATP binding site [chemical binding]; other site 557598005584 Q-loop/lid; other site 557598005585 ABC transporter signature motif; other site 557598005586 Walker B; other site 557598005587 D-loop; other site 557598005588 H-loop/switch region; other site 557598005589 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 557598005590 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 557598005591 dimer interface [polypeptide binding]; other site 557598005592 conserved gate region; other site 557598005593 ABC-ATPase subunit interface; other site 557598005594 ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]; Region: NlpA; COG1464 557598005595 NLPA lipoprotein; Region: Lipoprotein_9; pfam03180 557598005596 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 557598005597 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 557598005598 Walker A/P-loop; other site 557598005599 ATP binding site [chemical binding]; other site 557598005600 Q-loop/lid; other site 557598005601 ABC transporter signature motif; other site 557598005602 Walker B; other site 557598005603 D-loop; other site 557598005604 H-loop/switch region; other site 557598005605 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 557598005606 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 557598005607 FtsX-like permease family; Region: FtsX; pfam02687 557598005608 putative membrane fusion protein; Region: TIGR02828 557598005609 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 557598005610 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 557598005611 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 557598005612 active site 557598005613 3-methylcrotonyl-CoA carboxylase, beta chain; Region: PLN02820 557598005614 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 557598005615 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 557598005616 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 557598005617 carboxyltransferase (CT) interaction site; other site 557598005618 biotinylation site [posttranslational modification]; other site 557598005619 Isopropylmalate/homocitrate/citramalate synthases [Amino acid transport and metabolism]; Region: LeuA; COG0119 557598005620 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 557598005621 active site 557598005622 catalytic residues [active] 557598005623 metal binding site [ion binding]; metal-binding site 557598005624 acetoacetyl-CoA synthetase; Provisional; Region: PRK03584 557598005625 Acetoacetyl-CoA synthetase (acetoacetate-CoA ligase, AACS); Region: AACS; cd05943 557598005626 acyl-activating enzyme (AAE) consensus motif; other site 557598005627 putative AMP binding site [chemical binding]; other site 557598005628 putative active site [active] 557598005629 putative CoA binding site [chemical binding]; other site 557598005630 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 557598005631 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 557598005632 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 557598005633 active site 557598005634 catalytic residues [active] 557598005635 metal binding site [ion binding]; metal-binding site 557598005636 propionyl-CoA synthetase; Provisional; Region: prpE; PRK10524 557598005637 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 557598005638 acyl-activating enzyme (AAE) consensus motif; other site 557598005639 AMP binding site [chemical binding]; other site 557598005640 active site 557598005641 CoA binding site [chemical binding]; other site 557598005642 Predicted Fe-S-cluster oxidoreductase [General function prediction only]; Region: COG0727 557598005643 tRNA-dihydrouridine synthase C; Provisional; Region: PRK10550 557598005644 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 557598005645 FMN binding site [chemical binding]; other site 557598005646 active site 557598005647 catalytic residues [active] 557598005648 substrate binding site [chemical binding]; other site 557598005649 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 557598005650 Zn2+ binding site [ion binding]; other site 557598005651 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 557598005652 non-specific DNA binding site [nucleotide binding]; other site 557598005653 salt bridge; other site 557598005654 sequence-specific DNA binding site [nucleotide binding]; other site 557598005655 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 557598005656 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 557598005657 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 557598005658 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 557598005659 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 557598005660 CDP-diglyceride synthase; Provisional; Region: cdsA; PRK11624 557598005661 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 557598005662 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 557598005663 Undecaprenyl pyrophosphate synthase [Lipid metabolism]; Region: UppS; COG0020 557598005664 catalytic residue [active] 557598005665 putative FPP diphosphate binding site; other site 557598005666 putative FPP binding hydrophobic cleft; other site 557598005667 dimer interface [polypeptide binding]; other site 557598005668 putative IPP diphosphate binding site; other site 557598005669 ribosome recycling factor; Reviewed; Region: frr; PRK00083 557598005670 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 557598005671 hinge region; other site 557598005672 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 557598005673 putative nucleotide binding site [chemical binding]; other site 557598005674 uridine monophosphate binding site [chemical binding]; other site 557598005675 homohexameric interface [polypeptide binding]; other site 557598005676 elongation factor Ts; Provisional; Region: tsf; PRK09377 557598005677 UBA/TS-N domain; Region: UBA; pfam00627 557598005678 Elongation factor TS; Region: EF_TS; pfam00889 557598005679 Elongation factor TS; Region: EF_TS; pfam00889 557598005680 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 557598005681 rRNA interaction site [nucleotide binding]; other site 557598005682 S8 interaction site; other site 557598005683 putative laminin-1 binding site; other site 557598005684 transcriptional regulator NarL; Provisional; Region: PRK10651 557598005685 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 557598005686 active site 557598005687 phosphorylation site [posttranslational modification] 557598005688 intermolecular recognition site; other site 557598005689 dimerization interface [polypeptide binding]; other site 557598005690 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 557598005691 DNA binding residues [nucleotide binding] 557598005692 dimerization interface [polypeptide binding]; other site 557598005693 Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]; Region: NarQ; COG3850 557598005694 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 557598005695 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 557598005696 dimerization interface [polypeptide binding]; other site 557598005697 GAF domain; Region: GAF_3; pfam13492 557598005698 Histidine kinase; Region: HisKA_3; pfam07730 557598005699 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 557598005700 ATP binding site [chemical binding]; other site 557598005701 Mg2+ binding site [ion binding]; other site 557598005702 G-X-G motif; other site 557598005703 ferredoxin-type protein; Provisional; Region: PRK10194 557598005704 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 557598005705 NapD protein; Region: NapD; pfam03927 557598005706 nitrate reductase catalytic subunit; Provisional; Region: PRK13532 557598005707 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 557598005708 [4Fe-4S] binding site [ion binding]; other site 557598005709 molybdopterin cofactor binding site; other site 557598005710 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 557598005711 molybdopterin cofactor binding site; other site 557598005712 quinol dehydrogenase periplasmic component; Provisional; Region: napG; PRK09476 557598005713 quinol dehydrogenase membrane component; Provisional; Region: napH; PRK09477 557598005714 4Fe-4S binding domain; Region: Fer4_5; pfam12801 557598005715 4Fe-4S binding domain; Region: Fer4_5; pfam12801 557598005716 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 557598005717 Nitrate reductase cytochrome c-type subunit (NapB); Region: NapB; pfam03892 557598005718 periplasmic nitrate (or nitrite) reductase c-type cytochrome, NapC/NirT family; Region: napC_nirT; TIGR02161 557598005719 NapC/NirT cytochrome c family, N-terminal region; Region: Cytochrom_NNT; pfam03264 557598005720 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13538 557598005721 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 557598005722 Walker A/P-loop; other site 557598005723 ATP binding site [chemical binding]; other site 557598005724 Q-loop/lid; other site 557598005725 ABC transporter signature motif; other site 557598005726 Walker B; other site 557598005727 D-loop; other site 557598005728 H-loop/switch region; other site 557598005729 CcmB protein; Region: CcmB; pfam03379 557598005730 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 557598005731 Heme exporter protein D (CcmD); Region: CcmD; cl11475 557598005732 cytochrome c-type biogenesis protein CcmE; Reviewed; Region: PRK13254 557598005733 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: CcmF; COG1138 557598005734 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 557598005735 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 557598005736 catalytic residues [active] 557598005737 central insert; other site 557598005738 Cytochrome C biogenesis protein; Region: CcmH; pfam03918 557598005739 cytochrome c-type biogenesis protein CcmI; Region: cytochro_ccmI; TIGR03142 557598005740 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: COG4235 557598005741 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 557598005742 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 557598005743 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 557598005744 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 557598005745 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 557598005746 DNA-binding site [nucleotide binding]; DNA binding site 557598005747 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 557598005748 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557598005749 homodimer interface [polypeptide binding]; other site 557598005750 catalytic residue [active] 557598005751 ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]; Region: LivK; COG0683 557598005752 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 557598005753 dimerization interface [polypeptide binding]; other site 557598005754 ligand binding site [chemical binding]; other site 557598005755 Rec8/ScpA/Scc1-like protein (kleisin family) [Replication, recombination, and repair]; Region: scpA; COG1354 557598005756 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 557598005757 active site 557598005758 HIGH motif; other site 557598005759 dimer interface [polypeptide binding]; other site 557598005760 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 557598005761 active site 557598005762 KMSKS motif; other site 557598005763 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 557598005764 Peptidase family M50; Region: Peptidase_M50; pfam02163 557598005765 active site 557598005766 putative substrate binding region [chemical binding]; other site 557598005767 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 557598005768 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 557598005769 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 557598005770 active site 557598005771 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 557598005772 Oxidoreductase-like protein, N-terminal; Region: Oxidored-like; pfam09791 557598005773 S4 domain; Region: S4_2; pfam13275 557598005774 Type I (cytosolic) bacterial L-asparaginase; Region: L-asparaginase_I; cd08963 557598005775 active site 557598005776 homodimer interface [polypeptide binding]; other site 557598005777 Diacylglycerol kinase [Cell envelope biogenesis, outer membrane]; Region: DgkA; COG0818 557598005778 O-succinylhomoserine sulfhydrylase; Validated; Region: PRK08133 557598005779 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 557598005780 homodimer interface [polypeptide binding]; other site 557598005781 substrate-cofactor binding pocket; other site 557598005782 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557598005783 catalytic residue [active] 557598005784 amidophosphoribosyltransferase; Provisional; Region: PRK09246 557598005785 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 557598005786 active site 557598005787 tetramer interface [polypeptide binding]; other site 557598005788 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 557598005789 active site 557598005790 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 557598005791 Colicin V production protein; Region: Colicin_V; pfam02674 557598005792 Sporulation related domain; Region: SPOR; pfam05036 557598005793 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 557598005794 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 557598005795 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 557598005796 ABC transporter ATPase component; Reviewed; Region: PRK11147 557598005797 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 557598005798 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 557598005799 ABC transporter; Region: ABC_tran_2; pfam12848 557598005800 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 557598005801 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 557598005802 NlpC/P60 family; Region: NLPC_P60; pfam00877 557598005803 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 557598005804 AMP binding site [chemical binding]; other site 557598005805 metal binding site [ion binding]; metal-binding site 557598005806 active site 557598005807 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 557598005808 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 557598005809 Coenzyme A binding pocket [chemical binding]; other site 557598005810 Plasmid replication region DNA-binding N-term; Region: KfrA_N; pfam11740 557598005811 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 557598005812 Int/Topo IB signature motif; other site 557598005813 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit [Inorganic ion transport and metabolism / General function prediction only]; Region: HcaE; COG4638 557598005814 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 557598005815 [2Fe-2S] cluster binding site [ion binding]; other site 557598005816 C-terminal catalytic domain of the oxygenase alpha subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases; Region: RHO_alpha_C; cd00680 557598005817 alpha subunit interface [polypeptide binding]; other site 557598005818 active site 557598005819 substrate binding site [chemical binding]; other site 557598005820 Fe binding site [ion binding]; other site 557598005821 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 557598005822 putative substrate translocation pore; other site 557598005823 Protein of unknown function (DUF342); Region: DUF342; pfam03961 557598005824 Protein of unknown function (DUF342); Region: DUF342; pfam03961 557598005825 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 557598005826 multidrug efflux system transporter AcrA; Provisional; Region: PRK15030 557598005827 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 557598005828 HlyD family secretion protein; Region: HlyD_3; pfam13437 557598005829 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 557598005830 Protein export membrane protein; Region: SecD_SecF; cl14618 557598005831 copper/silver efflux system outer membrane protein CusC; Provisional; Region: PRK09837 557598005832 transcriptional regulator BetI; Validated; Region: PRK00767 557598005833 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 557598005834 Bacterial transcriptional repressor; Region: TetR_C_6; pfam13977 557598005835 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_ox_2; pfam12900 557598005836 ATP-dependent DNA helicase DinG; Provisional; Region: dinG; PRK11747 557598005837 CRISPR/Cas system-associated DinG family helicase Csf4; Region: Csf4_U; cl17460 557598005838 DEAD_2; Region: DEAD_2; pfam06733 557598005839 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 557598005840 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 557598005841 Periplasmic binding protein domain; Region: Peripla_BP_4; pfam13407 557598005842 ligand binding site [chemical binding]; other site 557598005843 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608 557598005844 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 557598005845 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 557598005846 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 557598005847 Aminopeptidase P, N-terminal domain; Region: AMP_N; pfam05195 557598005848 proline aminopeptidase P II; Provisional; Region: PRK10879 557598005849 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 557598005850 active site 557598005851 acyl-CoA synthetase; Validated; Region: PRK08162 557598005852 Fatty acyl-CoA synthetases similar to LC-FACS from Thermus thermophiles and Arabidopsis; Region: ttLC_FACS_AEE21_like; cd12118 557598005853 acyl-activating enzyme (AAE) consensus motif; other site 557598005854 putative active site [active] 557598005855 AMP binding site [chemical binding]; other site 557598005856 putative CoA binding site [chemical binding]; other site 557598005857 protease TldD; Provisional; Region: tldD; PRK10735 557598005858 nitrilase; Region: PLN02798 557598005859 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 557598005860 putative active site [active] 557598005861 catalytic triad [active] 557598005862 dimer interface [polypeptide binding]; other site 557598005863 TIGR02099 family protein; Region: TIGR02099 557598005864 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 557598005865 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed; Region: PRK11072 557598005866 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 557598005867 metal binding triad; other site 557598005868 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 557598005869 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 557598005870 metal binding triad; other site 557598005871 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 557598005872 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 557598005873 homodimer interface [polypeptide binding]; other site 557598005874 substrate-cofactor binding pocket; other site 557598005875 catalytic residue [active] 557598005876 Zinc-finger domain; Region: zf-CHCC; cl01821 557598005877 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 557598005878 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 557598005879 putative active site [active] 557598005880 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 557598005881 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 557598005882 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 557598005883 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 557598005884 G1 box; other site 557598005885 putative GEF interaction site [polypeptide binding]; other site 557598005886 GTP/Mg2+ binding site [chemical binding]; other site 557598005887 Switch I region; other site 557598005888 G2 box; other site 557598005889 G3 box; other site 557598005890 Switch II region; other site 557598005891 G4 box; other site 557598005892 G5 box; other site 557598005893 Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to...; Region: Translation_Factor_II_like; cl02787 557598005894 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 557598005895 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 557598005896 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 557598005897 active site 557598005898 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 557598005899 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 557598005900 substrate binding site [chemical binding]; other site 557598005901 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 557598005902 substrate binding site [chemical binding]; other site 557598005903 ligand binding site [chemical binding]; other site 557598005904 aconitate hydratase; Validated; Region: PRK09277 557598005905 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 557598005906 substrate binding site [chemical binding]; other site 557598005907 ligand binding site [chemical binding]; other site 557598005908 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 557598005909 substrate binding site [chemical binding]; other site 557598005910 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 557598005911 Beta-eliminating lyase; Region: Beta_elim_lyase; pfam01212 557598005912 tetramer interface [polypeptide binding]; other site 557598005913 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557598005914 catalytic residue [active] 557598005915 EamA-like transporter family; Region: EamA; pfam00892 557598005916 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 557598005917 PAS fold; Region: PAS_3; pfam08447 557598005918 putative active site [active] 557598005919 heme pocket [chemical binding]; other site 557598005920 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 557598005921 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 557598005922 Hydrolases of the alpha/beta superfamily [General function prediction only]; Region: COG1073 557598005923 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 557598005924 Uncharacterized conserved protein [Function unknown]; Region: COG4925 557598005925 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 557598005926 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 557598005927 putative substrate translocation pore; other site 557598005928 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557598005929 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 557598005930 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 557598005931 putative effector binding pocket; other site 557598005932 putative dimerization interface [polypeptide binding]; other site 557598005933 Cache domain; Region: Cache_1; pfam02743 557598005934 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 557598005935 dimerization interface [polypeptide binding]; other site 557598005936 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 557598005937 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557598005938 dimer interface [polypeptide binding]; other site 557598005939 putative CheW interface [polypeptide binding]; other site 557598005940 putative NAD(P)H quinone oxidoreductase, PIG3 family; Region: quinone_pig3; TIGR02824 557598005941 PIG3 p53-inducible quinone oxidoreductase; Region: p53_inducible_oxidoreductase; cd05276 557598005942 NAD(P) binding site [chemical binding]; other site 557598005943 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 557598005944 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 557598005945 N-carbamoylputrescine amidohydrolase (CPA) (class 11 nitrilases); Region: CPA; cd07573 557598005946 N-carbamoylputrescine amidase; Region: agmatine_aguB; TIGR03381 557598005947 putative active site; other site 557598005948 catalytic triad [active] 557598005949 putative dimer interface [polypeptide binding]; other site 557598005950 argininosuccinate synthase; Provisional; Region: PRK13820 557598005951 Argininosuccinate synthase. The Argininosuccinate synthase is a urea cycle enzyme that catalyzes the penultimate step in arginine biosynthesis: the ATP-dependent ligation of citrulline to aspartate to form argininosuccinate, AMP and pyrophosphate . In...; Region: Argininosuccinate_Synthase; cd01999 557598005952 ANP binding site [chemical binding]; other site 557598005953 Substrate Binding Site II [chemical binding]; other site 557598005954 Substrate Binding Site I [chemical binding]; other site 557598005955 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 557598005956 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 557598005957 putative substrate translocation pore; other site 557598005958 DNA-binding transcriptional regulator HcaR; Provisional; Region: PRK09906 557598005959 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 557598005960 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 557598005961 dimerization interface [polypeptide binding]; other site 557598005962 substrate binding pocket [chemical binding]; other site 557598005963 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 557598005964 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 557598005965 IHF dimer interface [polypeptide binding]; other site 557598005966 IHF - DNA interface [nucleotide binding]; other site 557598005967 Predicted glutamine amidotransferase [General function prediction only]; Region: COG0121 557598005968 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 557598005969 putative active site [active] 557598005970 putative dimer interface [polypeptide binding]; other site 557598005971 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 557598005972 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 557598005973 putative C-terminal domain interface [polypeptide binding]; other site 557598005974 putative GSH binding site (G-site) [chemical binding]; other site 557598005975 putative dimer interface [polypeptide binding]; other site 557598005976 C-terminal, alpha helical domain of an unknown subfamily 3 of Glutathione S-transferases; Region: GST_C_3; cd03194 557598005977 putative substrate binding pocket (H-site) [chemical binding]; other site 557598005978 putative N-terminal domain interface [polypeptide binding]; other site 557598005979 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 557598005980 active site 557598005981 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 557598005982 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 557598005983 dimerization interface [polypeptide binding]; other site 557598005984 domain crossover interface; other site 557598005985 redox-dependent activation switch; other site 557598005986 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK11790 557598005987 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_3; cd12176 557598005988 ligand binding site [chemical binding]; other site 557598005989 NAD binding site [chemical binding]; other site 557598005990 tetramer interface [polypeptide binding]; other site 557598005991 catalytic site [active] 557598005992 C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria; Region: ACT_3PGDH; cd04901 557598005993 L-serine binding site [chemical binding]; other site 557598005994 ACT domain interface; other site 557598005995 Predicted membrane protein [Function unknown]; Region: COG2119 557598005996 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 557598005997 Uncharacterized protein family UPF0016; Region: UPF0016; pfam01169 557598005998 Acylphosphatase; Region: Acylphosphatase; pfam00708 557598005999 transcription elongation factor GreB; Reviewed; Region: greB; PRK01885 557598006000 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 557598006001 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 557598006002 NlpE N-terminal domain; Region: NlpE; pfam04170 557598006003 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 557598006004 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 557598006005 RNA binding surface [nucleotide binding]; other site 557598006006 Pseudouridine synthase, Escherichia coli RluB like; Region: PseudoU_synth_RluB; cd02556 557598006007 probable active site [active] 557598006008 Putative transcriptional regulators (Ypuh-like); Region: DUF387; pfam04079 557598006009 nucleoside diphosphate kinase regulator; Provisional; Region: PRK05753 557598006010 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 557598006011 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 557598006012 active site 557598006013 