-- dump date 20140619_163044 -- class Genbank::misc_feature -- table misc_feature_note -- id note 940296000001 conjugal transfer relaxase TraI; Provisional; Region: PRK13878 940296000002 Relaxase/Mobilisation nuclease domain; Region: Relaxase; pfam03432 940296000003 conjugal transfer coupling protein TraG; Provisional; Region: PRK13880 940296000004 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 940296000005 Walker A motif; other site 940296000006 ATP binding site [chemical binding]; other site 940296000007 Walker B motif; other site 940296000008 conjugal transfer peptidase TraF; Provisional; Region: PRK13884 940296000009 conjugal transfer pilin processing protease TraF; Provisional; Region: PRK13838 940296000010 DNA topoisomerase III; Provisional; Region: PRK07726 940296000011 TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving...; Region: TOPRIM_TopoIA_TopoIII; cd03362 940296000012 active site 940296000013 putative interdomain interaction site [polypeptide binding]; other site 940296000014 putative metal-binding site [ion binding]; other site 940296000015 putative nucleotide binding site [chemical binding]; other site 940296000016 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; cl11986 940296000017 domain I; other site 940296000018 DNA binding groove [nucleotide binding] 940296000019 phosphate binding site [ion binding]; other site 940296000020 domain II; other site 940296000021 domain III; other site 940296000022 nucleotide binding site [chemical binding]; other site 940296000023 catalytic site [active] 940296000024 domain IV; other site 940296000025 Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]; Region: TopA; COG0551 940296000026 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 940296000027 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 940296000028 Antirestriction protein [DNA replication, recombination, and repair]; Region: COG4227 940296000029 Domain of unknown function (DUF1738); Region: DUF1738; pfam08401 940296000030 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4643 940296000031 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 940296000032 active site 940296000033 metal binding site [ion binding]; metal-binding site 940296000034 interdomain interaction site; other site 940296000035 Peptidase M15; Region: Peptidase_M15_3; cl01194 940296000036 DNA methylase; Region: N6_N4_Mtase; cl17433 940296000037 integral membrane protein, PqiA family; Region: pqiA_fam; TIGR00155 940296000038 Zeta toxin; Region: Zeta_toxin; pfam06414 940296000039 multiple promoter invertase; Provisional; Region: mpi; PRK13413 940296000040 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 940296000041 catalytic residues [active] 940296000042 catalytic nucleophile [active] 940296000043 Presynaptic Site I dimer interface [polypeptide binding]; other site 940296000044 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 940296000045 Synaptic Flat tetramer interface [polypeptide binding]; other site 940296000046 Synaptic Site I dimer interface [polypeptide binding]; other site 940296000047 DNA binding site [nucleotide binding] 940296000048 Uncharacterized virulence-associated protein D [Function unknown]; Region: VapD; COG3309 940296000049 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 940296000050 N-acetyl-D-glucosamine binding site [chemical binding]; other site 940296000051 catalytic residue [active] 940296000052 conjugal transfer protein TrbM; Provisional; Region: PRK13893 940296000053 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 940296000054 conjugal transfer protein TrbJ; Provisional; Region: PRK13879 940296000055 conjugal transfer protein TrbI; Provisional; Region: PRK13881 940296000056 Bacterial conjugation TrbI-like protein; Region: TrbI; pfam03743 940296000057 conjugal transfer protein TrbH; Provisional; Region: PRK13883 940296000058 Conjugal transfer protein TrbH; Region: TrbH; pfam07283 940296000059 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 940296000060 VirB7 interaction site; other site 940296000061 VirB8 protein; Region: VirB8; cl01500 940296000062 conjugal transfer protein TrbE; Provisional; Region: PRK13891 940296000063 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 940296000064 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 940296000065 Walker A motif; other site 940296000066 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 940296000067 Walker B; other site 940296000068 D-loop; other site 940296000069 H-loop/switch region; other site 940296000070 Type IV secretory pathway, VirB3-like protein; Region: VirB3; cl01501 940296000071 conjugal transfer protein TrbC; Provisional; Region: PRK13892 940296000072 conjugal transfer ATPase TrbB; Provisional; Region: PRK13894 940296000073 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 940296000074 ATP binding site [chemical binding]; other site 940296000075 Walker A motif; other site 940296000076 hexamer interface [polypeptide binding]; other site 940296000077 Walker B motif; other site 940296000078 conjugal transfer protein TrbA; Provisional; Region: PRK13890 940296000079 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 940296000080 sequence-specific DNA binding site [nucleotide binding]; other site 940296000081 salt bridge; other site 940296000082 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 940296000083 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 940296000084 dimer interface [polypeptide binding]; other site 940296000085 ssDNA binding site [nucleotide binding]; other site 940296000086 tetramer (dimer of dimers) interface [polypeptide binding]; other site 940296000087 TrfA protein; Region: TrfA; pfam07042 940296000088 Replication initiator protein A; Region: RPA; cl17860 940296000089 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 940296000090 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 940296000091 P-loop; other site 940296000092 Magnesium ion binding site [ion binding]; other site 940296000093 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 940296000094 Magnesium ion binding site [ion binding]; other site 940296000095 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 940296000096 ParB-like nuclease domain; Region: ParBc; pfam02195 940296000097 KorB domain; Region: KorB; pfam08535 940296000098 KorB C-terminal beta-barrel domain; Region: KorB_C; pfam06613 940296000099 Transcriptional activator TraM; Region: Activator-TraM; cl11943 940296000100 conjugal transfer protein TraL; Provisional; Region: PRK13886 940296000101 conjugal transfer relaxosome component TraJ; Provisional; Region: PRK13877 940296000102 triosephosphate isomerase; Provisional; Region: PRK14567 940296000103 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 940296000104 substrate binding