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3127 557598006014 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG3127 557598006015 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG4181 557598006016 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 557598006017 Walker A/P-loop; other site 557598006018 ATP binding site [chemical binding]; other site 557598006019 Q-loop/lid; other site 557598006020 ABC transporter signature motif; other site 557598006021 Walker B; other site 557598006022 D-loop; other site 557598006023 H-loop/switch region; other site 557598006024 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 557598006025 active site 557598006026 catalytic triad [active] 557598006027 oxyanion hole [active] 557598006028 switch loop; other site 557598006029 Protein of unknown function (DUF2799); Region: DUF2799; pfam10973 557598006030 Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which...; Region: ZnMc; cl00064 557598006031 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 557598006032 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 557598006033 dimer interface [polypeptide binding]; other site 557598006034 phosphorylation site [posttranslational modification] 557598006035 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 557598006036 ATP binding site [chemical binding]; other site 557598006037 Mg2+ binding site [ion binding]; other site 557598006038 G-X-G motif; other site 557598006039 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 557598006040 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 557598006041 active site 557598006042 phosphorylation site [posttranslational modification] 557598006043 intermolecular recognition site; other site 557598006044 dimerization interface [polypeptide binding]; other site 557598006045 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 557598006046 DNA binding site [nucleotide binding] 557598006047 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 557598006048 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 557598006049 Methyltransferase domain; Region: Methyltransf_18; pfam12847 557598006050 flagellar motor protein MotB; Validated; Region: motB; PRK09041 557598006051 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 557598006052 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 557598006053 ligand binding site [chemical binding]; other site 557598006054 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 557598006055 flagellar motor protein MotA; Validated; Region: PRK09110 557598006056 Glutamine synthetase [Amino acid transport and metabolism]; Region: GlnA; COG0174 557598006057 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 557598006058 putative aminotransferase; Validated; Region: PRK07480 557598006059 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 557598006060 inhibitor-cofactor binding pocket; inhibition site 557598006061 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557598006062 catalytic residue [active] 557598006063 Peptidase C26; Region: Peptidase_C26; pfam07722 557598006064 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 557598006065 catalytic triad [active] 557598006066 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 557598006067 Alanine dehydrogenase NAD-binding and catalytic domains; Region: L-AlaDH; cd05305 557598006068 hexamer interface [polypeptide binding]; other site 557598006069 ligand binding site [chemical binding]; other site 557598006070 putative active site [active] 557598006071 NAD(P) binding site [chemical binding]; other site 557598006072 Cupin domain; Region: Cupin_2; pfam07883 557598006073 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase; Provisional; Region: PRK09847 557598006074 Escherichia coli NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PuuC-like; Region: ALDH_GABALDH-PuuC; cd07112 557598006075 NAD(P) binding site [chemical binding]; other site 557598006076 catalytic residues [active] 557598006077 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 557598006078 active site residue [active] 557598006079 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 557598006080 dimerization interface [polypeptide binding]; other site 557598006081 putative DNA binding site [nucleotide binding]; other site 557598006082 putative Zn2+ binding site [ion binding]; other site 557598006083 Uncharacterized homolog of gamma-carboxymuconolactone decarboxylase subunit [Function unknown]; Region: COG0599 557598006084 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 557598006085 Uncharacterized conserved protein [Function unknown]; Region: COG1434 557598006086 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 557598006087 putative active site [active] 557598006088 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 557598006089 pseudouridine synthase, RluA family; Region: rluA_subfam; TIGR00005 557598006090 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 557598006091 RNA binding surface [nucleotide binding]; other site 557598006092 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 557598006093 active site 557598006094 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 557598006095 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 557598006096 Protein of unknown function (DUF2946); Region: DUF2944; pfam11161 557598006097 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 557598006098 DNA-binding site [nucleotide binding]; DNA binding site 557598006099 RNA-binding motif; other site 557598006100 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 557598006101 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 557598006102 dimer interface [polypeptide binding]; other site 557598006103 conserved gate region; other site 557598006104 putative PBP binding loops; other site 557598006105 ABC-ATPase subunit interface; other site 557598006106 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 557598006107 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 557598006108 substrate binding pocket [chemical binding]; other site 557598006109 membrane-bound complex binding site; other site 557598006110 hinge residues; other site 557598006111 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 557598006112 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 557598006113 Likely ribonuclease with RNase H fold; Region: YqgFc; smart00732 557598006114 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 557598006115 RNA binding site [nucleotide binding]; other site 557598006116 Protein of unknown function (DUF3478); Region: DUF3478; pfam11964 557598006117 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 557598006118 EamA-like transporter family; Region: EamA; pfam00892 557598006119 putative sulfite oxidase subunit YedZ; Reviewed; Region: PRK05419 557598006120 TMAO/DMSO reductase; Reviewed; Region: PRK05363 557598006121 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 557598006122 Moco binding site; other site 557598006123 metal coordination site [ion binding]; other site 557598006124 Putative p-aminobenzoyl-glutamate transporter [Coenzyme metabolism]; Region: AbgT; COG2978 557598006125 p-Aminobenzoyl-glutamate transporter family; Region: ydaH; TIGR00819 557598006126 Di- and tripeptidases [Amino acid transport and metabolism]; Region: PepD; COG2195 557598006127 M20 Peptidase T specifically cleaves tripeptides; Region: M20_peptT; cd03892 557598006128 metal binding site [ion binding]; metal-binding site 557598006129 dimer interface [polypeptide binding]; other site 557598006130 YhgE/Pip N-terminal domain; Region: pip_yhgE_Nterm; TIGR03061 557598006131 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 557598006132 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 557598006133 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 557598006134 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 557598006135 Walker A/P-loop; other site 557598006136 ATP binding site [chemical binding]; other site 557598006137 Q-loop/lid; other site 557598006138 ABC transporter signature motif; other site 557598006139 Walker B; other site 557598006140 D-loop; other site 557598006141 H-loop/switch region; other site 557598006142 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 557598006143 Walker A/P-loop; other site 557598006144 ATP binding site [chemical binding]; other site 557598006145 Q-loop/lid; other site 557598006146 ABC transporter signature motif; other site 557598006147 Walker B; other site 557598006148 D-loop; other site 557598006149 H-loop/switch region; other site 557598006150 YhgE/Pip N-terminal domain; Region: pip_yhgE_Nterm; TIGR03061 557598006151 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 557598006152 ABC-2 family transporter protein; Region: ABC2_membrane_2; pfam12679 557598006153 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 557598006154 putative efflux pump membrane fusion protein; Provisional; Region: PRK03598 557598006155 HlyD family secretion protein; Region: HlyD_3; pfam13437 557598006156 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 557598006157 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 557598006158 dihydroxy-acid dehydratase; Provisional; Region: PRK12448 557598006159 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 557598006160 Cytochrome oxidase maturation protein cbb3-type; Region: CcoS; pfam03597 557598006161 Na+/H+ antiporter family; Region: Na_H_antiporter; pfam03553 557598006162 CYTH-like Clostridium thermocellum TTM-like subgroup 1; Region: CYTH-like_CthTTM-like_1; cd07891 557598006163 putative active site [active] 557598006164 putative metal binding residues [ion binding]; other site 557598006165 signature motif; other site 557598006166 putative dimer interface [polypeptide binding]; other site 557598006167 putative phosphate binding site [ion binding]; other site 557598006168 PAS fold; Region: PAS_4; pfam08448 557598006169 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 557598006170 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 557598006171 Walker A motif; other site 557598006172 ATP binding site [chemical binding]; other site 557598006173 Walker B motif; other site 557598006174 arginine finger; other site 557598006175 cytochrome d terminal oxidase subunit 1; Provisional; Region: PRK15097 557598006176 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 557598006177 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 557598006178 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 557598006179 This CD represents a family of iron-molybdenum cluster-binding proteins that includes NifB, NifX, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. This...; Region: NifX_NifB; cd00562 557598006180 Membrane bound YbgT-like protein; Region: YbgT_YccB; pfam08173 557598006181 Cyd operon protein YbgE (Cyd_oper_YbgE); Region: Cyd_oper_YbgE; cl11451 557598006182 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK09263 557598006183 ATP cone domain; Region: ATP-cone; pfam03477 557598006184 Class III ribonucleotide reductase; Region: RNR_III; cd01675 557598006185 effector binding site; other site 557598006186 active site 557598006187 Zn binding site [ion binding]; other site 557598006188 glycine loop; other site 557598006189 anaerobic ribonucleotide reductase-activating protein; Provisional; Region: nrdG; PRK11121 557598006190 4Fe-4S single cluster domain; Region: Fer4_12; pfam13353 557598006191 adenosine nucleotide hydrolase NudE; Provisional; Region: nudE; PRK11762 557598006192 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 557598006193 dimer interface [polypeptide binding]; other site 557598006194 ADP-ribose binding site [chemical binding]; other site 557598006195 active site 557598006196 nudix motif; other site 557598006197 metal binding site [ion binding]; metal-binding site 557598006198 Uncharacterized protein conserved in bacteria (DUF2062); Region: DUF2062; pfam09835 557598006199 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 557598006200 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 557598006201 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 557598006202 active site 557598006203 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 557598006204 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 557598006205 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 557598006206 Serine dehydratase alpha chain; Region: SDH_alpha; pfam03313 557598006207 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 557598006208 putative active site [active] 557598006209 dimerization interface [polypeptide binding]; other site 557598006210 putative tRNAtyr binding site [nucleotide binding]; other site 557598006211 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 557598006212 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 557598006213 homotrimer interaction site [polypeptide binding]; other site 557598006214 putative active site [active] 557598006215 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed; Region: PRK11856 557598006216 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 557598006217 E3 interaction surface; other site 557598006218 lipoyl attachment site [posttranslational modification]; other site 557598006219 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 557598006220 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 557598006221 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 557598006222 alpha subunit interface [polypeptide binding]; other site 557598006223 TPP binding site [chemical binding]; other site 557598006224 heterodimer interface [polypeptide binding]; other site 557598006225 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 557598006226 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_x; TIGR03181 557598006227 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 557598006228 tetramer interface [polypeptide binding]; other site 557598006229 TPP-binding site [chemical binding]; other site 557598006230 heterodimer interface [polypeptide binding]; other site 557598006231 phosphorylation loop region [posttranslational modification] 557598006232 Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; Region: DNA_polB_like1_exo; cd05782 557598006233 active site 557598006234 catalytic site [active] 557598006235 substrate binding site [chemical binding]; other site 557598006236 Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; Region: DNA_pol_B_exo2; pfam10108 557598006237 alpha/beta hydrolase fold; Region: Abhydrolase_1; pfam00561 557598006238 Serine hydrolase; Region: Ser_hydrolase; cl17834 557598006239 CHASE domain; Region: CHASE; pfam03924 557598006240 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 557598006241 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 557598006242 putative active site [active] 557598006243 heme pocket [chemical binding]; other site 557598006244 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 557598006245 dimer interface [polypeptide binding]; other site 557598006246 phosphorylation site [posttranslational modification] 557598006247 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 557598006248 ATP binding site [chemical binding]; other site 557598006249 Mg2+ binding site [ion binding]; other site 557598006250 G-X-G motif; other site 557598006251 Response regulator [Signal transduction mechanisms]; Region: TtrR; COG4566 557598006252 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 557598006253 active site 557598006254 phosphorylation site [posttranslational modification] 557598006255 intermolecular recognition site; other site 557598006256 dimerization interface [polypeptide binding]; other site 557598006257 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 557598006258 DNA binding residues [nucleotide binding] 557598006259 dimerization interface [polypeptide binding]; other site 557598006260 ATP-dependent helicase HrpA; Region: DEAH_box_HrpA; TIGR01967 557598006261 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 557598006262 ATP binding site [chemical binding]; other site 557598006263 putative Mg++ binding site [ion binding]; other site 557598006264 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 557598006265 nucleotide binding region [chemical binding]; other site 557598006266 Helicase associated domain (HA2); Region: HA2; pfam04408 557598006267 Oligonucleotide/oligosaccharide-binding (OB)-fold; Region: OB_NTP_bind; pfam07717 557598006268 Domain of unknown function (DUF3418); Region: DUF3418; pfam11898 557598006269 formate--tetrahydrofolate ligase; Provisional; Region: PRK13505 557598006270 Formyltetrahydrofolate synthetase (FTHFS) catalyzes the ATP-dependent activation of formate ion via its addition to the N10 position of tetrahydrofolate. FTHFS is a highly expressed key enzyme in both the Wood-Ljungdahl pathway of autotrophic CO2...; Region: FTHFS; cd00477 557598006271 Potassium binding sites [ion binding]; other site 557598006272 Cesium cation binding sites [ion binding]; other site 557598006273 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 557598006274 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 557598006275 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 557598006276 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 557598006277 active site 557598006278 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 557598006279 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 557598006280 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 557598006281 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 557598006282 trimer interface [polypeptide binding]; other site 557598006283 active site 557598006284 UDP-GlcNAc binding site [chemical binding]; other site 557598006285 lipid binding site [chemical binding]; lipid-binding site 557598006286 periplasmic chaperone; Provisional; Region: PRK10780 557598006287 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 557598006288 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 557598006289 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 557598006290 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 557598006291 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 557598006292 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 557598006293 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 557598006294 Surface antigen; Region: Bac_surface_Ag; pfam01103 557598006295 zinc metallopeptidase RseP; Provisional; Region: PRK10779 557598006296 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 557598006297 active site 557598006298 PDZ domain of bacterial and plant zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ...; Region: PDZ_metalloprotease; cd00989 557598006299 PDZ domain of bacterial and plant zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ...; Region: PDZ_metalloprotease; cd00989 557598006300 protein binding site [polypeptide binding]; other site 557598006301 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 557598006302 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 557598006303 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557598006304 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 557598006305 The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold; Region: PBP2_YofA_SoxR_like; cd08442 557598006306 putative dimerization interface [polypeptide binding]; other site 557598006307 Protein of unknown function (DUF1228); Region: DUF1228; pfam06779 557598006308 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 557598006309 active site 1 [active] 557598006310 dimer interface [polypeptide binding]; other site 557598006311 hexamer interface [polypeptide binding]; other site 557598006312 active site 2 [active] 557598006313 Uncharacterized membrane protein, required for spore maturation in B.subtilis. [General function prediction only]; Region: SpmA; COG2715 557598006314 Uncharacterized membrane protein [Function unknown]; Region: SpmB; cl17667 557598006315 Uncharacterized membrane protein [Function unknown]; Region: SpmB; cl17667 557598006316 Chorismate mutase type II; Region: CM_2; cl00693 557598006317 Multiple antibiotic transporter [Intracellular trafficking and secretion]; Region: MarC; COG2095 557598006318 multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed; Region: cca; PRK10885 557598006319 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 557598006320 active site 557598006321 NTP binding site [chemical binding]; other site 557598006322 metal binding triad [ion binding]; metal-binding site 557598006323 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 557598006324 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; smart00471 557598006325 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2258 557598006326 MOSC domain; Region: MOSC; pfam03473 557598006327 hypothetical protein; Validated; Region: PRK02101 557598006328 putative cation:proton antiport protein; Provisional; Region: PRK10669 557598006329 Kef-type K+ transport system, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: RosB; COG4651 557598006330 TrkA-N domain; Region: TrkA_N; pfam02254 557598006331 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 557598006332 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 557598006333 dimer interface [polypeptide binding]; other site 557598006334 putative functional site; other site 557598006335 putative MPT binding site; other site 557598006336 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 557598006337 Walker A motif; other site 557598006338 hypothetical protein; Provisional; Region: PRK08960 557598006339 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 557598006340 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557598006341 homodimer interface [polypeptide binding]; other site 557598006342 catalytic residue [active] 557598006343 GMC oxidoreductase; Region: GMC_oxred_N; pfam00732 557598006344 dehydrogenase, Rv0697 family; Region: Rv0697; TIGR03970 557598006345 GMC oxidoreductase; Region: GMC_oxred_C; pfam05199 557598006346 Coniferyl aldehyde dehydrogenase-like; Region: ALDH_CALDH_CalB; cd07133 557598006347 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 557598006348 NAD(P) binding site [chemical binding]; other site 557598006349 catalytic residues [active] 557598006350 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3825 557598006351 YfaZ precursor; Region: YfaZ; pfam07437 557598006352 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 557598006353 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 557598006354 tetramer interface [polypeptide binding]; other site 557598006355 active site 557598006356 Mg2+/Mn2+ binding site [ion binding]; other site 557598006357 Cupin domain; Region: Cupin_2; pfam07883 557598006358 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 557598006359 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 557598006360 dimer interface [polypeptide binding]; other site 557598006361 active site 557598006362 citrylCoA binding site [chemical binding]; other site 557598006363 oxalacetate/citrate binding site [chemical binding]; other site 557598006364 coenzyme A binding site [chemical binding]; other site 557598006365 catalytic triad [active] 557598006366 2-methylisocitrate dehydratase, Fe/S-dependent; Region: 2met_isocit_dHY; TIGR02333 557598006367 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 557598006368 substrate binding site [chemical binding]; other site 557598006369 ligand binding site [chemical binding]; other site 557598006370 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 557598006371 substrate binding site [chemical binding]; other site 557598006372 probable AcnD-accessory protein PrpF; Region: prpF; TIGR02334 557598006373 Integrase core domain; Region: rve; pfam00665 557598006374 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 557598006375 Integrase core domain; Region: rve_3; pfam13683 557598006376 Competence-damaged protein; Region: CinA; pfam02464 557598006377 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 557598006378 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 557598006379 active site 557598006380 dimer interface [polypeptide binding]; other site 557598006381 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 557598006382 dimer interface [polypeptide binding]; other site 557598006383 active site 557598006384 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 557598006385 active site 557598006386 substrate binding site [chemical binding]; other site 557598006387 catalytic site [active] 557598006388 short chain dehydrogenase; Provisional; Region: PRK05993 557598006389 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 557598006390 NADP binding site [chemical binding]; other site 557598006391 active site 557598006392 steroid binding site; other site 557598006393 integral membrane protein, TerC family; Region: R_switched_Alx; TIGR03718 557598006394 Long-chain fatty acid transport protein [Lipid metabolism]; Region: FadL; COG2067 557598006395 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 557598006396 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 557598006397 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 557598006398 substrate binding pocket [chemical binding]; other site 557598006399 chain length determination region; other site 557598006400 substrate-Mg2+ binding site; other site 557598006401 catalytic residues [active] 557598006402 aspartate-rich region 1; other site 557598006403 active site lid residues [active] 557598006404 aspartate-rich region 2; other site 557598006405 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 557598006406 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 557598006407 TPP-binding site; other site 557598006408 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 557598006409 PYR/PP interface [polypeptide binding]; other site 557598006410 dimer interface [polypeptide binding]; other site 557598006411 TPP binding site [chemical binding]; other site 557598006412 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 557598006413 Predicted membrane protein [Function unknown]; Region: COG3174 557598006414 Domain of unknown function (DUF4010); Region: DUF4010; pfam13194 557598006415 putative GTP cyclohydrolase; Provisional; Region: PRK13674 557598006416 thiamine biosynthesis protein ThiH; Reviewed; Region: thiH; PRK09240 557598006417 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 557598006418 FeS/SAM binding site; other site 557598006419 Biotin and Thiamin Synthesis associated domain; Region: BATS; pfam06968 557598006420 [FeFe] hydrogenase H-cluster maturation GTPase HydF; Region: GTP_HydF; TIGR03918 557598006421 E. coli Ras-like protein (Era)-like GTPase; Region: Era_like; cd00880 557598006422 G1 box; other site 557598006423 GTP/Mg2+ binding site [chemical binding]; other site 557598006424 Switch I region; other site 557598006425 G2 box; other site 557598006426 Switch II region; other site 557598006427 G3 box; other site 557598006428 G4 box; other site 557598006429 G5 box; other site 557598006430 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 557598006431 catalytic loop [active] 557598006432 iron binding site [ion binding]; other site 557598006433 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 557598006434 [FeFe] hydrogenase, group A; Region: FeFe_hydrog_A; TIGR02512 557598006435 4Fe-4S binding domain; Region: Fer4; pfam00037 557598006436 Iron only hydrogenase large subunit, C-terminal domain; Region: Fe_hyd_lg_C; pfam02906 557598006437 Iron hydrogenase small subunit; Region: Fe_hyd_SSU; pfam02256 557598006438 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; pfam10589 557598006439 putative oxidoreductase; Provisional; Region: PRK12831 557598006440 biotin synthase; Provisional; Region: PRK07094 557598006441 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 557598006442 FeS/SAM binding site; other site 557598006443 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 557598006444 Periplasmic lysozyme inhibitor, I-type (PliI) and similar proteins; Region: PliI_like; cd09632 557598006445 dimer interface [polypeptide binding]; other site 557598006446 putative inhibitory loop; other site 557598006447 Bacterial inner membrane protein; Region: Imp-YgjV; pfam10688 557598006448 hypothetical protein; Provisional; Region: PRK01254 557598006449 Radical SAM N-terminal; Region: Radical_SAM_N; pfam08497 557598006450 Domain of unknown function (DUF3362); Region: DUF3362; pfam11842 557598006451 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 557598006452 feedback inhibition sensing region; other site 557598006453 homohexameric interface [polypeptide binding]; other site 557598006454 nucleotide binding site [chemical binding]; other site 557598006455 N-acetyl-L-glutamate binding site [chemical binding]; other site 557598006456 N-acetylglutamate synthase; Validated; Region: PRK05279 557598006457 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 557598006458 putative feedback inhibition sensing region; other site 557598006459 putative nucleotide binding site [chemical binding]; other site 557598006460 putative substrate binding site [chemical binding]; other site 557598006461 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 557598006462 Coenzyme A binding pocket [chemical binding]; other site 557598006463 Quinol:fumarate reductase (QFR) Type B subfamily, transmembrane subunit; QFR couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, the opposite reaction to that catalyzed by the related protein, succinate:quinone...; Region: QFR_TypeB_TM; cd00581 557598006464 Iron-sulfur protein interface; other site 557598006465 proximal heme binding site [chemical binding]; other site 557598006466 distal heme binding site [chemical binding]; other site 557598006467 dimer interface [polypeptide binding]; other site 557598006468 fumarate reductase flavoprotein subunit; Provisional; Region: PRK08626 557598006469 L-aspartate oxidase; Provisional; Region: PRK06175 557598006470 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 557598006471 fumarate reductase iron-sulfur subunit; Provisional; Region: frdB; PRK13552 557598006472 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 557598006473 catalytic loop [active] 557598006474 iron binding site [ion binding]; other site 557598006475 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 557598006476 SurA N-terminal domain; Region: SurA_N_3; cl07813 557598006477 periplasmic folding chaperone; Provisional; Region: PRK10788 557598006478 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 557598006479 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 557598006480 IHF dimer interface [polypeptide binding]; other site 557598006481 IHF - DNA interface [nucleotide binding]; other site 557598006482 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 557598006483 Found in ATP-dependent protease La (LON); Region: LON; smart00464 557598006484 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 557598006485 Walker A motif; other site 557598006486 ATP binding site [chemical binding]; other site 557598006487 Walker B motif; other site 557598006488 arginine finger; other site 557598006489 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 557598006490 hypothetical protein; Validated; Region: PRK00110 557598006491 flagellar biosynthesis protein FliR; Reviewed; Region: fliR; PRK05701 557598006492 flagellar biosynthesis protein FliQ; Validated; Region: fliQ; PRK05700 557598006493 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 557598006494 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK05699 557598006495 Flagellar biosynthesis protein, FliO; Region: FliO; cl01247 557598006496 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 557598006497 flagellar motor switch protein; Validated; Region: fliN; PRK05698 557598006498 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 557598006499 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 557598006500 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 557598006501 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 557598006502 Flagellar biosynthesis chaperone [Cell motility and secretion / Intracellular trafficking and secretion / Posttranslational modification, protein turnover, chaperones]; Region: FliJ; COG2882 557598006503 flagellar biosynthesis chaperone; Validated; Region: fliJ; PRK05689 557598006504 flagellar protein export ATPase FliI; Region: FliI_clade1; TIGR03496 557598006505 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 557598006506 Walker A motif/ATP binding site; other site 557598006507 Walker B motif; other site 557598006508 Flagellar assembly protein FliH; Region: FliH; pfam02108 557598006509 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 557598006510 MgtE intracellular N domain; Region: MgtE_N; cl15244 557598006511 FliG C-terminal domain; Region: FliG_C; pfam01706 557598006512 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 557598006513 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; pfam01514 557598006514 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 557598006515 flagellar hook-basal body protein FliE; Reviewed; Region: fliE; PRK00253 557598006516 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 557598006517 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 557598006518 active site 557598006519 phosphorylation site [posttranslational modification] 557598006520 intermolecular recognition site; other site 557598006521 dimerization interface [polypeptide binding]; other site 557598006522 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 557598006523 Walker A motif; other site 557598006524 ATP binding site [chemical binding]; other site 557598006525 Walker B motif; other site 557598006526 arginine finger; other site 557598006527 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 557598006528 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 557598006529 CheB methylesterase; Region: CheB_methylest; pfam01339 557598006530 PAS fold; Region: PAS_3; pfam08447 557598006531 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 557598006532 PAS domain; Region: PAS_9; pfam13426 557598006533 putative active site [active] 557598006534 heme pocket [chemical binding]; other site 557598006535 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 557598006536 PAS domain; Region: PAS_9; pfam13426 557598006537 putative active site [active] 557598006538 heme pocket [chemical binding]; other site 557598006539 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 557598006540 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557598006541 metal binding site [ion binding]; metal-binding site 557598006542 active site 557598006543 I-site; other site 557598006544 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 557598006545 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 557598006546 Low molecular weight phosphatase family; Region: LMWPc; cd00115 557598006547 active site 557598006548 OsmC-like protein; Region: OsmC; cl00767 557598006549 UGMP family protein; Validated; Region: PRK09604 557598006550 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 557598006551 recombination factor protein RarA; Reviewed; Region: PRK13342 557598006552 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 557598006553 Walker A motif; other site 557598006554 ATP binding site [chemical binding]; other site 557598006555 Walker B motif; other site 557598006556 arginine finger; other site 557598006557 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 557598006558 Acyltransferase family; Region: Acyl_transf_3; pfam01757 557598006559 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 557598006560 putative active site [active] 557598006561 class III alcohol dehydrogenases; Region: alcohol_DH_class_III; cd08300 557598006562 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase; Region: adh_III_F_hyde; TIGR02818 557598006563 substrate binding site [chemical binding]; other site 557598006564 catalytic Zn binding site [ion binding]; other site 557598006565 NAD binding site [chemical binding]; other site 557598006566 structural Zn binding site [ion binding]; other site 557598006567 dimer interface [polypeptide binding]; other site 557598006568 S-formylglutathione hydrolase; Region: PLN02442 557598006569 S-formylglutathione hydrolase; Region: fghA_ester_D; TIGR02821 557598006570 protoporphyrinogen oxidase; Region: PLN02576 557598006571 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 557598006572 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 557598006573 acyl-CoA binding pocket [chemical binding]; other site 557598006574 CoA binding site [chemical binding]; other site 557598006575 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 557598006576 tetramer interfaces [polypeptide binding]; other site 557598006577 binuclear metal-binding site [ion binding]; other site 557598006578 thiamine monophosphate kinase; Provisional; Region: PRK05731 557598006579 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 557598006580 ATP binding site [chemical binding]; other site 557598006581 dimerization interface [polypeptide binding]; other site 557598006582 transcription antitermination protein NusB; Reviewed; Region: nusB; PRK00202 557598006583 putative RNA binding site [nucleotide binding]; other site 557598006584 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 557598006585 homopentamer interface [polypeptide binding]; other site 557598006586 active site 557598006587 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein; Provisional; Region: PRK14019 557598006588 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 557598006589 GTP cyclohydrolase II; Region: GTP_cyclohydro2; pfam00925 557598006590 dimerization interface [polypeptide binding]; other site 557598006591 active site 557598006592 Predicted ATPases of PP-loop superfamily [General function prediction only]; Region: COG2102 557598006593 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_IV; cd01994 557598006594 Ligand Binding Site [chemical binding]; other site 557598006595 riboflavin synthase subunit alpha; Provisional; Region: PRK13020 557598006596 Lumazine binding domain; Region: Lum_binding; pfam00677 557598006597 Lumazine binding domain; Region: Lum_binding; pfam00677 557598006598 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 557598006599 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 557598006600 G1 box; other site 557598006601 putative GEF interaction site [polypeptide binding]; other site 557598006602 GTP/Mg2+ binding site [chemical binding]; other site 557598006603 Switch I region; other site 557598006604 G2 box; other site 557598006605 G3 box; other site 557598006606 Switch II region; other site 557598006607 G4 box; other site 557598006608 G5 box; other site 557598006609 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 557598006610 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 557598006611 Mechanosensitive ion channel; Region: MS_channel; pfam00924 557598006612 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 557598006613 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 557598006614 Bacterial transcriptional repressor; Region: TetR; pfam13972 557598006615 ssDNA exonuclease RecJ; Provisional; Region: PRK11070 557598006616 DHH family; Region: DHH; pfam01368 557598006617 DHHA1 domain; Region: DHHA1; pfam02272 557598006618 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4255 557598006619 putative peptidase; Provisional; Region: PRK11649 557598006620 Peptidase family M23; Region: Peptidase_M23; pfam01551 557598006621 anhydro-N-acetylmuramic acid kinase; Reviewed; Region: anmK; PRK09585 557598006622 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 557598006623 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 557598006624 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 557598006625 ferrochelatase; Reviewed; Region: hemH; PRK00035 557598006626 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 557598006627 C-terminal domain interface [polypeptide binding]; other site 557598006628 active site 557598006629 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 557598006630 active site 557598006631 N-terminal domain interface [polypeptide binding]; other site 557598006632 aminopeptidase N; Provisional; Region: pepN; PRK14015 557598006633 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_1; cd09600 557598006634 active site 557598006635 Zn binding site [ion binding]; other site 557598006636 SCP-2 sterol transfer family; Region: SCP2; pfam02036 557598006637 Transcriptional regulators [Transcription]; Region: GntR; COG1802 557598006638 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 557598006639 DNA-binding site [nucleotide binding]; DNA binding site 557598006640 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 557598006641 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 557598006642 ligand binding site [chemical binding]; other site 557598006643 flexible hinge region; other site 557598006644 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 557598006645 non-specific DNA interactions [nucleotide binding]; other site 557598006646 DNA binding site [nucleotide binding] 557598006647 sequence specific DNA binding site [nucleotide binding]; other site 557598006648 putative cAMP binding site [chemical binding]; other site 557598006649 putative 23S rRNA C2498 ribose 2'-O-ribose methyltransferase; Provisional; Region: PRK11760 557598006650 FtsJ-like methyltransferase; Region: FtsJ; pfam01728 557598006651 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 557598006652 CoA binding domain; Region: CoA_binding; smart00881 557598006653 CoA-ligase; Region: Ligase_CoA; pfam00549 557598006654 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 557598006655 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 557598006656 CoA-ligase; Region: Ligase_CoA; pfam00549 557598006657 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 557598006658 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 557598006659 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 557598006660 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 557598006661 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 557598006662 E3 interaction surface; other site 557598006663 lipoyl attachment site [posttranslational modification]; other site 557598006664 e3 binding domain; Region: E3_binding; pfam02817 557598006665 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 557598006666 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 557598006667 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 557598006668 TPP-binding site [chemical binding]; other site 557598006669 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 557598006670 dimer interface [polypeptide binding]; other site 557598006671 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 557598006672 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 557598006673 dimer interface [polypeptide binding]; other site 557598006674 active site 557598006675 citrylCoA binding site [chemical binding]; other site 557598006676 NADH binding [chemical binding]; other site 557598006677 cationic pore residues; other site 557598006678 oxalacetate/citrate binding site [chemical binding]; other site 557598006679 coenzyme A binding site [chemical binding]; other site 557598006680 catalytic triad [active] 557598006681 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 557598006682 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 557598006683 Uncharacterized conserved protein [Function unknown]; Region: COG2938 557598006684 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK07057 557598006685 L-aspartate oxidase; Provisional; Region: PRK06175 557598006686 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 557598006687 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 557598006688 SdhC subunit interface [polypeptide binding]; other site 557598006689 proximal heme binding site [chemical binding]; other site 557598006690 cardiolipin binding site; other site 557598006691 Iron-sulfur protein interface; other site 557598006692 proximal quinone binding site [chemical binding]; other site 557598006693 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 557598006694 Iron-sulfur protein interface; other site 557598006695 proximal quinone binding site [chemical binding]; other site 557598006696 SdhD (CybS) interface [polypeptide binding]; other site 557598006697 proximal heme binding site [chemical binding]; other site 557598006698 Transcriptional regulators [Transcription]; Region: PhnF; COG2188 557598006699 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 557598006700 DNA-binding site [nucleotide binding]; DNA binding site 557598006701 UTRA domain; Region: UTRA; pfam07702 557598006702 malate dehydrogenase; Provisional; Region: PRK05442 557598006703 Chloroplast-like malate dehydrogenases; Region: MDH_choloroplast_like; cd01338 557598006704 NAD(P) binding site [chemical binding]; other site 557598006705 dimer interface [polypeptide binding]; other site 557598006706 malate binding site [chemical binding]; other site 557598006707 peptide chain release factor 2; Validated; Region: prfB; PRK00578 557598006708 This domain is found in peptide chain release factors; Region: PCRF; smart00937 557598006709 RF-1 domain; Region: RF-1; pfam00472 557598006710 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 557598006711 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 557598006712 dimer interface [polypeptide binding]; other site 557598006713 putative anticodon binding site; other site 557598006714 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 557598006715 motif 1; other site 557598006716 active site 557598006717 motif 2; other site 557598006718 motif 3; other site 557598006719 Cache domain; Region: Cache_1; pfam02743 557598006720 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 557598006721 dimerization interface [polypeptide binding]; other site 557598006722 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 557598006723 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557598006724 dimer interface [polypeptide binding]; other site 557598006725 putative CheW interface [polypeptide binding]; other site 557598006726 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 557598006727 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 557598006728 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 557598006729 active site 557598006730 phosphorylation site [posttranslational modification] 557598006731 intermolecular recognition site; other site 557598006732 dimerization interface [polypeptide binding]; other site 557598006733 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; cd00588 557598006734 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 557598006735 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 557598006736 active site 557598006737 phosphorylation site [posttranslational modification] 557598006738 intermolecular recognition site; other site 557598006739 dimerization interface [polypeptide binding]; other site 557598006740 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 557598006741 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 557598006742 active site 557598006743 phosphorylation site [posttranslational modification] 557598006744 intermolecular recognition site; other site 557598006745 dimerization interface [polypeptide binding]; other site 557598006746 Chemotaxis phosphatase, CheZ; Region: CheZ; cl01219 557598006747 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 557598006748 putative binding surface; other site 557598006749 active site 557598006750 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 557598006751 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 557598006752 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 557598006753 ATP binding site [chemical binding]; other site 557598006754 Mg2+ binding site [ion binding]; other site 557598006755 G-X-G motif; other site 557598006756 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 557598006757 catalase/hydroperoxidase HPI(I); Provisional; Region: PRK15061 557598006758 N-terminal catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_1; cd00649 557598006759 dimer interface [polypeptide binding]; other site 557598006760 active site 557598006761 heme binding site [chemical binding]; other site 557598006762 C-terminal non-catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_2; cd08200 557598006763 Domain of unknown function (DUF3482); Region: DUF3482; pfam11981 557598006764 Di-haem cytochrome c peroxidase; Region: CCP_MauG; pfam03150 557598006765 Cytochrome c peroxidase [Inorganic ion transport and metabolism]; Region: MauG; COG1858 557598006766 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 557598006767 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557598006768 metal binding site [ion binding]; metal-binding site 557598006769 active site 557598006770 I-site; other site 557598006771 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 557598006772 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 557598006773 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 557598006774 trimer interface [polypeptide binding]; other site 557598006775 eyelet of channel; other site 557598006776 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 557598006777 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 557598006778 putative catalytic site [active] 557598006779 putative phosphate binding site [ion binding]; other site 557598006780 active site 557598006781 metal binding site A [ion binding]; metal-binding site 557598006782 DNA binding site [nucleotide binding] 557598006783 putative AP binding site [nucleotide binding]; other site 557598006784 putative metal binding site B [ion binding]; other site 557598006785 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 557598006786 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 557598006787 dimer interface [polypeptide binding]; other site 557598006788 anticodon binding site; other site 557598006789 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 557598006790 homodimer interface [polypeptide binding]; other site 557598006791 motif 1; other site 557598006792 active site 557598006793 motif 2; other site 557598006794 GAD domain; Region: GAD; pfam02938 557598006795 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 557598006796 motif 3; other site 557598006797 Uncharacterized conserved protein [Function unknown]; Region: COG2928 557598006798 putative regulatory protein, FmdB family; Region: CxxC_CxxC_SSSS; TIGR02605 557598006799 phosphate acetyltransferase; Provisional; Region: PRK11890 557598006800 bifunctional enoyl-CoA hydratase/phosphate acetyltransferase; Validated; Region: PRK08190 557598006801 Acetokinase family; Region: Acetate_kinase; cl17229 557598006802 propionate/acetate kinase; Provisional; Region: PRK12379 557598006803 ABC transporter transmembrane region 2; Region: ABC_membrane_2; cl00549 557598006804 ABC-type transport system involved in cytochrome c biogenesis, ATPase component [Posttranslational modification, protein turnover, chaperones]; Region: CcmA; COG4133 557598006805 ATP-binding cassette domain of peroxisomal transporter, subfamily D; Region: ABCD_peroxisomal_ALDP; cd03223 557598006806 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557598006807 dimer interface [polypeptide binding]; other site 557598006808 putative CheW interface [polypeptide binding]; other site 557598006809 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 557598006810 DNA-binding transcriptional regulator ModE; Provisional; Region: PRK10676 557598006811 N-terminal domain of molybdenum-binding protein [General function prediction only]; Region: ModE; COG2005 557598006812 molybdenum-pterin binding domain; Region: Mop; TIGR00638 557598006813 molybdenum-pterin binding domain; Region: Mop; TIGR00638 557598006814 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 557598006815 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 557598006816 TOBE domain; Region: TOBE; cl01440 557598006817 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 557598006818 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 557598006819 dimer interface [polypeptide binding]; other site 557598006820 conserved gate region; other site 557598006821 putative PBP binding loops; other site 557598006822 ABC-ATPase subunit interface; other site 557598006823 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 557598006824 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 557598006825 Walker A/P-loop; other site 557598006826 ATP binding site [chemical binding]; other site 557598006827 Q-loop/lid; other site 557598006828 ABC transporter signature motif; other site 557598006829 Walker B; other site 557598006830 D-loop; other site 557598006831 H-loop/switch region; other site 557598006832 Uncharacterized conserved protein [Function unknown]; Region: COG1683 557598006833 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 557598006834 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 557598006835 active site 557598006836 Int/Topo IB signature motif; other site 557598006837 Phage regulatory protein Rha (Phage_pRha); Region: Phage_pRha; cl10713 557598006838 Toprim domain; Region: Toprim_3; pfam13362 557598006839 Superfamily II helicase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG5519 557598006840 insertion element IS2 transposase InsD; Provisional; Region: PRK14702 557598006841 DoxX-like family; Region: DoxX_2; pfam13564 557598006842 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 557598006843 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 557598006844 catalytic residues [active] 557598006845 hypothetical protein; Region: PHA00675 557598006846 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 557598006847 signal recognition particle protein; Provisional; Region: PRK10867 557598006848 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 557598006849 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 557598006850 GTP binding site [chemical binding]; other site 557598006851 Signal peptide binding domain; Region: SRP_SPB; pfam02978 557598006852 ATP-grasp domain; Region: ATP-grasp_4; cl17255 557598006853 adenylosuccinate lyase; Provisional; Region: PRK09285 557598006854 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 557598006855 tetramer interface [polypeptide binding]; other site 557598006856 active site 557598006857 DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]; Region: ComEA; COG1555 557598006858 Helix-hairpin-helix motif; Region: HHH; pfam00633 557598006859 Periplasmic protein with OB-fold [Function unknown]; Region: COG3111 557598006860 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 557598006861 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 557598006862 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 557598006863 Domain of unknown function (DUF4102); Region: DUF4102; pfam13356 557598006864 aminotransferase AlaT; Validated; Region: PRK09265 557598006865 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 557598006866 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557598006867 homodimer interface [polypeptide binding]; other site 557598006868 catalytic residue [active] 557598006869 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 557598006870 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 557598006871 substrate binding site [chemical binding]; other site 557598006872 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 557598006873 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 557598006874 anaerobic dimethyl sulfoxide reductase, A subunit, DmsA/YnfE family; Region: dmsA_ynfE; TIGR02166 557598006875 This CD (MopB_DmsA-EC) includes the DmsA enzyme of the dmsABC operon encoding the anaerobic dimethylsulfoxide reductase (DMSOR) of Escherichia coli and other related DMSOR-like enzymes. Unlike other DMSOR-like enzymes, this group has a predicted...; Region: MopB_DmsA-EC; cd02770 557598006876 putative [Fe4-S4] binding site [ion binding]; other site 557598006877 putative molybdopterin cofactor binding site [chemical binding]; other site 557598006878 The MopB_CT_DmsA-EC CD includes the DmsA enzyme of