site [chemical binding]; other site 940296000105 dimer interface [polypeptide binding]; other site 940296000106 catalytic triad [active] 940296000107 GAF domain-containing protein [Signal transduction mechanisms]; Region: COG1956 940296000108 Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: Pcm; COG2518 940296000109 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 940296000110 S-adenosylmethionine binding site [chemical binding]; other site 940296000111 Member of the Rhodanese Homology Domain superfamily, subgroup 2. Subgroup 2 includes uncharacterized putative rhodanese-related domains; Region: RHOD_2; cd01528 940296000112 active site residue [active] 940296000113 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 940296000114 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 940296000115 N-terminal plug; other site 940296000116 ligand-binding site [chemical binding]; other site 940296000117 Mannose-6-phosphate isomerase [Carbohydrate transport and metabolism]; Region: {ManC}; COG0662 940296000118 ABC-type enterochelin transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: CeuA; COG4607 940296000119 Siderophore binding protein FatB. These proteins have been shown to function as ABC-type initial receptors in the siderophore-mediated iron uptake in some eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins...; Region: FatB; cd01140 940296000120 putative ligand binding residues [chemical binding]; other site 940296000121 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 940296000122 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 940296000123 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 940296000124 amino-acid N-acetyltransferase; Region: N-Ac-Glu-synth; TIGR01890 940296000125 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 940296000126 putative feedback inhibition sensing region; other site 940296000127 putative nucleotide binding site [chemical binding]; other site 940296000128 putative substrate binding site [chemical binding]; other site 940296000129 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 940296000130 Coenzyme A binding pocket [chemical binding]; other site 940296000131 zinc-ribbon domain; Region: zinc_ribbon_5; cl11777 940296000132 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 940296000133 active site 940296000134 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 940296000135 active site 940296000136 Fe-S cluster binding site [ion binding]; other site 940296000137 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214 940296000138 Glycoprotease family; Region: Peptidase_M22; pfam00814 940296000139 Lipoprotein GNA1870 C terminal like; Region: Lipoprot_C; pfam08794 940296000140 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 940296000141 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 940296000142 intersubunit interface [polypeptide binding]; other site 940296000143 active site 940296000144 zinc binding site [ion binding]; other site 940296000145 Na+ binding site [ion binding]; other site 940296000146 Site-specific recombinase XerC [DNA replication, recombination, and repair]; Region: XerC; COG4973 940296000147 XerD and XerC integrases, DNA breaking-rejoining enzymes, N- and C-terminal domains. XerD-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination...; Region: INT_XerDC; cd00798 940296000148 active site 940296000149 Int/Topo IB signature motif; other site 940296000150 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 940296000151 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 940296000152 TPP-binding site; other site 940296000153 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 940296000154 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 940296000155 PYR/PP interface [polypeptide binding]; other site 940296000156 dimer interface [polypeptide binding]; other site 940296000157 TPP binding site [chemical binding]; other site 940296000158 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 940296000159 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 940296000160 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 940296000161 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 940296000162 FeS/SAM binding site; other site 940296000163 TRAM domain; Region: TRAM; pfam01938 940296000164 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 940296000165 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 940296000166 inhibitor-cofactor binding pocket; inhibition site 940296000167 pyridoxal 5'-phosphate binding site [chemical binding]; other site 940296000168 catalytic residue [active] 940296000169 DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins; Region: Orn; cd06135 940296000170 catalytic site [active] 940296000171 putative active site [active] 940296000172 putative substrate binding site [chemical binding]; other site 940296000173 dimer interface [polypeptide binding]; other site 940296000174 Ribosomal protein L11 methyltransferase (PrmA); Region: PrmA; pfam06325 940296000175 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 940296000176 S-adenosylmethionine binding site [chemical binding]; other site 940296000177 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 940296000178 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 940296000179 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 940296000180 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 940296000181 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 940296000182 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 940296000183 carboxyltransferase (CT) interaction site; other site 940296000184 biotinylation site [posttranslational modification]; other site 940296000185 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 940296000186 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 940296000187 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 940296000188 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 940296000189 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 940296000190 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 940296000191 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 940296000192 ATP-grasp domain; Region: ATP-grasp_4; cl17255 940296000193 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 940296000194 IMP binding site; other site 940296000195 dimer interface [polypeptide binding]; other site 940296000196 interdomain contacts; other site 940296000197 partial ornithine binding site; other site 940296000198 Domain of unknown function, appears to be related to a diverse group of endonucleases; Region: Endonuclease_DUF559; cd01038 940296000199 putative active site [active] 940296000200 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 940296000201 dimer interface [polypeptide binding]; other site 940296000202 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 940296000203 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 940296000204 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; smart01097 940296000205 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 940296000206 catalytic site [active] 940296000207 subunit interface [polypeptide binding]; other site 940296000208 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; Region: GIY-YIG_unchar_3; cd10448 940296000209 putative active site [active] 940296000210 putative metal binding site [ion binding]; other site 940296000211 Tfp pilus assembly protein, tip-associated adhesin PilY1 [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilY1; COG3419 940296000212 Neisseria PilC beta-propeller domain; Region: Neisseria_PilC; pfam05567 940296000213 Neisseria PilC beta-propeller domain; Region: Neisseria_PilC; pfam05567 940296000214 Tfp pilus assembly protein, tip-associated adhesin PilY1 [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilY1; COG3419 940296000215 Neisseria PilC beta-propeller domain; Region: Neisseria_PilC; pfam05567 940296000216 Tfp pilus assembly protein, tip-associated adhesin PilY1 [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilY1; COG3419 940296000217 antiporter inner membrane protein; Provisional; Region: PRK11670 940296000218 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 940296000219 Walker A motif; other site 940296000220 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 940296000221 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 940296000222 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 940296000223 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 940296000224 Substrate binding site; other site 940296000225 metal-binding site 940296000226 Predicted membrane protein [Function unknown]; Region: COG2510 940296000227 formate--tetrahydrofolate ligase; Provisional; Region: PRK13505 940296000228 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 940296000229 Potassium binding sites [ion binding]; other site 940296000230 Cesium cation binding sites [ion binding]; other site 940296000231 GTP-binding protein YchF; Reviewed; Region: PRK09601 940296000232 YchF GTPase; Region: YchF; cd01900 940296000233 G1 box; other site 940296000234 GTP/Mg2+ binding site [chemical binding]; other site 940296000235 Switch I region; other site 940296000236 G2 box; other site 940296000237 Switch II region; other site 940296000238 G3 box; other site 940296000239 G4 box; other site 940296000240 G5 box; other site 940296000241 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 940296000242 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 940296000243 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 940296000244 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 940296000245 active site 940296000246 HIGH motif; other site 940296000247 dimer interface [polypeptide binding]; other site 940296000248 KMSKS motif; other site 940296000249 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 940296000250 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 940296000251 active site 940296000252 Riboflavin kinase; Region: Flavokinase; smart00904 940296000253 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 940296000254 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 940296000255 active site 940296000256 HIGH motif; other site 940296000257 nucleotide binding site [chemical binding]; other site 940296000258 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 940296000259 active site 940296000260 KMSKS motif; other site 940296000261 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 940296000262 tRNA binding surface [nucleotide binding]; other site 940296000263 anticodon binding site; other site 940296000264 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 940296000265 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl17254 940296000266 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 940296000267 lipoprotein signal peptidase; Provisional; Region: PRK14787 940296000268 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 940296000269 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism]; Region: lytB; COG0761 940296000270 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 940296000271 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 940296000272 motif II; other site 940296000273 HAD-hyrolase-like; Region: Hydrolase_like; pfam13242 940296000274 Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]; Region: FhuE; COG4773 940296000275 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 940296000276 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2819 940296000277 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 940296000278 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 940296000279 putative active site [active] 940296000280 putative PHP Thumb interface [polypeptide binding]; other site 940296000281 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 940296000282 generic binding surface II; other site 940296000283 generic binding surface I; other site 940296000284 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 940296000285 RNA binding surface [nucleotide binding]; other site 940296000286 Predicted metal-dependent phosphoesterases (PHP family) [General function prediction only]; Region: COG0613 940296000287 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 940296000288 active site 940296000289 Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound; Region: PHP_HisPPase_AMP; cd07438 940296000290 Alanine-alpha-ketoisovalerate (or valine-pyruvate) aminotransferase [Amino acid transport and metabolism]; Region: COG3977 940296000291 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 940296000292 pyridoxal 5'-phosphate binding site [chemical binding]; other site 940296000293 homodimer interface [polypeptide binding]; other site 940296000294 catalytic residue [active] 940296000295 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 940296000296 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 940296000297 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 940296000298 NAD(P) binding site [chemical binding]; other site 940296000299 homodimer interface [polypeptide binding]; other site 940296000300 substrate binding site [chemical binding]; other site 940296000301 active site 940296000302 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 940296000303 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 940296000304 inhibitor-cofactor binding pocket; inhibition site 940296000305 pyridoxal 5'-phosphate binding site [chemical binding]; other site 940296000306 catalytic residue [active] 940296000307 Bacterial