the dmsABC operon encoding the anaerobic dimethylsulfoxide reductase (DMSOR) of Escherichia coli and other related DMSOR-like enzymes. Unlike other DMSOR-like enzymes, this group has a predicted...; Region: MopB_CT_DmsA-EC; cd02794 557598006879 putative molybdopterin cofactor binding site; other site 557598006880 DMSO reductase, iron-sulfur subunit; Region: DMSO_dmsB; TIGR02951 557598006881 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 557598006882 DMSO reductase anchor subunit (DmsC); Region: DmsC; cl17519 557598006883 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 557598006884 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 557598006885 sensor protein ZraS; Provisional; Region: PRK10364 557598006886 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]; Region: COG4567 557598006887 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 557598006888 active site 557598006889 phosphorylation site [posttranslational modification] 557598006890 intermolecular recognition site; other site 557598006891 dimerization interface [polypeptide binding]; other site 557598006892 PucR C-terminal helix-turn-helix domain; Region: HTH_30; pfam13556 557598006893 glutamate racemase; Provisional; Region: PRK00865 557598006894 epoxyqueuosine reductase; Region: TIGR00276 557598006895 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 557598006896 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 557598006897 AMIN domain; Region: AMIN; pfam11741 557598006898 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 557598006899 active site 557598006900 metal binding site [ion binding]; metal-binding site 557598006901 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 557598006902 Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is...; Region: SLC13_permease; cd01115 557598006903 transmembrane helices; other site 557598006904 SlyX; Region: SlyX; pfam04102 557598006905 Predicted membrane protein [Function unknown]; Region: COG4125 557598006906 Bacterial Transmembrane Pair family; Region: BTP; pfam05232 557598006907 Bacterial Transmembrane Pair family; Region: BTP; pfam05232 557598006908 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557598006909 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 557598006910 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 557598006911 dimerization interface [polypeptide binding]; other site 557598006912 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 557598006913 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 557598006914 nucleoside/Zn binding site; other site 557598006915 dimer interface [polypeptide binding]; other site 557598006916 catalytic motif [active] 557598006917 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 557598006918 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 557598006919 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 557598006920 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 557598006921 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 557598006922 Protein of unknown function (DUF2721); Region: DUF2721; pfam11026 557598006923 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 557598006924 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 557598006925 Tetramer interface [polypeptide binding]; other site 557598006926 active site 557598006927 FMN-binding site [chemical binding]; other site 557598006928 Predicted proline hydroxylase [Posttranslational modification, protein turnover, chaperones]; Region: EGL-9; COG3751 557598006929 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy_3; pfam13640 557598006930 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 557598006931 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 557598006932 P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimD; COG3188 557598006933 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 557598006934 Spore Coat Protein U domain; Region: SCPU; pfam05229 557598006935 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 557598006936 active site 557598006937 catalytic site [active] 557598006938 substrate binding site [chemical binding]; other site 557598006939 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 557598006940 GIY-YIG motif/motif A; other site 557598006941 active site 557598006942 catalytic site [active] 557598006943 putative DNA binding site [nucleotide binding]; other site 557598006944 metal binding site [ion binding]; metal-binding site 557598006945 Phasin protein; Region: Phasin_2; pfam09361 557598006946 septum formation inhibitor; Reviewed; Region: minC; PRK04516 557598006947 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 557598006948 Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]; Region: MinD; COG2894 557598006949 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 557598006950 Switch I; other site 557598006951 Switch II; other site 557598006952 cell division topological specificity factor MinE; Provisional; Region: PRK13989 557598006953 DNA-binding transcriptional regulator OxyR; Provisional; Region: PRK11151 557598006954 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 557598006955 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 557598006956 dimerization interface [polypeptide binding]; other site 557598006957 multidrug efflux protein; Reviewed; Region: PRK01766 557598006958 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Vibrio cholerae NorM; Region: MATE_NorM_like; cd13131 557598006959 cation binding site [ion binding]; other site 557598006960 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK00046 557598006961 FAD binding domain; Region: FAD_binding_4; pfam01565 557598006962 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 557598006963 L,D-transpeptidase catalytic domain; Region: YkuD_2; pfam13645 557598006964 hypothetical protein; Provisional; Region: PRK06132 557598006965 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 557598006966 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 557598006967 Phosphate transporter family; Region: PHO4; cl00396 557598006968 putative transporter; Provisional; Region: PRK10504 557598006969 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 557598006970 putative substrate translocation pore; other site 557598006971 Transposase DDE domain; Region: DDE_Tnp_1_5; pfam13737 557598006972 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 557598006973 Fumarate hydratase (Fumerase); Region: Fumerase; pfam05681 557598006974 Fumarase C-terminus; Region: Fumerase_C; pfam05683 557598006975 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 557598006976 MarR family; Region: MarR_2; pfam12802 557598006977 NAD-dependent deacetylase; Provisional; Region: PRK00481 557598006978 SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+; Region: SIR2; cl00195 557598006979 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 557598006980 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 557598006981 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557598006982 catalytic residue [active] 557598006983 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 557598006984 DEAD-like helicases superfamily; Region: DEXDc; smart00487 557598006985 ATP binding site [chemical binding]; other site 557598006986 Mg++ binding site [ion binding]; other site 557598006987 motif III; other site 557598006988 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 557598006989 nucleotide binding region [chemical binding]; other site 557598006990 ATP-binding site [chemical binding]; other site 557598006991 CobD/CbiB family protein; Provisional; Region: PRK07630 557598006992 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 557598006993 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 557598006994 hinge; other site 557598006995 active site 557598006996 BolA-like protein; Region: BolA; cl00386 557598006997 ABC-2 type transporter; Region: ABC2_membrane; cl17235 557598006998 ABC-2 type transporter; Region: ABC2_membrane; cl17235 557598006999 prephenate dehydrogenase; Validated; Region: PRK08507 557598007000 Prephenate dehydrogenase; Region: PDH; pfam02153 557598007001 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 557598007002 ADCL_like: 4-Amino-4-deoxychorismate lyase: is a member of the fold-type IV of PLP dependent enzymes that converts 4-amino-4-deoxychorismate (ADC) to p-aminobenzoate and pyruvate. Based on the information available from the crystal structure, most...; Region: ADCL_like; cd01559 557598007003 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557598007004 catalytic residue [active] 557598007005 Uncharacterized conserved protein [Function unknown]; Region: COG5495 557598007006 Rossmann-like domain; Region: Rossmann-like; pfam10727 557598007007 Domain of unknown function (DUF2520); Region: DUF2520; pfam10728 557598007008 O-acetylhomoserine aminocarboxypropyltransferase; Validated; Region: PRK06084 557598007009 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 557598007010 homodimer interface [polypeptide binding]; other site 557598007011 substrate-cofactor binding pocket; other site 557598007012 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557598007013 catalytic residue [active] 557598007014 FOG: CBS domain [General function prediction only]; Region: COG0517 557598007015 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with a PAS domain, a GGDEF (DiGuanylate-Cyclase (DGC) domain, and a DUF1 domain downstream. PAS domains have been found to bind ligands, and to act...; Region: CBS_pair_PAS_GGDEF_DUF1_assoc; cd04611 557598007016 FOG: CBS domain [General function prediction only]; Region: COG0517 557598007017 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with a PAS domain, a GGDEF (DiGuanylate-Cyclase (DGC) domain, and a DUF1 domain downstream. PAS domains have been found to bind ligands, and to act...; Region: CBS_pair_PAS_GGDEF_DUF1_assoc; cd04611 557598007018 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 557598007019 PAS domain; Region: PAS_9; pfam13426 557598007020 putative active site [active] 557598007021 heme pocket [chemical binding]; other site 557598007022 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 557598007023 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557598007024 metal binding site [ion binding]; metal-binding site 557598007025 active site 557598007026 I-site; other site 557598007027 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 557598007028 LTXXQ motif family protein; Region: LTXXQ; pfam07813 557598007029 seryl-tRNA synthetase; Provisional; Region: PRK05431 557598007030 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 557598007031 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 557598007032 dimer interface [polypeptide binding]; other site 557598007033 active site 557598007034 motif 1; other site 557598007035 motif 2; other site 557598007036 motif 3; other site 557598007037 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 557598007038 EamA-like transporter family; Region: EamA; pfam00892 557598007039 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 557598007040 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 557598007041 large-conductance mechanosensitive channel; Provisional; Region: mscL; PRK13952 557598007042 Uncharacterized protein family UPF0547; Region: UPF0547; pfam10571 557598007043 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 557598007044 FAD binding domain; Region: FAD_binding_4; pfam01565 557598007045 Domain of unknown function (DUF3488); Region: DUF3488; pfam11992 557598007046 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]; Region: COG1305 557598007047 Transglutaminase-like superfamily; Region: Transglut_core; pfam01841 557598007048 Protein of unknown function DUF58; Region: DUF58; pfam01882 557598007049 MoxR-like ATPases [General function prediction only]; Region: COG0714 557598007050 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 557598007051 Walker A motif; other site 557598007052 ATP binding site [chemical binding]; other site 557598007053 Walker B motif; other site 557598007054 arginine finger; other site 557598007055 ribonuclease R; Region: RNase_R; TIGR02063 557598007056 Ribonuclease B OB domain; Region: OB_RNB; pfam08206 557598007057 RNB domain; Region: RNB; pfam00773 557598007058 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 557598007059 RNA binding site [nucleotide binding]; other site 557598007060 The tRNA binding domain is also known as the Myf domain in literature. This domain is found in a diverse collection of tRNA binding proteins, including prokaryotic phenylalanyl tRNA synthetases (PheRS), methionyl-tRNA synthetases (MetRS), human...; Region: tRNA_bindingDomain; cl00320 557598007061 putative tRNA-binding site [nucleotide binding]; other site 557598007062 B12 binding domain; Region: B12-binding; pfam02310 557598007063 B12 binding site [chemical binding]; other site 557598007064 Radical SAM superfamily; Region: Radical_SAM; pfam04055 557598007065 SGNH_hydrolase, or GDSL_hydrolase, is 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 active site closely...; Region: SGNH_hydrolase; cl01053 557598007066 active site 557598007067 catalytic triad [active] 557598007068 oxyanion hole [active] 557598007069 EamA-like transporter family; Region: EamA; pfam00892 557598007070 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 557598007071 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 557598007072 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 557598007073 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557598007074 putative DNA-binding transcriptional regulator; Provisional; Region: PRK09775 557598007075 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 557598007076 putative DNA binding site [nucleotide binding]; other site 557598007077 putative Zn2+ binding site [ion binding]; other site 557598007078 HipA-like N-terminal domain; Region: HipA_N; pfam07805 557598007079 HipA-like C-terminal domain; Region: HipA_C; pfam07804 557598007080 portal vertex protein; Provisional; Region: Q; PHA02536 557598007081 Phage portal protein; Region: Phage_portal; pfam04860 557598007082 terminase ATPase subunit; Provisional; Region: P; PHA02535 557598007083 Putative ATPase subunit of terminase (gpP-like); Region: Terminase_5; pfam06056 557598007084 Mu-like prophage FluMu protein gp28 [General function prediction only]; Region: COG4373 557598007085 Phage capsid scaffolding protein (GPO) serine peptidase; Region: Phage_GPO; cl15838 557598007086 Uncharacterized conserved protein [Function unknown]; Region: COG5484 557598007087 Putative ATPase subunit of terminase (gpP-like); Region: Terminase_5; pfam06056 557598007088 Mu-like prophage FluMu protein gp28 [General function prediction only]; Region: COG4373 557598007089 Phage capsid scaffolding protein (GPO) serine peptidase; Region: Phage_GPO; cl15838 557598007090 capsid protein; Provisional; Region: N; PHA02538 557598007091 terminase endonuclease subunit; Provisional; Region: M; PHA02537 557598007092 Phage small terminase subunit; Region: Phage_term_smal; pfam05944 557598007093 Phage head completion protein (GPL); Region: Phage_GPL; pfam05926 557598007094 Phage Tail Protein X; Region: Phage_tail_X; cl02088 557598007095 Protein of unknown function (DUF754); Region: DUF754; pfam05449 557598007096 Putative peptidoglycan-binding domain-containing protein [Cell envelope biogenesis, outer membrane]; Region: COG3409 557598007097 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 557598007098 Protein of unknown function (DUF3380); Region: DUF3380; pfam11860 557598007099 phage lysis regulatory protein, LysB family; Region: phage_LysB; TIGR03495 557598007100 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 557598007101 P2 phage tail completion protein R (GpR); Region: P2_Phage_GpR; pfam06891 557598007102 Phage virion morphogenesis family; Region: Phage_tail_S; pfam05069 557598007103 phage baseplate assembly protein V; Region: phage_P2_V; TIGR01644 557598007104 Phage P2 baseplate assembly protein gpV [General function prediction only]; Region: gpV; COG4540 557598007105 Gene 25-like lysozyme; Region: GPW_gp25; cl01403 557598007106 Baseplate J-like protein; Region: Baseplate_J; cl01294 557598007107 Bacteriophage P2-related tail formation protein [General function prediction only]; Region: gpI; COG4385 557598007108 Phage tail-collar fibre protein; Region: DUF3751; pfam12571 557598007109 Domain of unknown function (DUF4376); Region: DUF4376; pfam14301 557598007110 Mu-like prophage protein Com; Region: Mu-like_Com; cl11540 557598007111 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dam; COG0338 557598007112 major tail sheath protein; Provisional; Region: FI; PHA02560 557598007113 major tail tube protein; Provisional; Region: FII; PHA02600 557598007114 Mu-like prophage FluMu protein gp41; Region: FluMu_gp41; pfam10109 557598007115 Phage P2 GpE; Region: Phage_P2_GpE; pfam06528 557598007116 phage tail tape measure protein, TP901 family, core region; Region: tape_meas_TP901; TIGR01760 557598007117 Phage P2 GpU; Region: Phage_P2_GpU; pfam06995 557598007118 Phage late control gene D protein (GPD); Region: Phage_GPD; cl15796 557598007119 Protein of unknown function (DUF4231); Region: DUF4231; pfam14015 557598007120 MTH538 TIR-like domain (DUF1863); Region: DUF1863; pfam08937 557598007121 Archaea-specific editing domain of threonyl-tRNA synthetase; Region: tRNA-Thr_ED; pfam08915 557598007122 Ogr/Delta-like zinc finger; Region: Ogr_Delta; pfam04606 557598007123 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 557598007124 non-specific DNA binding site [nucleotide binding]; other site 557598007125 salt bridge; other site 557598007126 sequence-specific DNA binding site [nucleotide binding]; other site 557598007127 Bacteriophage replication gene A protein (GPA); Region: Phage_GPA; cl15276 557598007128 Helix-turn-helix domain; Region: HTH_17; pfam12728 557598007129 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 557598007130 active site 557598007131 DNA binding site [nucleotide binding] 557598007132 Int/Topo IB signature motif; other site 557598007133 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 557598007134 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 557598007135 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 557598007136 GIY-YIG motif/motif A; other site 557598007137 active site 557598007138 catalytic site [active] 557598007139 putative DNA binding site [nucleotide binding]; other site 557598007140 metal binding site [ion binding]; metal-binding site 557598007141 UvrB/uvrC motif; Region: UVR; pfam02151 557598007142 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 557598007143 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 557598007144 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 557598007145 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 557598007146 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 557598007147 active site 557598007148 Cupin superfamily protein; Region: Cupin_4; pfam08007 557598007149 Cupin-like domain; Region: Cupin_8; pfam13621 557598007150 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK15095 557598007151 Uncharacterized protein conserved in bacteria (DUF2325); Region: DUF2325; cl01811 557598007152 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 557598007153 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 557598007154 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 557598007155 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 557598007156 dimer interface [polypeptide binding]; other site 557598007157 conserved gate region; other site 557598007158 putative PBP binding loops; other site 557598007159 ABC-ATPase subunit interface; other site 557598007160 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 557598007161 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 557598007162 ATP-binding cassette domain of the carbohydrate and solute transporters-like; Region: ABC_Carb_Solutes_like; cd03259 557598007163 Walker A/P-loop; other site 557598007164 ATP binding site [chemical binding]; other site 557598007165 Q-loop/lid; other site 557598007166 ABC transporter signature motif; other site 557598007167 Walker B; other site 557598007168 D-loop; other site 557598007169 H-loop/switch region; other site 557598007170 TOBE domain; Region: TOBE_2; pfam08402 557598007171 acetoacetate metabolism regulatory protein AtoC; Provisional; Region: PRK11361 557598007172 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 557598007173 Walker A motif; other site 557598007174 ATP binding site [chemical binding]; other site 557598007175 Walker B motif; other site 557598007176 arginine finger; other site 557598007177 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 557598007178 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 557598007179 putative active site [active] 557598007180 ribonuclease PH; Reviewed; Region: rph; PRK00173 557598007181 Ribonuclease PH; Region: RNase_PH_bact; cd11362 557598007182 hexamer interface [polypeptide binding]; other site 557598007183 active site 557598007184 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 557598007185 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 557598007186 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 557598007187 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557598007188 metal binding site [ion binding]; metal-binding site 557598007189 active site 557598007190 I-site; other site 557598007191 ribosome biogenesis GTP-binding protein YlqF; Region: GTPase_YlqF; TIGR03596 557598007192 Circularly permuted YlqF GTPase; Region: YlqF; cd01856 557598007193 GTP/Mg2+ binding site [chemical binding]; other site 557598007194 G4 box; other site 557598007195 G5 box; other site 557598007196 G1 box; other site 557598007197 Switch I region; other site 557598007198 G2 box; other site 557598007199 G3 box; other site 557598007200 Switch II region; other site 557598007201 Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]; Region: PhrB; COG0415 557598007202 DNA photolyase; Region: DNA_photolyase; pfam00875 557598007203 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 557598007204 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 557598007205 FMN binding site [chemical binding]; other site 557598007206 active site 557598007207 substrate binding site [chemical binding]; other site 557598007208 catalytic residue [active] 557598007209 Sulfate transporter family; Region: Sulfate_transp; pfam00916 557598007210 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 557598007211 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: Unknown ABO13168; Region: LPLAT_ABO13168-like; cd07988 557598007212 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 557598007213 putative acyl-acceptor binding pocket; other site 557598007214 putative protease; Provisional; Region: PRK15452 557598007215 Peptidase family U32; Region: Peptidase_U32; pfam01136 557598007216 Collagenase; Region: DUF3656; pfam12392 557598007217 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 557598007218 PAS fold; Region: PAS_4; pfam08448 557598007219 putative active site [active] 557598007220 heme pocket [chemical binding]; other site 557598007221 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 557598007222 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557598007223 metal binding site [ion binding]; metal-binding site 557598007224 active site 557598007225 I-site; other site 557598007226 Protein of unknown function (DUF917); Region: DUF917; cl17829 557598007227 Protein of unknown function (DUF917); Region: DUF917; cl17829 557598007228 Acyltransferase family; Region: Acyl_transf_3; pfam01757 557598007229 thiamine biosynthesis protein ThiC; Provisional; Region: PRK09284 557598007230 ThiC-associated domain; Region: ThiC-associated; pfam13667 557598007231 Thiamine biosynthesis protein ThiC [Coenzyme metabolism]; Region: ThiC; COG0422 557598007232 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 557598007233 dimer interface [polypeptide binding]; other site 557598007234 substrate binding site [chemical binding]; other site 557598007235 ATP binding site [chemical binding]; other site 557598007236 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 557598007237 thiamine phosphate binding site [chemical binding]; other site 557598007238 active site 557598007239 pyrophosphate binding site [ion binding]; other site 557598007240 4-methyl-5-beta-hydroxyethylthiazole (Thz) kinase catalyzes the phosphorylation of the hydroxylgroup of Thz. A reaction that allows cells to recycle Thz into the thiamine biosynthesis pathway, as an alternative to its synthesis from cysteine, tyrosine...; Region: THZ_kinase; cd01170 557598007241 substrate binding site [chemical binding]; other site 557598007242 multimerization interface [polypeptide binding]; other site 557598007243 ATP binding site [chemical binding]; other site 557598007244 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 557598007245 EamA-like transporter family; Region: EamA; pfam00892 557598007246 EamA-like transporter family; Region: EamA; pfam00892 557598007247 phosphoenolpyruvate synthase; Validated; Region: PRK06464 557598007248 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 557598007249 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 557598007250 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 557598007251 Cytochrome c peroxidase [Inorganic ion transport and metabolism]; Region: MauG; COG1858 557598007252 Uncharacterized oxidoreductases, Fe-dependent alcohol dehydrogenase family [Energy production and conversion]; Region: COG1979 557598007253 Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process; Region: BDH; cd08187 557598007254 dimer interface [polypeptide binding]; other site 557598007255 active site 557598007256 metal binding site [ion binding]; metal-binding site 557598007257 PEP synthetase regulatory protein; Provisional; Region: PRK05339 557598007258 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 557598007259 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 557598007260 active site 557598007261 HIGH motif; other site 557598007262 dimer interface [polypeptide binding]; other site 557598007263 KMSKS motif; other site 557598007264 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 557598007265 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 557598007266 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 557598007267 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 557598007268 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 557598007269 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 557598007270 dimer interface [polypeptide binding]; other site 557598007271 conserved gate region; other site 557598007272 putative PBP binding loops; other site 557598007273 ABC-ATPase subunit interface; other site 557598007274 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 557598007275 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 557598007276 dimer interface [polypeptide binding]; other site 557598007277 conserved gate region; other site 557598007278 putative PBP binding loops; other site 557598007279 ABC-ATPase subunit interface; other site 557598007280 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 557598007281 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 557598007282 ABC transporter signature motif; other site 557598007283 Walker B; other site 557598007284 D-loop; other site 557598007285 H-loop/switch region; other site 557598007286 TOBE domain; Region: TOBE_2; pfam08402 557598007287 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 557598007288 Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan...; Region: Trp-synth-beta_II; cl00342 557598007289 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 557598007290 catalytic residue [active] 557598007291 Outer membrane protein W [Cell envelope biogenesis, outer membrane]; Region: OmpW; COG3047 557598007292 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 557598007293 Uncharacterized conserved protein related to dihydrodipicolinate reductase [Function unknown]; Region: COG3804 557598007294 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 557598007295 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 557598007296 S-adenosylmethionine binding site [chemical binding]; other site 557598007297 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 557598007298 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 557598007299 Ligand Binding Site [chemical binding]; other site 557598007300 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 557598007301 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 557598007302 FMN binding site [chemical binding]; other site 557598007303 substrate binding site [chemical binding]; other site 557598007304 putative catalytic residue [active] 557598007305 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 557598007306 dimerization interface [polypeptide binding]; other site 557598007307 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 557598007308 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557598007309 dimer interface [polypeptide binding]; other site 557598007310 putative CheW interface [polypeptide binding]; other site 557598007311 Cache domain; Region: Cache_1; pfam02743 557598007312 AzlC protein; Region: AzlC; pfam03591 557598007313 Branched-chain amino acid transport protein (AzlD); Region: AzlD; pfam05437 557598007314 EamA-like transporter family; Region: EamA; pfam00892 557598007315 putative hydrolase; Provisional; Region: PRK02113 557598007316 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 557598007317 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 557598007318 active site 557598007319 DNA polymerase III subunit delta'; Validated; Region: PRK08699 557598007320 thymidylate kinase; Validated; Region: tmk; PRK00698 557598007321 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 557598007322 TMP-binding site; other site 557598007323 ATP-binding site [chemical binding]; other site 557598007324 YceG-like family; Region: YceG; pfam02618 557598007325 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 557598007326 dimerization interface [polypeptide binding]; other site 557598007327 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 557598007328 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 557598007329 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 557598007330 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 557598007331 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 557598007332 Flagellar capping protein [Cell motility and secretion]; Region: FliD; COG1345 557598007333 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 557598007334 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 557598007335 FlaG protein; Region: FlaG; pfam03646 557598007336 flagellin; Provisional; Region: PRK12802 557598007337 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 557598007338 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 557598007339 Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones]; Region: Spy; COG3914 557598007340 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 557598007341 Methyltransferase domain; Region: Methyltransf_23; pfam13489 557598007342 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 557598007343 S-adenosylmethionine binding site [chemical binding]; other site 557598007344 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 557598007345 Integrase core domain; Region: rve; pfam00665 557598007346 Integrase core domain; Region: rve_3; pfam13683 557598007347 Transposase DDE domain; Region: DDE_Tnp_1_2; pfam13586 557598007348 Transposase DDE domain; Region: DDE_Tnp_1_5; pfam13737 557598007349 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 557598007350 G1P_cytidylyltransferase catalyzes the production of CDP-D-Glucose; Region: G1P_cytidylyltransferase; cd02524 557598007351 substrate binding site; other site 557598007352 CDP-glucose 4,6-dehydratase; Region: CDP_4_6_dhtase; TIGR02622 557598007353 CDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: CDP_GD_SDR_e; cd05252 557598007354 NAD binding site [chemical binding]; other site 557598007355 homotetramer interface [polypeptide binding]; other site 557598007356 homodimer interface [polypeptide binding]; other site 557598007357 substrate binding site [chemical binding]; other site 557598007358 active site 557598007359 Putative zinc binding domain; Region: Methyltransf_13; pfam08421 557598007360 Methyltransferase domain; Region: Methyltransf_23; pfam13489 557598007361 Methyltransferase domain; Region: Methyltransf_12; pfam08242 557598007362 C-methyltransferase C-terminal domain; Region: Methyltransf_14; pfam08484 557598007363 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 557598007364 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 557598007365 inhibitor-cofactor binding pocket; inhibition site 557598007366 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557598007367 catalytic residue [active] 557598007368 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 557598007369 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 557598007370 HTH-like domain; Region: HTH_21; pfam13276 557598007371 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 557598007372 Integrase core domain; Region: rve; pfam00665 557598007373 Integrase core domain; Region: rve_3; pfam13683 557598007374 Transposase; Region: HTH_Tnp_1; pfam01527 557598007375 glycine dehydrogenase; Provisional; Region: PRK05367 557598007376 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 557598007377 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 557598007378 catalytic residue [active] 557598007379 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 557598007380 tetramer interface [polypeptide binding]; other site 557598007381 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557598007382 catalytic residue [active] 557598007383 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 557598007384 lipoyl attachment site [posttranslational modification]; other site 557598007385 glycine cleavage system aminomethyltransferase T; Reviewed; Region: gcvT; PRK00389 557598007386 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 557598007387 heme binding pocket [chemical binding]; other site 557598007388 heme ligand [chemical binding]; other site 557598007389 Heme oxygenase catalyzes the rate limiting step in the degradation of heme to bilirubin, it is essential for recycling of iron from heme. Heme is used as a substrate and cofactor for its own degradation to biliverdin, iron, and carbon monoxide. This...; Region: HemeO; cl17299 557598007390 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 557598007391 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 557598007392 AAK_CK: Carbamate kinase (CK) catalyzes both the ATP-phosphorylation of carbamate and carbamoyl phosphate (CP) utilization with the production of ATP from ADP and CP. Both CK (this CD) and nonhomologous CP synthetase synthesize carbamoyl phosphate, an...; Region: AAK_CK; cd04235 557598007393 putative substrate binding site [chemical binding]; other site 557598007394 nucleotide binding site [chemical binding]; other site 557598007395 nucleotide binding site [chemical binding]; other site 557598007396 homodimer interface [polypeptide binding]; other site 557598007397 ornithine carbamoyltransferase; Validated; Region: PRK02102 557598007398 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 557598007399 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 557598007400 arginine deiminase; Provisional; Region: PRK01388 557598007401 arginine-ornithine antiporter; Region: arg_ornith_anti; TIGR03810 557598007402 arginine-ornithine antiporter; Region: arg_ornith_anti; TIGR03810 557598007403 carbamate kinase-like carbamoyl phosphate synthetase; Reviewed; Region: PRK12454 557598007404 AAK_CK: Carbamate kinase (CK) catalyzes both the ATP-phosphorylation of carbamate and carbamoyl phosphate (CP) utilization with the production of ATP from ADP and CP. Both CK (this CD) and nonhomologous CP synthetase synthesize carbamoyl phosphate, an...; Region: AAK_CK; cd04235 557598007405 putative substrate binding site [chemical binding]; other site 557598007406 nucleotide binding site [chemical binding]; other site 557598007407 nucleotide binding site [chemical binding]; other site 557598007408 homodimer interface [polypeptide binding]; other site 557598007409 ornithine carbamoyltransferase; Validated; Region: PRK02102 557598007410 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 557598007411 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 557598007412 arginine deiminase; Provisional; Region: PRK01388 557598007413 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 557598007414 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 557598007415 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 557598007416 metal ion-dependent adhesion site (MIDAS); other site 557598007417 RTX toxins and related Ca2+-binding proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2931 557598007418 type I secretion C-terminal target domain (VC_A0849 subclass); Region: T1SS_VCA0849; TIGR03661 557598007419 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 557598007420 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 557598007421 chaperone protein DnaJ; Provisional; Region: PRK10767 557598007422 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 557598007423 HSP70 interaction site [polypeptide binding]; other site 557598007424 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 557598007425 substrate binding site [polypeptide binding]; other site 557598007426 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 557598007427 Zn binding sites [ion binding]; other site 557598007428 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 557598007429 dimer interface [polypeptide binding]; other site 557598007430 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 557598007431 Nucleotide-binding domain of human HSPA9, Escherichia coli DnaK, and similar proteins; Region: HSPA9-like_NBD; cd11733 557598007432 nucleotide binding site [chemical binding]; other site 557598007433 NEF interaction site [polypeptide binding]; other site 557598007434 SBD interface [polypeptide binding]; other site 557598007435 heat shock protein GrpE; Provisional; Region: PRK14140 557598007436 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 557598007437 dimer interface [polypeptide binding]; other site 557598007438 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 557598007439 isocitrate lyase; Provisional; Region: PRK15063 557598007440 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 557598007441 tetramer interface [polypeptide binding]; other site 557598007442 active site 557598007443 Mg2+/Mn2+ binding site [ion binding]; other site 557598007444 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 557598007445 Walker A/P-loop; other site 557598007446 ATP binding site [chemical binding]; other site 557598007447 Q-loop/lid; other site 557598007448 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 557598007449 dimer interface [polypeptide binding]; other site 557598007450 conserved gate region; other site 557598007451 putative PBP binding loops; other site 557598007452 ABC-ATPase subunit interface; other site 557598007453 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 557598007454 dimer interface [polypeptide binding]; other site 557598007455 conserved gate region; other site 557598007456 putative PBP binding loops; other site 557598007457 ABC-ATPase subunit interface; other site 557598007458 PBP superfamily domain; Region: PBP_like_2; cl17296 557598007459 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 557598007460 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 557598007461 DNA binding residues [nucleotide binding] 557598007462 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 557598007463 IHF - DNA interface [nucleotide binding]; other site 557598007464 IHF dimer interface [polypeptide binding]; other site 557598007465 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 557598007466 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 557598007467 putative tRNA-binding site [nucleotide binding]; other site 557598007468 B3/4 domain; Region: B3_4; pfam03483 557598007469 tRNA synthetase B5 domain; Region: B5; smart00874 557598007470 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 557598007471 dimer interface [polypeptide binding]; other site 557598007472 motif 1; other site 557598007473 motif 3; other site 557598007474 motif 2; other site 557598007475 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 557598007476 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 557598007477 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 557598007478 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 557598007479 dimer interface [polypeptide binding]; other site 557598007480 motif 1; other site 557598007481 active site 557598007482 motif 2; other site 557598007483 motif 3; other site 557598007484 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 557598007485 23S rRNA binding site [nucleotide binding]; other site 557598007486 L21 binding site [polypeptide binding]; other site 557598007487 L13 binding site [polypeptide binding]; other site 557598007488 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 557598007489 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 557598007490 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 557598007491 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 557598007492 The TGS domain, named after the ThrRS, GTPase, and SpoT/RelA proteins where it occurs, is structurally similar to ubiquitin. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information...; Region: TGS; cl15768 557598007493 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 557598007494 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 557598007495 active site 557598007496 dimer interface [polypeptide binding]; other site 557598007497 motif 1; other site 557598007498 motif 2; other site 557598007499 motif 3; other site 557598007500 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 557598007501 anticodon binding site; other site 557598007502 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 557598007503 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 557598007504 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 557598007505 SecD export protein N-terminal TM region; Region: SecD-TM1; pfam13721 557598007506 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 557598007507 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 557598007508 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 557598007509 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 557598007510 dimerization interface [polypeptide binding]; other site 557598007511 putative DNA binding site [nucleotide binding]; other site 557598007512 putative Zn2+ binding site [ion binding]; other site 557598007513 phosphoglyceromutase; Provisional; Region: PRK05434 557598007514 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 557598007515 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]; Region: COG4942 557598007516 Peptidase family M23; Region: Peptidase_M23; pfam01551 557598007517 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 557598007518 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 557598007519 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 557598007520 protein binding site [polypeptide binding]; other site 557598007521 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 557598007522 Catalytic dyad [active] 557598007523 N-acetylglutamate synthase; Validated; Region: PRK05279 557598007524 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 557598007525 putative feedback inhibition sensing region; other site 557598007526 putative nucleotide binding site [chemical binding]; other site 557598007527 putative substrate binding site [chemical binding]; other site 557598007528 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 557598007529 Coenzyme A binding pocket [chemical binding]; other site 557598007530 UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]; Region: GalE; COG1087 557598007531 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 557598007532 NAD binding site [chemical binding]; other site 557598007533 homodimer interface [polypeptide binding]; other site 557598007534 active site 557598007535 substrate binding site [chemical binding]; other site 557598007536 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 557598007537 heterotetramer interface [polypeptide binding]; other site 557598007538 active site pocket [active] 557598007539 cleavage site 557598007540 ATP-dependent DNA helicase RecQ; Region: recQ; TIGR01389 557598007541 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 557598007542 ATP binding site [chemical binding]; other site 557598007543 putative Mg++ binding site [ion binding]; other site 557598007544 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 557598007545 nucleotide binding region [chemical binding]; other site 557598007546 ATP-binding site [chemical binding]; other site 557598007547 This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure; Region: RQC; smart00956 557598007548 HRDC domain; Region: HRDC; pfam00570 557598007549 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 557598007550 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 557598007551 P-loop; other site 557598007552 Magnesium ion binding site [ion binding]; other site 557598007553 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 557598007554 Magnesium ion binding site [ion binding]; other site 557598007555 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 557598007556 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 557598007557 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 557598007558 ssDNA binding site; other site 557598007559 generic binding surface II; other site 557598007560 DEAD-like helicases superfamily; Region: DEXDc; smart00487 557598007561 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 557598007562 ATP binding site [chemical binding]; other site 557598007563 putative Mg++ binding site [ion binding]; other site 557598007564 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 557598007565 nucleotide binding region [chemical binding]; other site 557598007566 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 557598007567 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 557598007568 23S rRNA interface [nucleotide binding]; other site 557598007569 L3 interface [polypeptide binding]; other site 557598007570 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 557598007571 HD domain; Region: HD_4; pfam13328 557598007572 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 557598007573 synthetase active site [active] 557598007574 NTP binding site [chemical binding]; other site 557598007575 metal binding site [ion binding]; metal-binding site 557598007576 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 557598007577 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 557598007578 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 557598007579 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 557598007580 minor groove reading motif; other site 557598007581 helix-hairpin-helix signature motif; other site 557598007582 substrate binding pocket [chemical binding]; other site 557598007583 active site 557598007584 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 557598007585 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 557598007586 DNA binding and oxoG recognition site [nucleotide binding] 557598007587 Predicted N6-adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0116 557598007588 THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Region: THUMP_AdoMetMT; cd11715 557598007589 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 557598007590 MarC family integral membrane protein; Region: MarC; cl00919 557598007591 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 557598007592 Polysaccharide biosynthesis protein; Region: Polysacc_synt_2; pfam02719 557598007593 NAD(P) binding site [chemical binding]; other site 557598007594 homodimer interface [polypeptide binding]; other site 557598007595 substrate binding site [chemical binding]; other site 557598007596 active site 557598007597 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 557598007598 The members of this subfamily catalyze the formation of a phosphodiester bond between a membrane-associated undecaprenyl-phosphate (Und-P) molecule and N-acetylhexosamine 1-phosphate, which is usually donated by a soluble UDP-N-acetylhexosamine precursor; Region: GT_WbpL_WbcO_like; cd06854 557598007599 Mg++ binding site [ion binding]; other site 557598007600 putative catalytic motif [active] 557598007601 putative substrate binding site [chemical binding]; other site 557598007602 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 557598007603 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 557598007604 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 557598007605 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 557598007606 This family is most closely related to the GT1 family of glycosyltransferases. wlbH in Bordetella parapertussis has been shown to be required for the biosynthesis of a trisaccharide that, when attached to the B. pertussis lipopolysaccharide (LPS) core; Region: GT1_wlbH_like; cd03798 557598007607 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 557598007608 Asparagine synthase (glutamine-hydrolyzing) [Amino acid transport and metabolism]; Region: AsnB; COG0367 557598007609 Glutamine amidotransferases class-II (GATase) asparagine synthase_B type. Asparagine synthetase B catalyses the ATP-dependent conversion of aspartate to asparagine. This enzyme is a homodimer, with each monomer composed of a glutaminase domain and a...; Region: AsnB; cd00712 557598007610 active site 557598007611 dimer interface [polypeptide binding]; other site 557598007612 The C-terminal domain of Asparagine Synthase B. This domain is always found associated n-terminal amidotransferase domain. Family members that contain this domain catalyse the conversion of aspartate to asparagine. Asparagine synthetase B catalyzes the...; Region: Asn_Synthase_B_C; cd01991 557598007613 Ligand Binding Site [chemical binding]; other site 557598007614 Molecular Tunnel; other site 557598007615 exosortase A system-associated amidotransferase 1; Region: eps_aminotran_1; TIGR03108 557598007616 Glutamine amidotransferases class-II (GATase) asparagine synthase_B type. Asparagine synthetase B catalyses the ATP-dependent conversion of aspartate to asparagine. This enzyme is a homodimer, with each monomer composed of a glutaminase domain and a...; Region: AsnB; cd00712 557598007617 active site 557598007618 dimer interface [polypeptide binding]; other site 557598007619 The C-terminal domain of Asparagine Synthase B. This domain is always found associated n-terminal amidotransferase domain. Family members that contain this domain catalyse the conversion of aspartate to asparagine. Asparagine synthetase B catalyzes the...; Region: Asn_Synthase_B_C; cd01991 557598007620 Ligand Binding Site [chemical binding]; other site 557598007621 Molecular Tunnel; other site 557598007622 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 557598007623 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 557598007624 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 557598007625 SGNH_hydrolase, or GDSL_hydrolase, is 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 active site closely...; Region: SGNH_hydrolase; cd00229 557598007626 active site 557598007627 catalytic triad [active] 557598007628 oxyanion hole [active] 557598007629 Formyl transferase catalytic core domain found in a group of proteins with unknown functions; Region: FMT_core_like_6; cd08820 557598007630 putative active site [active] 557598007631 putative substrate binding site [chemical binding]; other site 557598007632 putative cosubstrate binding site; other site 557598007633 catalytic site [active] 557598007634 ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagH; COG1134 557598007635 ATP-binding cassette component of polysaccharide transport system; Region: ABC_KpsT_Wzt; cd03220 557598007636 Walker A/P-loop; other site 557598007637 ATP binding site [chemical binding]; other site 557598007638 Q-loop/lid; other site 557598007639 ABC transporter signature motif; other site 557598007640 Walker B; other site 557598007641 D-loop; other site 557598007642 H-loop/switch region; other site 557598007643 C-Terminal domain of O-antigenic polysaccharide transporter protein Wzt and related proteins; Region: Wzt_C-like; cd10147 557598007644 putative carbohydrate binding site [chemical binding]; other site 557598007645 ABC-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagG; COG1682 557598007646 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 557598007647 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557598007648 NAD(P) binding site [chemical binding]; other site 557598007649 active site 557598007650 Bordetella bronchiseptica enzymes WbmH and WbmG-like, extended (e) SDRs; Region: WbmH_like_SDR_e; cd08957 557598007651 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 557598007652 NAD binding site [chemical binding]; other site 557598007653 homodimer interface [polypeptide binding]; other site 557598007654 active site 557598007655 putative substrate binding site [chemical binding]; other site 557598007656 Bordetella bronchiseptica enzymes WbmH and WbmG-like, extended (e) SDRs; Region: WbmH_like_SDR_e; cd08957 557598007657 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 557598007658 NAD binding site [chemical binding]; other site 557598007659 homodimer interface [polypeptide binding]; other site 557598007660 active site 557598007661 putative substrate binding site [chemical binding]; other site 557598007662 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 557598007663 active site 557598007664 UDP-N-acetylglucosamine 2-epimerase; Region: Epimerase_2; pfam02350 557598007665 homodimer interface [polypeptide binding]; other site 557598007666 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 557598007667 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 557598007668 inhibitor-cofactor binding pocket; inhibition site 557598007669 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557598007670 catalytic residue [active] 557598007671 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 557598007672 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 557598007673 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 557598007674 Vi polysaccharide biosynthesis protein TviB; Provisional; Region: PRK15182 557598007675 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 557598007676 UDP binding domain; Region: UDPG_MGDP_dh_C; smart00984 557598007677 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 557598007678 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 557598007679 putative DNA binding site [nucleotide binding]; other site 557598007680 putative Zn2+ binding site [ion binding]; other site 557598007681 AsnC family; Region: AsnC_trans_reg; pfam01037 557598007682 Dipeptide/tripeptide permease [Amino acid transport and metabolism]; Region: PTR2; COG3104 557598007683 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 557598007684 POT family; Region: PTR2; cl17359 557598007685 Transcriptional regulators RcnR and FrmR, and related domains; this domain family was previously known as part of DUF156; Region: RcnR-FrmR-like_DUF156; cd10153 557598007686 putative metal binding site [ion binding]; other site 557598007687 putative homodimer interface [polypeptide binding]; other site 557598007688 putative homotetramer interface [polypeptide binding]; other site 557598007689 putative homodimer-homodimer interface [polypeptide binding]; other site 557598007690 putative allosteric switch controlling residues; other site 