sugar transferase; Region: Bac_transf; pfam02397 940296000308 Putative Acyltransferase (AT), Left-handed parallel beta-Helix (LbH) domain; This group is composed of mostly uncharacterized proteins containing an N-terminal helical subdomain followed by a LbH domain. The alignment contains 6 turns, each containing...; Region: LbH_AT_putative; cd03360 940296000309 sugar O-acyltransferase, sialic acid O-acetyltransferase NeuD family; Region: NeuD_NnaD; TIGR03570 940296000310 putative trimer interface [polypeptide binding]; other site 940296000311 putative CoA binding site [chemical binding]; other site 940296000312 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 940296000313 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 940296000314 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 940296000315 Multidrug and toxic compound extrusion family and similar proteins; Region: MATE_like; cl09326 940296000316 bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional; Region: ribD; PRK10786 940296000317 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 940296000318 catalytic motif [active] 940296000319 Zn binding site [ion binding]; other site 940296000320 RibD C-terminal domain; Region: RibD_C; cl17279 940296000321 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 940296000322 ATP cone domain; Region: ATP-cone; pfam03477 940296000323 Predicted glutamine amidotransferase [General function prediction only]; Region: COG0121 940296000324 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 940296000325 putative dimer interface [polypeptide binding]; other site 940296000326 putative active site [active] 940296000327 AMIN domain; Region: AMIN; pfam11741 940296000328 type IV pilus secretin (or competence protein) PilQ; Region: IV_pilus_PilQ; TIGR02515 940296000329 Secretin and TonB N terminus short domain; Region: STN; pfam07660 940296000330 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 940296000331 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 940296000332 Pilus assembly protein, PilP; Region: PilP; pfam04351 940296000333 Pilus assembly protein, PilO; Region: PilO; cl01234 940296000334 Tfp pilus assembly protein PilN [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilN; COG3166 940296000335 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 940296000336 Tfp pilus assembly protein, ATPase PilM [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilM; COG4972 940296000337 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 940296000338 Transglycosylase; Region: Transgly; pfam00912 940296000339 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 940296000340 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 940296000341 G1 box; other site 940296000342 GTP/Mg2+ binding site [chemical binding]; other site 940296000343 Switch I region; other site 940296000344 G2 box; other site 940296000345 G3 box; other site 940296000346 Switch II region; other site 940296000347 G4 box; other site 940296000348 G5 box; other site 940296000349 Cytochrome c553 [Energy production and conversion]; Region: COG2863 940296000350 Cytochrome c; Region: Cytochrom_C; cl11414 940296000351 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; COG1333 940296000352 ResB-like family; Region: ResB; pfam05140 940296000353 cytochrome c-type biogenesis protein CcsB; Region: cytochr_II_ccsB; TIGR03144 940296000354 UGMP family protein; Validated; Region: PRK09604 940296000355 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 940296000356 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 940296000357 putative acyl-acceptor binding pocket; other site 940296000358 S-adenosylmethionine synthetase; Validated; Region: PRK05250 940296000359 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 940296000360 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 940296000361 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 940296000362 D-Ala-D-Ala carboxypeptidase 3 (S13) family; Region: Peptidase_S13; pfam02113 940296000363 Predicted flavoprotein [General function prediction only]; Region: COG0431 940296000364 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 940296000365 H+/citrate symporter [Energy production and conversion]; Region: CitM; COG2851 940296000366 Citrate transporter; Region: CitMHS; pfam03600 940296000367 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 940296000368 DNA-binding transcriptional regulator BasR; Provisional; Region: PRK10643 940296000369 active site 940296000370 phosphorylation site [posttranslational modification] 940296000371 intermolecular recognition site; other site 940296000372 dimerization interface [polypeptide binding]; other site 940296000373 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 940296000374 DNA binding site [nucleotide binding] 940296000375 sensor protein QseC; Provisional; Region: PRK10337 940296000376 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 940296000377 dimer interface [polypeptide binding]; other site 940296000378 phosphorylation site [posttranslational modification] 940296000379 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 940296000380 ATP binding site [chemical binding]; other site 940296000381 Mg2+ binding site [ion binding]; other site 940296000382 G-X-G motif; other site 940296000383 ribonuclease G; Provisional; Region: PRK11712 940296000384 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 940296000385 homodimer interface [polypeptide binding]; other site 940296000386 oligonucleotide binding site [chemical binding]; other site 940296000387 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 940296000388 GSH binding site [chemical binding]; other site 940296000389 catalytic residues [active] 940296000390 Preprotein translocase subunit SecB. SecB is a cytoplasmic component of the multisubunit membrane-bound enzyme termed Sec protein translocase, which is the main constituent of the General Secretory (type II) Pathway involved in translocation of nascent...; Region: Translocase_SecB; cl00251 940296000391 SecA binding site; other site 940296000392 Preprotein binding site; other site 940296000393 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 940296000394 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 940296000395 generic binding surface II; other site 940296000396 ssDNA binding site; other site 940296000397 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 940296000398 ATP binding site [chemical binding]; other site 940296000399 putative Mg++ binding site [ion binding]; other site 940296000400 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 940296000401 nucleotide binding region [chemical binding]; other site 940296000402 ATP-binding site [chemical binding]; other site 940296000403 N-acetyl-gamma-glutamyl-phosphate