557598007691 High-affinity nickel-transport protein; Region: NicO; cl00964 557598007692 High-affinity nickel-transport protein; Region: NicO; cl00964 557598007693 N-Utilization Substance G (NusG) N-terminal (NGN) domain Superfamily; Region: NGN; cl02766 557598007694 transcriptional activator RfaH; Region: RfaH; TIGR01955 557598007695 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 557598007696 heterodimer interface [polypeptide binding]; other site 557598007697 homodimer interface [polypeptide binding]; other site 557598007698 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 557598007699 PAS domain; Region: PAS_9; pfam13426 557598007700 putative active site [active] 557598007701 heme pocket [chemical binding]; other site 557598007702 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 557598007703 HAMP domain; Region: HAMP; pfam00672 557598007704 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 557598007705 Membrane-bound lytic murein transglycosylase [Cell envelope biogenesis, outer membrane]; Region: MltA; COG2821 557598007706 MltA specific insert domain; Region: MltA; smart00925 557598007707 3D domain; Region: 3D; pfam06725 557598007708 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 557598007709 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 557598007710 HlyD family secretion protein; Region: HlyD_3; pfam13437 557598007711 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 557598007712 Protein export membrane protein; Region: SecD_SecF; cl14618 557598007713 methylcobalamin:coenzyme M methyltransferase; Validated; Region: PRK06252 557598007714 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 557598007715 substrate binding site [chemical binding]; other site 557598007716 active site 557598007717 primosome assembly protein PriA; Validated; Region: PRK05580 557598007718 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 557598007719 ATP binding site [chemical binding]; other site 557598007720 putative Mg++ binding site [ion binding]; other site 557598007721 helicase superfamily c-terminal domain; Region: HELICc; smart00490 557598007722 ATP-binding site [chemical binding]; other site 557598007723 succinic semialdehyde dehydrogenase; Region: PLN02278 557598007724 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 557598007725 tetramerization interface [polypeptide binding]; other site 557598007726 NAD(P) binding site [chemical binding]; other site 557598007727 catalytic residues [active] 557598007728 4-aminobutyrate aminotransferase; Provisional; Region: PRK07495 557598007729 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 557598007730 inhibitor-cofactor binding pocket; inhibition site 557598007731 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557598007732 catalytic residue [active] 557598007733 outer membrane channel protein; Reviewed; Region: tolC; PRK09465 557598007734 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 557598007735 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 557598007736 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 557598007737 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 557598007738 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 557598007739 feedback inhibition sensing region; other site 557598007740 homohexameric interface [polypeptide binding]; other site 557598007741 nucleotide binding site [chemical binding]; other site 557598007742 N-acetyl-L-glutamate binding site [chemical binding]; other site 557598007743 FOG: CBS domain [General function prediction only]; Region: COG0517 557598007744 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_10; cd04623 557598007745 pyrimidine 5'-nucleotidase; Region: Pyr-5-nucltdase; TIGR01993 557598007746 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 557598007747 motif II; other site 557598007748 VanZ like family; Region: VanZ; cl01971 557598007749 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 557598007750 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557598007751 dimer interface [polypeptide binding]; other site 557598007752 putative CheW interface [polypeptide binding]; other site 557598007753 nitrate/nitrite transport protein NarU; Provisional; Region: PRK15034 557598007754 D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 4) [Cell envelope biogenesis, outer membrane]; Region: DacB; COG2027 557598007755 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 557598007756 GSH binding site [chemical binding]; other site 557598007757 catalytic residues [active] 557598007758 preprotein translocase subunit SecB; Validated; Region: PRK05751 557598007759 SecA binding site; other site 557598007760 Preprotein binding site; other site 557598007761 Bacterial SH3 domain; Region: SH3_4; pfam06347 557598007762 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 557598007763 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 557598007764 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 557598007765 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 557598007766 transcriptional regulator PdhR; Reviewed; Region: pdhR; PRK09464 557598007767 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 557598007768 DNA-binding site [nucleotide binding]; DNA binding site 557598007769 This entry represents the C-terminal ligand binding domain of many members of the GntR family; Region: FCD; smart00895 557598007770 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 557598007771 Cysteine-rich domain; Region: CCG; pfam02754 557598007772 Cysteine-rich domain; Region: CCG; pfam02754 557598007773 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 557598007774 Uncharacterized conserved protein containing a ferredoxin-like domain [Energy production and conversion]; Region: COG1139 557598007775 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 557598007776 Domain of unknown function (DUF3390); Region: DUF3390; pfam11870 557598007777 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 557598007778 FAD binding domain; Region: FAD_binding_4; pfam01565 557598007779 4Fe-4S dicluster domain; Region: Fer4_17; pfam13534 557598007780 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 557598007781 glutathione-regulated potassium-efflux system protein KefB; Provisional; Region: PRK03659 557598007782 transporter, monovalent cation:proton antiporter-2 (CPA2) family; Region: 2a37; TIGR00932 557598007783 TrkA-N domain; Region: TrkA_N; pfam02254 557598007784 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 557598007785 succinate CoA transferase; Region: YgfH_subfam; TIGR03458 557598007786 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 557598007787 RmuC family; Region: RmuC; pfam02646 557598007788 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 557598007789 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557598007790 metal binding site [ion binding]; metal-binding site 557598007791 active site 557598007792 I-site; other site 557598007793 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 557598007794 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 557598007795 trimer interface [polypeptide binding]; other site 557598007796 active site 557598007797 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01096 557598007798 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 557598007799 Zn2+ binding site [ion binding]; other site 557598007800 Mg2+ binding site [ion binding]; other site 557598007801 YcaC related amidohydrolases; E.coli YcaC is an homooctameric hydrolase with unknown specificity. Despite its weak sequence similarity, it is structurally related to other amidohydrolases and shares conserved active site residues with them; Region: YcaC_related; cd01012 557598007802 Isochorismatase family; Region: Isochorismatase; pfam00857 557598007803 catalytic triad [active] 557598007804 dimer interface [polypeptide binding]; other site 557598007805 conserved cis-peptide bond; other site 557598007806 Uncharacterized protein conserved in bacteria (DUF2322); Region: DUF2322; cl01820 557598007807 FeS assembly protein IscX; Region: iscX_yfhJ; TIGR03412 557598007808 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; cl00022 557598007809 putative deacylase active site [active] 557598007810 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 557598007811 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 557598007812 catalytic loop [active] 557598007813 iron binding site [ion binding]; other site 557598007814 chaperone protein HscA; Provisional; Region: hscA; PRK05183 557598007815 Nucleotide-binding domain of HscA and similar proteins; Region: HscA_like_NBD; cd10236 557598007816 nucleotide binding site [chemical binding]; other site 557598007817 putative NEF/HSP70 interaction site [polypeptide binding]; other site 557598007818 SBD interface [polypeptide binding]; other site 557598007819 co-chaperone HscB; Provisional; Region: hscB; PRK03578 557598007820 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 557598007821 HSP70 interaction site [polypeptide binding]; other site 557598007822 HSCB C-terminal oligomerisation domain; Region: HSCB_C; pfam07743 557598007823 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 557598007824 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 557598007825 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 557598007826 trimerization site [polypeptide binding]; other site 557598007827 active site 557598007828 cysteine desulfurase; Provisional; Region: PRK14012 557598007829 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 557598007830 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 557598007831 catalytic residue [active] 557598007832 iron-sulfur cluster assembly transcription factor IscR; Region: IscR; TIGR02010 557598007833 Rrf2 family protein; Region: rrf2_super; TIGR00738 557598007834 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 557598007835 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 557598007836 Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis]; Region: HemK; COG2890 557598007837 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 557598007838 Transcriptional regulator [Transcription]; Region: LysR; COG0583 557598007839 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 557598007840 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 557598007841 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 557598007842 NAD(P) binding site [chemical binding]; other site 557598007843 active site 557598007844 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 557598007845 active site 557598007846 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 557598007847 dTDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]; Region: RfbA; COG1209 557598007848 active site 557598007849 tetramer interface; other site 557598007850 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 557598007851 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 557598007852 nucleotide binding pocket [chemical binding]; other site 557598007853 K-X-D-G motif; other site 557598007854 catalytic site [active] 557598007855 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 557598007856 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 557598007857 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 557598007858 Dimer interface [polypeptide binding]; other site 557598007859 ZipA, C-terminal domain (FtsZ-binding); Region: ZipA_C; smart00771 557598007860 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 557598007861 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 557598007862 Walker A/P-loop; other site 557598007863 ATP binding site [chemical binding]; other site 557598007864 Q-loop/lid; other site 557598007865 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 557598007866 ABC transporter signature motif; other site 557598007867 Walker B; other site 557598007868 D-loop; other site 557598007869 H-loop/switch region; other site 557598007870 hypothetical protein; Validated; Region: PRK00228 557598007871 Uncharacterized protein family (UPF0081); Region: UPF0081; pfam03652 557598007872 Protein of unknown function (DUF3592); Region: DUF3592; pfam12158 557598007873 ClpXP protease specificity-enhancing factor; Provisional; Region: PRK11798 557598007874 stringent starvation protein A; Provisional; Region: sspA; PRK09481 557598007875 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 557598007876 C-terminal domain interface [polypeptide binding]; other site 557598007877 putative GSH binding site (G-site) [chemical binding]; other site 557598007878 dimer interface [polypeptide binding]; other site 557598007879 C-terminal, alpha helical domain of Stringent starvation protein A; Region: GST_C_SspA; cd03186 557598007880 dimer interface [polypeptide binding]; other site 557598007881 N-terminal domain interface [polypeptide binding]; other site 557598007882 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 557598007883 Cytochrome b subunit of the bc complex [Energy production and conversion]; Region: QcrB; COG1290 557598007884 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 557598007885 Qi binding site; other site 557598007886 intrachain domain interface; other site 557598007887 interchain domain interface [polypeptide binding]; other site 557598007888 heme bH binding site [chemical binding]; other site 557598007889 heme bL binding site [chemical binding]; other site 557598007890 Qo binding site; other site 557598007891 interchain domain interface [polypeptide binding]; other site 557598007892 intrachain domain interface; other site 557598007893 Qi binding site; other site 557598007894 Cytochrome b(C-terminal)/b6/petD; Region: Cytochrom_B_C; pfam00032 557598007895 Qo binding site; other site 557598007896 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 557598007897 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 557598007898 [2Fe-2S] cluster binding site [ion binding]; other site 557598007899 Uncharacterized conserved protein [Function unknown]; Region: COG0327 557598007900 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl15371 557598007901 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 557598007902 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 557598007903 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 557598007904 Glutaryl-CoA dehydrogenase; Region: GCD; cd01151 557598007905 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 557598007906 FAD binding site [chemical binding]; other site 557598007907 substrate binding pocket [chemical binding]; other site 557598007908 catalytic base [active] 557598007909 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 557598007910 dimer interface [polypeptide binding]; other site 557598007911 active site 557598007912 aspartate-rich active site metal binding site; other site 557598007913 allosteric magnesium binding site [ion binding]; other site 557598007914 Schiff base residues; other site 557598007915 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 557598007916 dimerization interface [polypeptide binding]; other site 557598007917 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 557598007918 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557598007919 metal binding site [ion binding]; metal-binding site 557598007920 active site 557598007921 I-site; other site 557598007922 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 557598007923 NMT1-like family; Region: NMT1_2; pfam13379 557598007924 ABC transporter, substrate-binding protein, aliphatic sulfonates family; Region: SsuA_fam; TIGR01728 557598007925 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 557598007926 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 557598007927 active site 557598007928 substrate binding site [chemical binding]; other site 557598007929 metal binding site [ion binding]; metal-binding site 557598007930 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 557598007931 dihydropteroate synthase; Region: DHPS; TIGR01496 557598007932 substrate binding pocket [chemical binding]; other site 557598007933 dimer interface [polypeptide binding]; other site 557598007934 inhibitor binding site; inhibition site 557598007935 ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]; Region: HflB; COG0465 557598007936 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 557598007937 Walker A motif; other site 557598007938 ATP binding site [chemical binding]; other site 557598007939 Walker B motif; other site 557598007940 arginine finger; other site 557598007941 Peptidase family M41; Region: Peptidase_M41; pfam01434 557598007942 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 557598007943 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 557598007944 S-adenosylmethionine binding site [chemical binding]; other site 557598007945 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]; Region: COG1534 557598007946 Domain of unknown function (DUF4149); Region: DUF4149; pfam13664 557598007947 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 557598007948 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 557598007949 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 557598007950 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 557598007951 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 557598007952 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 557598007953 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 557598007954 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 557598007955 ATP-grasp domain; Region: ATP-grasp_4; cl17255 557598007956 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 557598007957 IMP binding site; other site 557598007958 dimer interface [polypeptide binding]; other site 557598007959 interdomain contacts; other site 557598007960 partial ornithine binding site; other site 557598007961 leucine export protein LeuE; Provisional; Region: PRK10958 557598007962 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 557598007963 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; smart01097 557598007964 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 557598007965 catalytic site [active] 557598007966 subunit interface [polypeptide binding]; other site 557598007967 Sulfatase; Region: Sulfatase; cl17466 557598007968 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 557598007969 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 557598007970 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 557598007971 active site 557598007972 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 557598007973 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 557598007974 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 557598007975 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 557598007976 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 557598007977 Electron transfer flavoprotein domain; Region: ETF; pfam01012 557598007978 Ligand binding site [chemical binding]; other site 557598007979 (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 557598007980 dimer interaction site [polypeptide binding]; other site 557598007981 substrate-binding tunnel; other site 557598007982 active site 557598007983 catalytic site [active] 557598007984 substrate binding site [chemical binding]; other site 557598007985 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 557598007986 Bacterial transglutaminase-like cysteine proteinase BTLCP; Region: BTLCP; cl17596 557598007987 HAMP domain; Region: HAMP; pfam00672 557598007988 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557598007989 metal binding site [ion binding]; metal-binding site 557598007990 active site 557598007991 I-site; other site 557598007992 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 557598007993 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 557598007994 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 557598007995 metal ion-dependent adhesion site (MIDAS); other site 557598007996 RTX toxins and related Ca2+-binding proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2931 557598007997 PA14 domain; Region: PA14; cl08459 557598007998 type I secretion C-terminal target domain (VC_A0849 subclass); Region: T1SS_VCA0849; TIGR03661 557598007999 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 557598008000 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 557598008001 DNA binding residues [nucleotide binding] 557598008002 dimerization interface [polypeptide binding]; other site 557598008003 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 557598008004 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 557598008005 HlyD family secretion protein; Region: HlyD_3; pfam13437 557598008006 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_C39_likeD; cd02421 557598008007 type I secretion system ATPase, LssB family; Region: type_I_sec_LssB; TIGR03375 557598008008 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 557598008009 ATP-binding cassette domain of bacteriocin exporters, subfamily C; Region: ABCC_bacteriocin_exporters; cd03245 557598008010 Walker A/P-loop; other site 557598008011 ATP binding site [chemical binding]; other site 557598008012 Q-loop/lid; other site 557598008013 ABC transporter signature motif; other site 557598008014 Walker B; other site 557598008015 D-loop; other site 557598008016 H-loop/switch region; other site 557598008017 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 557598008018 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 557598008019 active site 557598008020 Zn binding site [ion binding]; other site 557598008021 Ion channel; Region: Ion_trans_2; pfam07885 557598008022 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 557598008023 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 557598008024 trimer interface [polypeptide binding]; other site 557598008025 putative metal binding site [ion binding]; other site 557598008026 Invasion gene expression up-regulator, SirB; Region: SirB; pfam04247 557598008027 DNA-binding transcriptional repressor AcrR; Provisional; Region: PRK10668 557598008028 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 557598008029 MAATS-type transcriptional repressor, C-terminal region; Region: TetR_C_2; pfam08361 557598008030 periplasmic multidrug efflux lipoprotein precursor; Reviewed; Region: PRK09578 557598008031 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 557598008032 HlyD family secretion protein; Region: HlyD_3; pfam13437 557598008033 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 557598008034 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 557598008035 putative aminotransferase; Provisional; Region: PRK09105 557598008036 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 557598008037 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557598008038 homodimer interface [polypeptide binding]; other site 557598008039 catalytic residue [active] 557598008040 Ammonia permease [Inorganic ion transport and metabolism]; Region: AmtB; COG0004 557598008041 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 557598008042 Nitrogen regulatory protein P-II; Region: P-II; smart00938 557598008043 Membrane fusogenic activity; Region: BMFP; pfam04380 557598008044 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 557598008045 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 557598008046 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 557598008047 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 557598008048 Sporulation related domain; Region: SPOR; pfam05036 557598008049 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 557598008050 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 557598008051 catalytic residues [active] 557598008052 hinge region; other site 557598008053 alpha helical domain; other site 557598008054 undecaprenyl pyrophosphate phosphatase; Reviewed; Region: PRK00281 557598008055 Cytochrome c5 [Energy production and conversion]; Region: CycB; COG3245 557598008056 Cytochrome c5 [Energy production and conversion]; Region: CycB; COG3245 557598008057 Predicted membrane protein [Function unknown]; Region: COG2855 557598008058 Protein of unknown function (DUF3025); Region: DUF3025; pfam11227 557598008059 Siroheme synthase (precorrin-2 oxidase/ferrochelatase domain) [Coenzyme metabolism]; Region: CysG; COG1648 557598008060 Putative NAD(P)-binding; Region: NAD_binding_7; pfam13241 557598008061 Sirohaem synthase dimerisation region; Region: CysG_dimeriser; pfam10414 557598008062 S-AdoMet dependent tetrapyrrole methylases; Region: TP_methylase; cl00304 557598008063 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 557598008064 active pocket/dimerization site; other site 557598008065 active site 557598008066 phosphorylation site [posttranslational modification] 557598008067 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 557598008068 dimerization domain swap beta strand [polypeptide binding]; other site 557598008069 regulatory protein interface [polypeptide binding]; other site 557598008070 active site 557598008071 regulatory phosphorylation site [posttranslational modification]; other site 557598008072 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 557598008073 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 557598008074 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 557598008075 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 557598008076 lipid A export permease/ATP-binding protein MsbA; Region: MsbA_lipidA; TIGR02203 557598008077 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 557598008078 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 557598008079 Walker A/P-loop; other site 557598008080 ATP binding site [chemical binding]; other site 557598008081 Q-loop/lid; other site 557598008082 ABC transporter signature motif; other site 557598008083 Walker B; other site 557598008084 D-loop; other site 557598008085 H-loop/switch region; other site 557598008086 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 557598008087 putative metal binding site; other site 557598008088 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 557598008089 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 557598008090 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 557598008091 Glycosyl transferase family 2; Region: Glycos_transf_2; pfam00535 557598008092 active site 557598008093 O-Antigen ligase; Region: Wzy_C; pfam04932 557598008094 Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimV; COG3170 557598008095 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 557598008096 active site 557598008097 dimer interface [polypeptide binding]; other site 557598008098 metal binding site [ion binding]; metal-binding site 557598008099 shikimate kinase; Reviewed; Region: aroK; PRK00131 557598008100 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 557598008101 ADP binding site [chemical binding]; other site 557598008102 magnesium binding site [ion binding]; other site 557598008103 putative shikimate binding site; other site 557598008104 penicillin-binding protein 1a; Provisional; Region: mrcA; PRK11636 557598008105 Transglycosylase; Region: Transgly; pfam00912 557598008106 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 557598008107 Methyltransferase domain; Region: Methyltransf_23; pfam13489 557598008108 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 557598008109 S-adenosylmethionine binding site [chemical binding]; other site 557598008110 homoserine O-acetyltransferase; Provisional; Region: metX; PRK00175 557598008111 homoserine O-acetyltransferase; Region: homoserO_Ac_trn; TIGR01392 557598008112 Predicted Fe-S oxidoreductase [General function prediction only]; Region: COG1242 557598008113 phosphoethanolamine transferase; Provisional; Region: PRK11560 557598008114 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 557598008115 Sulfatase; Region: Sulfatase; pfam00884 557598008116 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 557598008117 Mechanosensitive ion channel; Region: MS_channel; pfam00924 557598008118 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 557598008119 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 