reductase; Validated; Region: argC; PRK00436 940296000404 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 940296000405 ribonuclease BN/unknown domain fusion protein; Reviewed; Region: rbn; PRK04214 940296000406 Uncharacterized conserved protein [Function unknown]; Region: COG2850 940296000407 Cupin-like domain; Region: Cupin_8; pfam13621 940296000408 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 940296000409 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 940296000410 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 940296000411 HlyD family secretion protein; Region: HlyD_3; pfam13437 940296000412 ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]; Region: SunT; COG2274 940296000413 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_C39C; cd02419 940296000414 putative active site [active] 940296000415 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 940296000416 ATP-binding cassette domain of multidrug resistance protein-like transporters; Region: ABCC_MRP_Like; cd03228 940296000417 Walker A/P-loop; other site 940296000418 ATP binding site [chemical binding]; other site 940296000419 Q-loop/lid; other site 940296000420 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 940296000421 ABC transporter signature motif; other site 940296000422 Walker B; other site 940296000423 D-loop; other site 940296000424 H-loop/switch region; other site 940296000425 ribonuclease BN/unknown domain fusion protein; Reviewed; Region: rbn; PRK04214 940296000426 YihY family inner membrane protein; Region: yihY_not_rbn; TIGR00765 940296000427 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 940296000428 Ligand Binding Site [chemical binding]; other site 940296000429 6-pyruvoyl tetrahydropterin synthase; Region: PTPS; pfam01242 940296000430 active site 940296000431 Predicted membrane protein [Function unknown]; Region: COG3759 940296000432 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 940296000433 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 940296000434 FeS/SAM binding site; other site 940296000435 beta-hexosaminidase; Provisional; Region: PRK05337 940296000436 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 940296000437 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 940296000438 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 940296000439 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 940296000440 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 940296000441 protein binding site [polypeptide binding]; other site 940296000442 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 940296000443 protein binding site [polypeptide binding]; other site 940296000444 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 940296000445 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 940296000446 minor groove reading motif; other site 940296000447 helix-hairpin-helix signature motif; other site 940296000448 substrate binding pocket [chemical binding]; other site 940296000449 active site 940296000450 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 940296000451 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 940296000452 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 940296000453 putative substrate translocation pore; other site 940296000454 Na+/H+ antiporter family; Region: Na_H_antiporter; pfam03553 940296000455 Putative Mg2+ and Co2+ transporter CorC [Inorganic ion transport and metabolism]; Region: CorC; COG4535 940296000456 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 940296000457 Transporter associated domain; Region: CorC_HlyC; smart01091 940296000458 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG0319 940296000459 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 940296000460 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 940296000461 domain interfaces; other site 940296000462 active site 940296000463 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 940296000464 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 940296000465 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 940296000466 DEAD-like helicases superfamily; Region: DEXDc; smart00487 940296000467 ATP binding site [chemical binding]; other site 940296000468 Mg++ binding site [ion binding]; other site 940296000469 motif III; other site 940296000470 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 940296000471 nucleotide binding region [chemical binding]; other site 940296000472 ATP-binding site [chemical binding]; other site 940296000473 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 940296000474 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 940296000475 FMN binding site [chemical binding]; other site 940296000476 active site 940296000477 catalytic residues [active] 940296000478 substrate binding site [chemical binding]; other site 940296000479 DNA-binding protein Fis; Provisional; Region: PRK01905 940296000480 Factor for inversion stimulation Fis, transcriptional activator [Transcription / DNA replication, recombination, and repair]; Region: Fis; COG2901 940296000481 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 940296000482 active site 940296000483 putative DNA-binding cleft [nucleotide binding]; other site 940296000484 dimer interface [polypeptide binding]; other site 940296000485 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 940296000486 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 940296000487 putative acyl-acceptor binding pocket; other site 940296000488 Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; Region: DNA_polB_like1_exo; cd05782 940296000489 active site 940296000490 catalytic site [active] 940296000491 substrate binding site [chemical binding]; other site 940296000492 Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; Region: DNA_pol_B_exo2; pfam10108 940296000493 aminopeptidase N; Provisional; Region: pepN; PRK14015 940296000494 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_1; cd09600 940296000495 active site 940296000496 Zn binding site [ion binding]; other site 940296000497 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 940296000498 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 940296000499 metal binding site [ion binding]; metal-binding site 940296000500 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 940296000501 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 940296000502 ABC-ATPase subunit interface; other site 940296000503 dimer interface [polypeptide binding]; other site 940296000504 putative PBP binding regions; other site 940296000505 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 940296000506 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 940296000507 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 940296000508 