557598008120 substrate binding pocket [chemical binding]; other site 557598008121 chain length determination region; other site 557598008122 substrate-Mg2+ binding site; other site 557598008123 catalytic residues [active] 557598008124 aspartate-rich region 1; other site 557598008125 active site lid residues [active] 557598008126 aspartate-rich region 2; other site 557598008127 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 557598008128 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 557598008129 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 557598008130 GTPase CgtA; Reviewed; Region: obgE; PRK12299 557598008131 GTP1/OBG; Region: GTP1_OBG; pfam01018 557598008132 Obg GTPase; Region: Obg; cd01898 557598008133 G1 box; other site 557598008134 GTP/Mg2+ binding site [chemical binding]; other site 557598008135 Switch I region; other site 557598008136 G2 box; other site 557598008137 G3 box; other site 557598008138 Switch II region; other site 557598008139 G4 box; other site 557598008140 G5 box; other site 557598008141 Acetyl-coenzyme A transporter 1; Region: Acatn; pfam13000 557598008142 muropeptide transporter; Reviewed; Region: ampG; PRK11902 557598008143 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 557598008144 putative substrate translocation pore; other site 557598008145 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 557598008146 putative deacylase active site [active] 557598008147 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 557598008148 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 557598008149 putative substrate translocation pore; other site 557598008150 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 557598008151 ArsC family; Region: ArsC; pfam03960 557598008152 catalytic residues [active] 557598008153 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 557598008154 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 557598008155 ribonuclease BN/unknown domain fusion protein; Reviewed; Region: rbn; PRK04214 557598008156 Virulence factor BrkB; Region: Virul_fac_BrkB; cl07918 557598008157 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 557598008158 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 557598008159 EamA-like transporter family; Region: EamA; pfam00892 557598008160 EamA-like transporter family; Region: EamA; pfam00892 557598008161 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 557598008162 Domain of unknown function (DUF3391); Region: DUF3391; pfam11871 557598008163 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 557598008164 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 557598008165 Zn2+ binding site [ion binding]; other site 557598008166 Mg2+ binding site [ion binding]; other site 557598008167 DNA polymerase I; Provisional; Region: PRK05755 557598008168 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 557598008169 active site 557598008170 metal binding site 1 [ion binding]; metal-binding site 557598008171 putative 5' ssDNA interaction site; other site 557598008172 metal binding site 3; metal-binding site 557598008173 metal binding site 2 [ion binding]; metal-binding site 557598008174 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 557598008175 putative DNA binding site [nucleotide binding]; other site 557598008176 putative metal binding site [ion binding]; other site 557598008177 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 557598008178 active site 557598008179 catalytic site [active] 557598008180 substrate binding site [chemical binding]; other site 557598008181 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 557598008182 active site 557598008183 DNA binding site [nucleotide binding] 557598008184 catalytic site [active] 557598008185 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]; Region: COG1611 557598008186 Protein of unknown function (DUF2782); Region: DUF2782; pfam11191 557598008187 Putative homoserine kinase type II (protein kinase fold) [General function prediction only]; Region: COG2334 557598008188 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 557598008189 putative active site [active] 557598008190 putative substrate binding site [chemical binding]; other site 557598008191 ATP binding site [chemical binding]; other site 557598008192 TRAP-type mannitol/chloroaromatic compound transport system, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT1; COG4663 557598008193 Bacterial extracellular solute-binding protein, family 7; Region: SBP_bac_7; pfam03480 557598008194 TRAP-type mannitol/chloroaromatic compound transport system, small permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT2; COG4665 557598008195 TRAP-type mannitol/chloroaromatic compound transport system, large permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT3; COG4664 557598008196 TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]; Region: DctQ; cl17274 557598008197 Extended Signal Peptide of Type V secretion system; Region: ESPR; pfam13018 557598008198 Uncharacterized protein with a C-terminal OMP (outer membrane protein) domain [Function unknown]; Region: COG4625 557598008199 Autotransporter beta-domain; Region: Autotransporter; smart00869 557598008200 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 557598008201 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 557598008202 FAD binding pocket [chemical binding]; other site 557598008203 FAD binding motif [chemical binding]; other site 557598008204 phosphate binding motif [ion binding]; other site 557598008205 beta-alpha-beta structure motif; other site 557598008206 NAD binding pocket [chemical binding]; other site 557598008207 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: dTDP_sugar_isom; pfam00908 557598008208 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 557598008209 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 557598008210 substrate binding site; other site 557598008211 tetramer interface; other site 557598008212 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 557598008213 RmlD substrate binding domain; Region: RmlD_sub_bind; pfam04321 557598008214 NADP binding site [chemical binding]; other site 557598008215 active site 557598008216 putative substrate binding site [chemical binding]; other site 557598008217 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 557598008218 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 557598008219 NAD binding site [chemical binding]; other site 557598008220 substrate binding site [chemical binding]; other site 557598008221 homodimer interface [polypeptide binding]; other site 557598008222 active site 557598008223 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 557598008224 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 557598008225 glutaminase active site [active] 557598008226 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 557598008227 dimer interface [polypeptide binding]; other site 557598008228 active site 557598008229 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 557598008230 dimer interface [polypeptide binding]; other site 557598008231 active site 557598008232 N-acetylglucosamine-1-phosphate uridyltransferase (contains nucleotidyltransferase and I-patch acetyltransferase domains) [Cell envelope biogenesis, outer membrane]; Region: GlmU; COG1207 557598008233 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 557598008234 Substrate binding site; other site 557598008235 Mg++ binding site; other site 557598008236 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 557598008237 active site 557598008238 substrate binding site [chemical binding]; other site 557598008239 CoA binding site [chemical binding]; other site 557598008240 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 557598008241 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 557598008242 gamma subunit interface [polypeptide binding]; other site 557598008243 epsilon subunit interface [polypeptide binding]; other site 557598008244 LBP interface [polypeptide binding]; other site 557598008245 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 557598008246 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 557598008247 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 557598008248 alpha subunit interaction interface [polypeptide binding]; other site 557598008249 Walker A motif; other site 557598008250 ATP binding site [chemical binding]; other site 557598008251 Walker B motif; other site 557598008252 inhibitor binding site; inhibition site 557598008253 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 557598008254 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 557598008255 core domain interface [polypeptide binding]; other site 557598008256 delta subunit interface [polypeptide binding]; other site 557598008257 epsilon subunit interface [polypeptide binding]; other site 557598008258 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 557598008259 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 557598008260 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 557598008261 beta subunit interaction interface [polypeptide binding]; other site 557598008262 Walker A motif; other site 557598008263 ATP binding site [chemical binding]; other site 557598008264 Walker B motif; other site 557598008265 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 557598008266 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 557598008267 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 557598008268 F0F1 ATP synthase subunit B; Validated; Region: PRK05759 557598008269 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 557598008270 F0F1 ATP synthase subunit C; Validated; Region: PRK06876 557598008271 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 557598008272 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 557598008273 ATP synthase I chain; Region: ATP_synt_I; cl09170 557598008274 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 557598008275 ParB-like nuclease domain; Region: ParBc; pfam02195 557598008276 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 557598008277 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 557598008278 P-loop; other site 557598008279 Magnesium ion binding site [ion binding]; other site 557598008280 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 557598008281 Magnesium ion binding site [ion binding]; other site 557598008282 rRNA small subunit methyltransferase G; Region: GidB; pfam02527 557598008283 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 557598008284 S-adenosylmethionine binding site [chemical binding]; other site 557598008285 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 557598008286 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 557598008287 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 557598008288 Acetyltransferase (GNAT) domain; Region: Acetyltransf_5; cl17496 557598008289 Protein of unknown function (DUF445); Region: DUF445; pfam04286 557598008290 Escherichia coli YaeB and related proteins; Region: UPF0066; cd09281 557598008291 homodimer interaction site [polypeptide binding]; other site 557598008292 cofactor binding site; other site 557598008293 Tim44 is an essential component of the machinery that mediates the translocation of nuclear-encoded proteins across the mitochondrial inner membrane; Region: Tim44; smart00978 557598008294 Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]; Region: TerC; COG0861 557598008295 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 557598008296 Transporter associated domain; Region: CorC_HlyC; cl08393 557598008297 BON domain; Region: BON; cl02771 557598008298 Predicted periplasmic or secreted lipoprotein [General function prediction only]; Region: OsmY; COG2823 557598008299 BON domain; Region: BON; pfam04972 557598008300 Phosphoheptose isomerase is a member of the SIS (Sugar ISomerase) superfamily. Phosphoheptose isomerase catalyzes the isomerization of sedoheptulose 7-phosphate into D-glycero-D-mannoheptose 7-phosphate. This is the first step of the biosynthesis of...; Region: SIS_GmhA; cd05006 557598008301 dimer interface [polypeptide binding]; other site 557598008302 active site 557598008303 hypothetical protein; Reviewed; Region: PRK12497 557598008304 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 557598008305 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 557598008306 Predicted methyltransferases [General function prediction only]; Region: COG0313 557598008307 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 557598008308 putative SAM binding site [chemical binding]; other site 557598008309 putative homodimer interface [polypeptide binding]; other site 557598008310 Cache domain; Region: Cache_1; pfam02743 557598008311 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 557598008312 dimerization interface [polypeptide binding]; other site 557598008313 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 557598008314 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557598008315 dimer interface [polypeptide binding]; other site 557598008316 putative CheW interface [polypeptide binding]; other site 557598008317 DNA-binding transcriptional activator GcvA; Provisional; Region: PRK11139 557598008318 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 557598008319 The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in control of the expression of beta-lactamase gene ampC, contains the type 2 periplasmic binding fold; Region: PBP2_AmpR; cd08488 557598008320 putative dimerization interface [polypeptide binding]; other site 557598008321 putative substrate binding pocket [chemical binding]; other site 557598008322 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 557598008323 beta-lactamase/D-alanine carboxypeptidase; Provisional; Region: ampC; PRK11289 557598008324 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 557598008325 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 557598008326 active site 557598008327 serine/threonine transporter SstT; Provisional; Region: PRK13628 557598008328 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 557598008329 Transcriptional regulators CsoR (copper-sensitive operon repressor), RcnR, and FrmR, and related domains; this domain superfamily was previously known as DUF156; Region: CsoR-like_DUF156; cd10148 557598008330 putative homodimer interface [polypeptide binding]; other site 557598008331 putative homotetramer interface [polypeptide binding]; other site 557598008332 putative allosteric switch controlling residues; other site 557598008333 putative metal binding site [ion binding]; other site 557598008334 putative homodimer-homodimer interface [polypeptide binding]; other site 557598008335 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 557598008336 metal-binding site [ion binding] 557598008337 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 557598008338 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 557598008339 metal-binding site [ion binding] 557598008340 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 557598008341 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 557598008342 metal-binding site [ion binding] 557598008343 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 557598008344 Soluble P-type ATPase [General function prediction only]; Region: COG4087 557598008345 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 557598008346 4-hydroxythreonine-4-phosphate dehydrogenase; Region: pdxA; TIGR00557 557598008347 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK06943 557598008348 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 557598008349 inhibitor-cofactor binding pocket; inhibition site 557598008350 pyridoxal 5'-phosphate binding site [chemical binding]; other site 557598008351 catalytic residue [active] 557598008352 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 557598008353 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; cl17251 557598008354 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 557598008355 SEC-C motif; Region: SEC-C; pfam02810 557598008356 Lipid A 3-O-deacylase (PagL); Region: PagL; pfam09411 557598008357 FeoA domain; Region: FeoA; pfam04023 557598008358 ferrous iron transport protein B; Reviewed; Region: feoB; PRK09554 557598008359 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 557598008360 G1 box; other site 557598008361 GTP/Mg2+ binding site [chemical binding]; other site 557598008362 Switch I region; other site 557598008363 G2 box; other site 557598008364 G3 box; other site 557598008365 Switch II region; other site 557598008366 G4 box; other site 557598008367 G5 box; other site 557598008368 Nucleoside recognition; Region: Gate; pfam07670 557598008369 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 557598008370 Nucleoside recognition; Region: Gate; pfam07670 557598008371 FeoC like transcriptional regulator; Region: FeoC; cl17677 557598008372 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 557598008373 trimer interface [polypeptide binding]; other site 557598008374 dimer interface [polypeptide binding]; other site 557598008375 putative active site [active] 557598008376 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 557598008377 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 557598008378 cell division protein FtsZ; Validated; Region: PRK09330 557598008379 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 557598008380 nucleotide binding site [chemical binding]; other site 557598008381 SulA interaction site; other site 557598008382 cell division protein FtsA; Region: ftsA; TIGR01174 557598008383 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 557598008384 nucleotide binding site [chemical binding]; other site 557598008385 Cell division protein FtsA; Region: FtsA; pfam14450 557598008386 Cell division septal protein [Cell envelope biogenesis, outer membrane]; Region: FtsQ; COG1589 557598008387 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 557598008388 Cell division protein FtsQ; Region: FtsQ; pfam03799 557598008389 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 557598008390 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 557598008391 ATP-grasp domain; Region: ATP-grasp_4; cl17255 557598008392 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 557598008393 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 557598008394 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 557598008395 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 557598008396 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 557598008397 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 557598008398 active site 557598008399 homodimer interface [polypeptide binding]; other site 557598008400 cell division protein FtsW; Region: ftsW; TIGR02614 557598008401 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK04308 557598008402 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 557598008403 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 557598008404 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 557598008405 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 557598008406 Mg++ binding site [ion binding]; other site 557598008407 putative catalytic motif [active] 557598008408 putative substrate binding site [chemical binding]; other site 557598008409 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 557598008410 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 557598008411 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 557598008412 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 557598008413 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 557598008414 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 557598008415 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 557598008416 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 557598008417 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 557598008418 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 557598008419 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 557598008420 Cell division protein FtsL; Region: FtsL; pfam04999 557598008421 MraW methylase family; Region: Methyltransf_5; cl17771 557598008422 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 557598008423 MraZ protein; Region: MraZ; pfam02381 557598008424 cell division protein MraZ; Reviewed; Region: PRK00326 557598008425 MraZ protein; Region: MraZ; pfam02381 557598008426 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 557598008427 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 557598008428 GatB domain; Region: GatB_Yqey; smart00845 557598008429 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 557598008430 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 557598008431 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 557598008432 rod shape-determining protein MreB; Provisional; Region: PRK13927 557598008433 MreB and similar proteins; Region: MreB_like; cd10225 557598008434 nucleotide binding site [chemical binding]; other site 557598008435 Mg binding site [ion binding]; other site 557598008436 putative protofilament interaction site [polypeptide binding]; other site 557598008437 RodZ interaction site [polypeptide binding]; other site 557598008438 rod shape-determining protein MreC; Provisional; Region: PRK13922 557598008439 rod shape-determining protein MreC; Region: MreC; pfam04085 557598008440 rod shape-determining protein MreD; Region: shape_MreD; TIGR03426 557598008441 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 557598008442 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 557598008443 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 557598008444 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 557598008445 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 557598008446 EamA-like transporter family; Region: EamA; pfam00892 557598008447 EamA-like transporter family; Region: EamA; pfam00892 557598008448 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 557598008449 EamA-like transporter family; Region: EamA; pfam00892 557598008450 N-Dimethylarginine dimethylaminohydrolase [Amino acid transport and metabolism]; Region: COG1834 557598008451 Amidinotransferase; Region: Amidinotransf; cl12043 557598008452 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 557598008453 ATP binding site [chemical binding]; other site 557598008454 active site 557598008455 substrate binding site [chemical binding]; other site 557598008456 LabA_like proteins; Region: LabA_like; cd06167 557598008457 putative metal binding site [ion binding]; other site 557598008458 Uncharacterized conserved protein [Function unknown]; Region: COG1432 557598008459 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 557598008460 ATP-grasp domain; Region: ATP-grasp; pfam02222 557598008461 Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase [Nucleotide transport and metabolism]; Region: PurE; COG0041 557598008462 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 557598008463 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 557598008464 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 557598008465 substrate binding site [chemical binding]; other site 557598008466 ATP binding site [chemical binding]; other site 557598008467 glutamate--cysteine ligase, T. ferrooxidans family; Region: gshA_ferroox; TIGR02049 557598008468 Glutamate-cysteine ligase; Region: GshA; pfam08886 557598008469 Dihaem cytochrome c; Region: DHC; pfam09626 557598008470 Domain of unknown function (DUF1924); Region: DUF1924; pfam09086 557598008471 NADH:flavorubredoxin oxidoreductase; Provisional; Region: PRK04965 557598008472 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 557598008473 Rubredoxin [Energy production and conversion]; Region: COG1773 557598008474 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 557598008475 iron binding site [ion binding]; other site 557598008476 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; cl00859 557598008477 Protein of unknown function (DUF3313); Region: DUF3313; pfam11769 557598008478 glutathione synthetase; Provisional; Region: PRK05246 557598008479 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 557598008480 Prokaryotic glutathione synthetase, ATP-grasp domain; Region: GSH-S_ATP; pfam02955 557598008481 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 557598008482 ApbE family; Region: ApbE; pfam02424 557598008483 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 557598008484 G1 box; other site 557598008485 GTP/Mg2+ binding site [chemical binding]; other site 557598008486 Switch I region; other site 557598008487 G2 box; other site 557598008488 G3 box; other site 557598008489 Switch II region; other site 557598008490 G4 box; other site 557598008491 G5 box; other site 557598008492 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 557598008493 Cytochrome c553 [Energy production and conversion]; Region: COG2863 557598008494 Cytochrome c; Region: Cytochrom_C; cl11414 557598008495 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 557598008496 ResB-like family; Region: ResB; pfam05140 557598008497 ResB-like family; Region: ResB; pfam05140 557598008498 cytochrome c-type biogenesis protein CcsB; Region: cytochr_II_ccsB; TIGR03144 557598008499 AraC-type DNA-binding domain-containing proteins [Transcription]; Region: AraC; COG2207 557598008500 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557598008501 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 557598008502 glycerol kinase; Provisional; Region: glpK; PRK00047 557598008503 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 557598008504 N- and C-terminal domain interface [polypeptide binding]; other site 557598008505 active site 557598008506 MgATP binding site [chemical binding]; other site 557598008507 catalytic site [active] 557598008508 metal binding site [ion binding]; metal-binding site 557598008509 glycerol binding site [chemical binding]; other site 557598008510 homotetramer interface [polypeptide binding]; other site 557598008511 homodimer interface [polypeptide binding]; other site 557598008512 FBP binding site [chemical binding]; other site 557598008513 protein IIAGlc interface [polypeptide binding]; other site 557598008514 Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; Region: GlpR; COG1349 557598008515 helix_turn_helix, Deoxyribose operon repressor; Region: HTH_DEOR; smart00420 557598008516 DeoR C terminal sensor domain; Region: DeoRC; pfam00455 557598008517 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 557598008518 Ligand Binding Site [chemical binding]; other site 557598008519 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 557598008520 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 557598008521 S-adenosylmethionine binding site [chemical binding]; other site 557598008522 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 557598008523 Protein of unknown function (DUF454); Region: DUF454; cl01063 557598008524 peptide chain release factor 1; Validated; Region: prfA; PRK00591 557598008525 This domain is found in peptide chain release factors; Region: PCRF; smart00937 557598008526 RF-1 domain; Region: RF-1; pfam00472 557598008527 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 557598008528 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 557598008529 tRNA; other site 557598008530 putative tRNA binding site [nucleotide binding]; other site 557598008531 putative NADP binding site [chemical binding]; other site 557598008532 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 557598008533 Protein of unknown function (DUF3683); Region: DUF3683; pfam12447 557598008534 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 557598008535 FAD binding domain; Region: FAD_binding_4; pfam01565 557598008536 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 557598008537 4Fe-4S dicluster domain; Region: Fer4_8; pfam13183 557598008538 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 557598008539 Cysteine-rich domain; Region: CCG; pfam02754 557598008540 Cysteine-rich domain; Region: CCG; pfam02754 557598008541 Domain of unknown function (DUF3400); Region: DUF3400; pfam11880 557598008542 PAP2_like_2 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_2; cd03392 557598008543 active site 557598008544 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 557598008545 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 557598008546 RuvA N terminal domain; Region: RuvA_N; pfam01330 557598008547 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 557598008548 1,4-dihydroxy-2-naphthoate octaprenyltransferase [Coenzyme metabolism]; Region: MenA; cl17224 557598008549 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 557598008550 Patatin-like phospholipase domain containing protein 6, protein 7, and fungal NTE1; Region: Pat_PNPLA6_PNPLA7_NTE1_like; cd07205 557598008551 nucleophile elbow; other site 557598008552 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 557598008553 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 557598008554 S-adenosylmethionine binding site [chemical binding]; other site 557598008555 pimelyl-[acyl-carrier protein] methyl ester esterase; Region: bioH; TIGR01738 557598008556 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 557598008557 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 557598008558 S-adenosylmethionine binding site [chemical binding]; other site 557598008559 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 557598008560 active site 557598008561 intersubunit interface [polypeptide binding]; other site 557598008562 catalytic residue [active] 557598008563 Predicted membrane protein (DUF2061); Region: DUF2061; pfam09834 557598008564 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 557598008565 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557598008566 dimer interface [polypeptide binding]; other site 557598008567 Methyl-accepting chemotaxis protein (MCP) signalling domain; Region: MCPsignal; pfam00015 557598008568 putative CheW interface [polypeptide binding]; other site 557598008569 putative DMT superfamily transporter inner membrane protein; Provisional; Region: PRK11272 557598008570 EamA-like transporter family; Region: EamA; pfam00892 557598008571 EamA-like transporter family; Region: EamA; pfam00892 557598008572 argininosuccinate lyase; Provisional; Region: PRK00855 557598008573 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 557598008574 active sites [active] 557598008575 tetramer interface [polypeptide binding]; other site 557598008576 Protein of unknown function (DUF3460); Region: DUF3460; pfam11943 557598008577 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 557598008578 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 557598008579 dimerization interface [polypeptide binding]; other site 557598008580 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 557598008581 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557598008582 metal binding site [ion binding]; metal-binding site 557598008583 active site 557598008584 I-site; other site 557598008585 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 557598008586 Predicted deacylase [General function prediction only]; Region: COG3608 557598008587 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 557598008588 active site 557598008589 Zn binding site [ion binding]; other site 557598008590 CNP1-like family; Region: CNP1; pfam08750 557598008591 NRDE protein; Region: NRDE; cl01315 557598008592 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 557598008593 CPxP motif; other site 557598008594 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 557598008595 active site 557598008596 substrate binding pocket [chemical binding]; other site 557598008597 dimer interface [polypeptide binding]; other site 557598008598 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 557598008599 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 557598008600 ATP binding site [chemical binding]; other site 557598008601 Mg++ binding site [ion binding]; other site 557598008602 motif III; other site 557598008603 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 557598008604 nucleotide binding region [chemical binding]; other site 557598008605 ATP-binding site [chemical binding]; other site 557598008606 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 557598008607 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 557598008608 putative substrate translocation pore; other site 557598008609 multidrug efflux system protein EmrA; Provisional; Region: PRK15136 557598008610 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 557598008611 HlyD family secretion protein; Region: HlyD_3; pfam13437 557598008612 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 557598008613 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 557598008614 GAF domain; Region: GAF_3; pfam13492 557598008615 GAF domain; Region: GAF_2; pfam13185 557598008616 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 557598008617 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 557598008618 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 557598008619 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; cd00494 557598008620 domain interfaces; other site 557598008621 active site 557598008622 phosphoenolpyruvate carboxylase; Reviewed; Region: PRK00009 557598008623 Phosphoenolpyruvate carboxylase [Energy production and conversion]; Region: Ppc; COG2352 557598008624 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 557598008625 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 557598008626 Bacterial transcriptional repressor; Region: TetR_C_6; pfam13977 557598008627 Predicted membrane protein [Function unknown]; Region: COG4392 557598008628 Predicted branched-chain amino acid permease (azaleucine resistance) [Amino acid transport and metabolism]; Region: AzlC; COG1296 557598008629 DNA topoisomerase I; Validated; Region: PRK06599 557598008630 TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I. Type IA DNA topoisomerases remove (relax) negative supercoils in the...; Region: TOPRIM_TopoIA_TopoI; cd03363 557598008631 active site 557598008632 interdomain interaction site; other site 557598008633 putative metal-binding site [ion binding]; other site 557598008634 nucleotide binding site [chemical binding]; other site 557598008635 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 557598008636 domain I; other site 557598008637 DNA binding groove [nucleotide binding] 557598008638 phosphate binding site [ion binding]; other site 557598008639 domain II; other site 557598008640 domain III; other site 557598008641 nucleotide binding site [chemical binding]; other site 557598008642 catalytic site [active] 557598008643 domain IV; other site 557598008644 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 557598008645 Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]; Region: TopA; COG0551 557598008646 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 557598008647 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 557598008648 Protein of unknown function (DUF494); Region: DUF494; pfam04361 557598008649 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 557598008650 DNA protecting protein DprA; Region: dprA; TIGR00732 557598008651 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 557598008652 active site 557598008653 catalytic residues [active] 557598008654 metal binding site [ion binding]; metal-binding site 557598008655 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 557598008656 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 557598008657 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 557598008658 putative active site [active] 557598008659 putative cosubstrate binding site; other site 557598008660 substrate binding site [chemical binding]; other site 557598008661 catalytic site [active] 557598008662 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 557598008663 substrate binding site [chemical binding]; other site 557598008664 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 557598008665 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 557598008666 RNA binding surface [nucleotide binding]; other site 557598008667 FtsJ-like methyltransferase; Region: FtsJ; pfam01728 557598008668 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 557598008669 active site 557598008670 Ammonia permease [Inorganic ion transport and metabolism]; Region: AmtB; COG0004 557598008671 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 557598008672 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 557598008673 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 557598008674 putative ATP binding site [chemical binding]; other site 557598008675 putative substrate interface [chemical binding]; other site 557598008676 Domain of unknown function DUF302; Region: DUF302; pfam03625 557598008677 ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: Sbp; COG1613 557598008678 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 557598008679 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 557598008680 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 557598008681 dimer interface [polypeptide binding]; other site 557598008682 conserved gate region; other site 557598008683 putative PBP binding loops; other site 557598008684 ABC-ATPase subunit interface; other site 557598008685 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 557598008686 dimer interface [polypeptide binding]; other site 557598008687 conserved gate region; other site 557598008688 putative PBP binding loops; other site 557598008689 ABC-ATPase subunit interface; other site 557598008690 ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: CysA; COG1118 557598008691 ATP-binding cassette domain of the sulfate transporter; Region: ABC_CysA_sulfate_importer; cd03296 557598008692 Walker A/P-loop; other site 557598008693 ATP binding site [chemical binding]; other site 557598008694 Q-loop/lid; other site 557598008695 ABC transporter signature motif; other site 557598008696 Walker B; other site 557598008697 D-loop; other site 557598008698 H-loop/switch region; other site 557598008699 TOBE-like domain; Region: TOBE_3; pfam12857 557598008700 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 557598008701 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 557598008702 dimer interface [polypeptide binding]; other site 557598008703 putative CheW interface [polypeptide binding]; other site 557598008704 Endonuclease I; Region: Endonuclease_1; pfam04231 557598008705 Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases [Nucleotide transport and metabolism / Carbohydrate transport and metabolism / General function prediction only]; Region: Hit; COG0537 557598008706 nucleotide binding site/active site [active] 557598008707 HIT family signature motif; other site 557598008708 catalytic residue [active] 557598008709 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 557598008710 Domain of unknown function DUF21; Region: DUF21; pfam01595 557598008711 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 557598008712 Transporter associated domain; Region: CorC_HlyC; smart01091 557598008713 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 557598008714 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 557598008715 active site 557598008716 phosphorylation site [posttranslational modification] 557598008717 intermolecular recognition site; other site 557598008718 dimerization interface [polypeptide binding]; other site 557598008719 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 557598008720 Response regulator receiver domain; Region: Response_reg; pfam00072 557598008721 active site 557598008722 phosphorylation site [posttranslational modification] 557598008723 intermolecular recognition site; other site 557598008724 dimerization interface [polypeptide binding]; other site 557598008725 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 557598008726 binding surface 557598008727 Tetratricopeptide repeat; Region: TPR_16; pfam13432 557598008728 TPR motif; other site 557598008729 TPR repeat; Region: TPR_11; pfam13414 557598008730 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 557598008731 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 557598008732 ligand binding site [chemical binding]; other site 557598008733 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 557598008734 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 557598008735 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 557598008736 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 557598008737 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 557598008738 TonB C terminal; Region: TonB_2; pfam13103 557598008739 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 557598008740 TolR protein; Region: tolR; TIGR02801 557598008741 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 557598008742 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 557598008743 catalytic residues [active] 557598008744 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 557598008745 active site 557598008746 Uncharacterized protein conserved in bacteria (DUF2309); Region: DUF2309; pfam10070 557598008747 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 557598008748 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 557598008749 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 557598008750 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 557598008751 putative active site [active] 557598008752 heme pocket [chemical binding]; other site 557598008753 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 557598008754 putative active site [active] 557598008755 heme pocket [chemical binding]; other site 557598008756 PAS fold; Region: PAS; pfam00989 557598008757 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 557598008758 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 557598008759 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557598008760 metal binding site [ion binding]; metal-binding site 557598008761 active site 557598008762 I-site; other site 557598008763 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 557598008764 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 557598008765 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 557598008766 dimerization interface [polypeptide binding]; other site 557598008767 DPS ferroxidase diiron center [ion binding]; other site 557598008768 ion pore; other site 557598008769 Uncharacterized ACR, YggU family COG1872; Region: DUF167; cl00811 557598008770 phage T7 F exclusion suppressor FxsA; Reviewed; Region: fxsA; PRK11463 557598008771 Uncharacterized protein involved in tolerance to divalent cations [Inorganic ion transport and metabolism]; Region: CutA; COG1324 557598008772 thiol:disulfide interchange protein precursor; Provisional; Region: dipZ; PRK00293 557598008773 Disulphide bond corrector protein DsbC; Region: DsbC; pfam11412 557598008774 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 557598008775 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 557598008776 DsbD alpha interface [polypeptide binding]; other site 557598008777 catalytic residues [active] 557598008778 hypothetical protein; Provisional; Region: PRK13687 557598008779 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 557598008780 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 557598008781 Coenzyme A binding pocket [chemical binding]; other site 557598008782 SEC10/PgrA surface exclusion domain; Region: Surf_Exclu_PgrA; TIGR04320 557598008783 prolyl-tRNA synthetase; Provisional; Region: PRK09194 557598008784 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 557598008785 dimer interface [polypeptide binding]; other site 557598008786 motif 1; other site 557598008787 active site 557598008788 motif 2; other site 557598008789 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 557598008790 putative deacylase active site [active] 557598008791 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 557598008792 active site 557598008793 motif 3; other site 557598008794 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 557598008795 anticodon binding site; other site 557598008796 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 557598008797 active site 557598008798 putative DNA-binding cleft [nucleotide binding]; other site 557598008799 dimer interface [polypeptide binding]; other site 557598008800 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 557598008801 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 557598008802 Substrate binding site; other site 557598008803 metal-binding site 557598008804 Phosphotransferase enzyme family; Region: APH; pfam01636 557598008805 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family 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: APH_ChoK_like; cd05120 557598008806 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 557598008807 Organic solvent tolerance protein; Region: OstA_C; pfam04453 557598008808 peptidyl-prolyl cis-trans isomerase SurA; Provisional; Region: PRK10770 557598008809 SurA N-terminal domain; Region: SurA_N; pfam09312 557598008810 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 557598008811 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 557598008812 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 557598008813 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 557598008814 RNA binding surface [nucleotide binding]; other site 557598008815 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 557598008816 active site 557598008817 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 557598008818 dimerization interface [polypeptide binding]; other site 557598008819 Stage II sporulation protein E (SpoIIE); Region: SpoIIE; pfam07228 557598008820 Domain of unknown function (DUF1987); Region: DUF1987; pfam09345 557598008821 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 557598008822 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 557598008823 metal binding site [ion binding]; metal-binding site 557598008824 active site 557598008825 I-site; other site 557598008826 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4320 557598008827 Uncharacterized protein conserved in bacteria (DUF2252); Region: DUF2252; pfam10009 557598008828 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 557598008829 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 557598008830 putative catalytic cysteine [active] 557598008831 Protein of unknown function (DUF3422); Region: DUF3422; pfam11902 557598008832 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 557598008833 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 557598008834 FMN binding site [chemical binding]; other site 557598008835 active site 557598008836 catalytic residues [active] 557598008837 substrate binding site [chemical binding]; other site 557598008838 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 557598008839 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 557598008840 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 557598008841 purine monophosphate binding site [chemical binding]; other site 557598008842 dimer interface [polypeptide binding]; other site 557598008843 putative catalytic residues [active] 557598008844 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; smart00798 557598008845 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 557598008846 phospholipid:lipid A palmitoyltransferase; Provisional; Region: pagP; PRK11045 557598008847 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 557598008848 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 557598008849 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 557598008850 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 557598008851 Nitroreductase-like family 1. 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_1; cd02137 557598008852 dimer interface [polypeptide binding]; other site 557598008853 FMN binding site [chemical binding]; other site 557598008854 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 557598008855 active site 557598008856 Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Nape_like_AP-endo; cd10281 557598008857 putative active site [active] 557598008858 putative catalytic site [active] 557598008859 putative DNA binding site [nucleotide binding]; other site 557598008860 putative phosphate binding site [ion binding]; other site 557598008861 metal binding site A [ion binding]; metal-binding site 557598008862 putative AP binding site [nucleotide binding]; other site 557598008863 putative metal binding site B [ion binding]; other site 557598008864 Cobalamin-5-phosphate synthase; Region: CobS; cl00415 557598008865 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 557598008866 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 557598008867 5,10-methenyltetrahydrofolate synthetase; Region: MTHFS_bact; TIGR02727 557598008868 Cell division protein ZapA; Region: ZapA; pfam05164 557598008869 vitamin B12-transporter protein BtuF; Provisional; Region: PRK03379 557598008870 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 557598008871 cobalamin binding residues [chemical binding]; other site 557598008872 putative BtuC binding residues; other site 557598008873 dimer interface [polypeptide binding]; other site 557598008874 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 557598008875 homotrimer interface [polypeptide binding]; other site 557598008876 Walker A motif; other site 557598008877 GTP binding site [chemical binding]; other site 557598008878 Walker B motif; other site 557598008879 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 557598008880 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 557598008881 N-terminal plug; other site 557598008882 ligand-binding site [chemical binding]; other site 557598008883 Phosphoribosyltransferase; Region: DBI_PRT; pfam02277 557598008884 Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT; Region: DMB-PRT_CobT; cd02439 557598008885 putative dimer interface [polypeptide binding]; other site 557598008886 active site pocket [active] 557598008887 putative cataytic base [active] 557598008888 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 557598008889 catalytic core [active] 557598008890 Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP; cl11399 557598008891 catalytic core [active] 557598008892 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; COG1282 557598008893 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 557598008894 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 557598008895 Rubrum transdehydrogenase NAD-binding and catalytic domains; Region: Rubrum_tdh; cd05304 557598008896 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 557598008897 ligand binding site [chemical binding]; other site 557598008898 homodimer interface [polypeptide binding]; other site 557598008899 NAD(P) binding site [chemical binding]; other site 557598008900 trimer interface B [polypeptide binding]; other site 557598008901 trimer interface A [polypeptide binding]; other site 557598008902 hypothetical protein; Provisional; Region: PRK10621 557598008903 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 557598008904 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 557598008905 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 557598008906 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 557598008907 trmE is a tRNA modification GTPase; Region: trmE; cd04164 557598008908 G1 box; other site 557598008909 GTP/Mg2+ binding site [chemical binding]; other site 557598008910 Switch I region; other site 557598008911 G2 box; other site 557598008912 Switch II region; other site 557598008913 G3 box; other site 557598008914 G4 box; other site 557598008915 G5 box; other site 557598008916 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 557598008917 membrane protein insertase; Provisional; Region: PRK01318 557598008918 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 557598008919 Haemolytic domain; Region: Haemolytic; pfam01809 557598008920 ribonuclease P; Reviewed; Region: rnpA; PRK04390 557598008921 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 557598008922 DnaA N-terminal domain; Region: DnaA_N; pfam11638 557598008923 chromosomal replication initiator protein DnaA; Region: DnaA; TIGR00362 557598008924 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 557598008925 Walker A motif; other site 557598008926 ATP binding site [chemical binding]; other site 557598008927 Walker B motif; other site 557598008928 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 557598008929 arginine finger; other site 557598008930 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 557598008931 DnaA box-binding interface [nucleotide binding]; other site 557598008932 DNA polymerase III subunit beta; Validated; Region: PRK05643 557598008933 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 557598008934 putative DNA binding surface [nucleotide binding]; other site 557598008935 dimer interface [polypeptide binding]; other site 557598008936 beta-clamp/translesion DNA polymerase binding surface; other site 557598008937 beta-clamp/clamp loader binding surface; other site 557598008938 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 557598008939 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 557598008940 Mg2+ binding site [ion binding]; other site 557598008941 G-X-G motif; other site 557598008942 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 557598008943 anchoring element; other site 557598008944 dimer interface [polypeptide binding]; other site 557598008945 ATP binding site [chemical binding]; other site 557598008946 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 557598008947 active site 557598008948 putative metal-binding site [ion binding]; other site 557598008949 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 557598008950 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 557598008951 additional DNA contacts [nucleotide binding]; other site 557598008952 mismatch recognition site; other site 557598008953 active site 557598008954 zinc binding site [ion binding]; other site 557598008955 DNA intercalation site [nucleotide binding]; other site 557598008956 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 557598008957 DNA-methyltransferase (dcm); Region: dcm; TIGR00675 557598008958 cofactor binding site; other site 557598008959 DNA binding site [nucleotide binding] 557598008960 substrate interaction site [chemical binding]; other site 557598008961 LysR family transcriptional regulator; Provisional; Region: PRK14997 557598008962 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 557598008963 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 557598008964 putative effector binding pocket; other site 557598008965 putative dimerization interface [polypeptide binding]; other site 557598008966 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 557598008967 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 557598008968 Pirin-related protein [General function prediction only]; Region: COG1741 557598008969 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 557598008970 Ammonia permease [Inorganic ion transport and metabolism]; Region: AmtB; COG0004 557598008971 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cl00264 557598008972 dinuclear metal binding motif [ion binding]; other site 557598008973 ADP-heptose synthase, bifunctional sugar kinase/adenylyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaE; COG2870 557598008974 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 557598008975 active site 557598008976 HIGH motif; other site 557598008977 nucleotide binding site [chemical binding]; other site 557598008978 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional; Region: PRK11886 557598008979 Biotin operon repressor [Transcription]; Region: BirA; COG1654 557598008980 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 557598008981 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 557598008982 Type III pantothenate kinase; Region: Pan_kinase; cl17198 557598008983 Sporulation related domain; Region: SPOR; pfam05036 557598008984 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609