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 940296000509 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 940296000510 RimM N-terminal domain; Region: RimM; pfam01782 940296000511 PRC-barrel domain; Region: PRC; pfam05239 940296000512 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 940296000513 potential frameshift: common BLAST hit: gi|254804476|ref|YP_003082697.1| putative N-acetyltransferase 940296000514 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 940296000515 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 940296000516 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]; Region: COG1042 940296000517 CoA binding domain; Region: CoA_binding_2; pfam13380 940296000518 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 940296000519 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 940296000520 dimerization interface [polypeptide binding]; other site 940296000521 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 940296000522 dimer interface [polypeptide binding]; other site 940296000523 phosphorylation site [posttranslational modification] 940296000524 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 940296000525 ATP binding site [chemical binding]; other site 940296000526 Mg2+ binding site [ion binding]; other site 940296000527 G-X-G motif; other site 940296000528 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 940296000529 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 940296000530 active site 940296000531 phosphorylation site [posttranslational modification] 940296000532 intermolecular recognition site; other site 940296000533 dimerization interface [polypeptide binding]; other site 940296000534 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 940296000535 DNA binding site [nucleotide binding] 940296000536 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 940296000537 O-Antigen ligase; Region: Wzy_C; pfam04932 940296000538 Domain of unknown function (DUF3366); Region: DUF3366; pfam11846 940296000539 Predicted membrane protein [Function unknown]; Region: COG3308 940296000540 Maf-like protein; Region: Maf; pfam02545 940296000541 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 940296000542 active site 940296000543 dimer interface [polypeptide binding]; other site 940296000544 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 940296000545 sec-independent translocase; Provisional; Region: PRK00708 940296000546 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 940296000547 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 940296000548 nucleotide binding site/active site [active] 940296000549 HIT family signature motif; other site 940296000550 catalytic residue [active] 940296000551 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 940296000552 metal binding site [ion binding]; metal-binding site 940296000553 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 940296000554 (2R,3R)-2,3-butanediol dehydrogenase; Region: butanediol_DH_like; cd08233 940296000555 putative NAD(P) binding site [chemical binding]; other site 940296000556 catalytic Zn binding site [ion binding]; other site 940296000557 Transposase domain (DUF772); Region: DUF772; pfam05598 940296000558 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 940296000559 Transposase; Region: DEDD_Tnp_IS110; pfam01548 940296000560 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 940296000561 Putative SAM-dependent methyltransferase; Region: SAM_MT; pfam04445 940296000562 Predicted permeases [General function prediction only]; Region: COG0730 940296000563 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 940296000564 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 940296000565 Walker B motif; other site 940296000566 arginine finger; other site 940296000567 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 940296000568 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 940296000569 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 940296000570 CAP-like domain; other site 940296000571 active site 940296000572 primary dimer interface [polypeptide binding]; other site 940296000573 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 940296000574 catalytic core [active] 940296000575 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 940296000576 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 940296000577 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 940296000578 motif 1; other site 940296000579 active site 940296000580 motif 2; other site 940296000581 motif 3; other site 940296000582 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 940296000583 DHHA1 domain; Region: DHHA1; pfam02272 940296000584 putrescine transporter subunit: periplasmic-binding component of ABC superfamily; Provisional; Region: PRK10682 940296000585 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 940296000586 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 940296000587 EamA-like transporter family; Region: EamA; pfam00892 940296000588 Cupin; Region: Cupin_6; pfam12852 940296000589 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 940296000590 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 940296000591 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 940296000592 Uncharacterized homolog of gamma-carboxymuconolactone decarboxylase subunit [Function unknown]; Region: COG0599 940296000593 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 940296000594 Peptidase family S49 N-terminal; Region: Peptidase_S49_N; pfam08496 940296000595 putative inner membrane peptidase; Provisional; Region: PRK11778 940296000596 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 940296000597 tandem repeat interface [polypeptide binding]; other site 940296000598 oligomer interface [polypeptide binding]; other site 940296000599 active site residues [active] 940296000600 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 940296000601 ABC transporter transmembrane region; Region: ABC_membrane_3; pfam13748 940296000602 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 940296000603 MarR family; Region: MarR_2; pfam12802 940296000604 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 940296000605 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 940296000606 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 940296000607 putative active site pocket [active] 940296000608 4-fold oligomerization interface [polypeptide binding]; other site 940296000609 metal binding residues [ion binding]; metal-binding site 940296000610 3-fold/trimer interface [polypeptide binding]; other site 940296000611 histidinol-phosphate aminotransferase; Provisional; Region: PRK04870 940296000612 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 940296000613 pyridoxal 5'-phosphate binding site [chemical binding]; other site 940296000614 homodimer interface [polypeptide binding]; other site 940296000615 catalytic residue [active] 940296000616 Histidinol dehydrogenase [Amino acid transport and metabolism]; Region: HisD; COG0141 940296000617 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 940296000618 NAD binding site [chemical binding]; other site 940296000619 dimerization interface [polypeptide binding]; other site 940296000620 product binding site; other site 940296000621 substrate binding site [chemical binding]; other site 940296000622 zinc binding site [ion binding]; other site 940296000623 catalytic residues [active] 940296000624 GIY-YIG domain of uncharacterized proteins from bacteria and their eukaryotic homologs; Region: GIY-YIG_COG3680; cd10440 940296000625 GIY-YIG motif/motif A; other site 940296000626 putative active site [active] 940296000627 putative metal binding site [ion binding]; other site 940296000628 ATP phosphoribosyltransferase catalytic subunit; Reviewed; Region: hisG; PRK01686 940296000629 ATP phosphoribosyltransferase [Amino acid transport and metabolism]; Region: HisG; COG0040 940296000630 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 940296000631 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 940296000632 Cu(I) binding site [ion binding]; other site 940296000633 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK06965 940296000634 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 940296000635 PYR/PP interface [polypeptide binding]; other site 940296000636 dimer interface [polypeptide binding]; other site 940296000637 TPP binding site [chemical binding]; other site 940296000638 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 940296000639 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 940296000640 TPP-binding site [chemical binding]; other site 940296000641 dimer interface [polypeptide binding]; other site 940296000642 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 940296000643 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 940296000644 putative valine binding site [chemical binding]; other site 940296000645 dimer interface [polypeptide binding]; other site 940296000646 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 940296000647 Uncharacterized conserved protein [Function unknown]; Region: COG1359 940296000648 ketol-acid reductoisomerase; Provisional; Region: PRK05479 940296000649 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 940296000650 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 940296000651 ornithine carbamoyltransferase; Validated; Region: PRK02102 940296000652 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 940296000653 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 940296000654 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 940296000655 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 940296000656 substrate binding site [chemical binding]; other site 940296000657 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 940296000658 substrate binding site [chemical binding]; other site 940296000659 ligand binding site [chemical binding]; other site 940296000660 Predicted permeases [General function prediction only]; Region: COG0795 940296000661 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 940296000662 Predicted permeases [General function prediction only]; Region: COG0795 940296000663 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 940296000664 multifunctional aminopeptidase A; Provisional; Region: PRK00913 940296000665 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 940296000666 interface (dimer of trimers) [polypeptide binding]; other site 940296000667 Substrate-binding/catalytic site; other site 940296000668 Zn-binding sites [ion binding]; other site 940296000669 DNA polymerase III, chi subunit [DNA replication, recombination, and repair]; Region: HolC; COG2927 940296000670 FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]; Region: FkpA; COG0545 940296000671 Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; Region: FKBP_N; pfam01346 940296000672 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 940296000673 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 940296000674 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 940296000675 active site 940296000676 substrate binding site [chemical binding]; other site 940296000677 cosubstrate binding site; other site 940296000678 catalytic site [active] 940296000679 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 940296000680 OsmC-like protein; Region: OsmC; cl00767 940296000681 Transcriptional regulators [Transcription]; Region: GntR; COG1802 940296000682 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 940296000683 DNA-binding site [nucleotide binding]; DNA binding site 940296000684 This entry represents the C-terminal ligand binding domain of many members of the GntR family; Region: FCD; smart00895 940296000685 Predicted membrane protein [Function unknown]; Region: COG2431 940296000686 DNA-binding transcriptional activator FucR; Provisional; Region: PRK10411 940296000687 DeoR-like helix-turn-helix domain; Region: HTH_DeoR; pfam08220 940296000688 DeoR C terminal sensor domain; Region: DeoRC; pfam00455 940296000689 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 940296000690 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 940296000691 active site 940296000692 HIGH motif; other site 940296000693 nucleotide binding site [chemical binding]; other site 940296000694 catalytic core domain of glutaminyl-tRNA synthetase; Region: GlnRS_core; cd00807 940296000695 KMSKS motif; other site 940296000696 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 940296000697 glutathione synthetase; Provisional; Region: PRK05246 940296000698 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 940296000699 Prokaryotic glutathione synthetase, ATP-grasp domain; Region: GSH-S_ATP; pfam02955 940296000700 Diacylglycerol kinase [Cell envelope biogenesis, outer membrane]; Region: DgkA; COG0818 940296000701 Copper(I)-binding protein [Inorganic ion transport and metabolism]; Region: COG2847 940296000702 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 940296000703 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 940296000704 Ligand Binding Site [chemical binding]; other site 940296000705 Long-chain-fatty-acid--CoA ligase; Validated; Region: PRK07059 940296000706 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 940296000707 acyl-activating enzyme (AAE) consensus motif; other site 940296000708 putative AMP binding site [chemical binding]; other site 940296000709 putative active site [active] 940296000710 putative CoA binding site [chemical binding]; other site 940296000711 CTP synthetase; Validated; Region: pyrG; PRK05380 940296000712 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 940296000713 Catalytic site [active] 940296000714 active site 940296000715 UTP binding site [chemical binding]; other site 940296000716 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 940296000717 active site 940296000718 putative oxyanion hole; other site 940296000719 catalytic triad [active] 940296000720 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG1943 940296000721 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 940296000722 C-5 cytosine-specific DNA methylase; Region: DNA_methylase; pfam00145 940296000723 cofactor binding site; other site 940296000724 DNA binding site [nucleotide binding] 940296000725 substrate interaction site [chemical binding]; other site 940296000726 Catalytic GIY-YIG domain of type II restriction enzyme R.Eco29kI, R.NgoMIII, and similar proteins; Region: GIY-YIG_RE_Eco29kI_NgoMIII; cd10452 940296000727 homodimer interface [polypeptide binding]; other site 940296000728 GIY-YIG motif/motif A; other site 940296000729 active site 940296000730 DNA binding site [nucleotide binding] 940296000731 putative metal binding site [ion binding]; other site 940296000732 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 940296000733 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 940296000734 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 940296000735 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 940296000736 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 940296000737 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 940296000738 RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when...; Region: RhoGAP; cl02570 940296000739 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 940296000740 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 940296000741 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 940296000742 glutamine binding [chemical binding]; other site 940296000743 catalytic triad [active] 940296000744 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 940296000745 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 940296000746 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 940296000747 Transposase domain (DUF772); Region: DUF772; pfam05598 940296000748 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 940296000749 Histone deacetylases and histone-like deacetylases, classII; Region: HDAC_classII_2; cd11599 940296000750 putative active site [active] 940296000751 Zn binding site [ion binding]; other site 940296000752 Preprotein translocase subunit; Region: YajC; pfam02699 940296000753 SecD export protein N-terminal TM region; Region: SecD-TM1; pfam13721 940296000754 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 940296000755 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 940296000756 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 940296000757 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 940296000758 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 940296000759 Protein export membrane protein; Region: SecD_SecF; pfam02355 940296000760 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 940296000761 16S/18S rRNA binding site [nucleotide binding]; other site 940296000762 S13e-L30e interaction site [polypeptide binding]; other site 940296000763 25S rRNA binding site [nucleotide binding]; other site 940296000764 putrescine transporter ATP-binding subunit; Provisional; Region: potG; PRK11607 940296000765 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 940296000766 Walker A/P-loop; other site 940296000767 ATP binding site [chemical binding]; other site 940296000768 Q-loop/lid; other site 940296000769 ABC transporter signature motif; other site 940296000770 Walker B; other site 940296000771 D-loop; other site 940296000772 H-loop/switch region; other site 940296000773 TOBE domain; Region: TOBE_2; pfam08402 940296000774 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 940296000775 dimer interface [polypeptide binding]; other site 940296000776 conserved gate region; other site 940296000777 putative PBP binding loops; other site 940296000778 ABC-ATPase subunit interface; other site 940296000779 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 940296000780 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 940296000781 dimer interface [polypeptide binding]; other site 940296000782 conserved gate region; other site 940296000783 putative PBP binding loops; other site 940296000784 ABC-ATPase subunit interface; other site 940296000785 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 940296000786 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 940296000787 Ammonia permease [Inorganic ion transport and metabolism]; Region: AmtB; COG0004 940296000788 transcription termination factor Rho; Provisional; Region: rho; PRK09376 940296000789 Rho termination factor, N-terminal domain; Region: Rho_N; smart00959 940296000790 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 940296000791 RNA binding site [nucleotide binding]; other site 940296000792 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 940296000793 multimer interface [polypeptide binding]; other site 940296000794 Walker A motif; other site 940296000795 ATP binding site [chemical binding]; other site 940296000796 Walker B motif; other site 940296000797 phosphoenolpyruvate synthase; Validated; Region: PRK06464 940296000798 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 940296000799 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 940296000800 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 940296000801 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1806 940296000802 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 940296000803 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 940296000804 motif II; other site 940296000805 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 940296000806 dinuclear metal binding motif [ion binding]; other site 940296000807 Outer membrane lipoprotein-sorting protein [Cell envelope biogenesis, outer membrane]; Region: LolA; COG2834 940296000808 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 940296000809 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 940296000810 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 940296000811 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 940296000812 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 940296000813 active site 940296000814 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 940296000815 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 940296000816 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 940296000817 trimer interface [polypeptide binding]; other site 940296000818 putative metal binding site [ion binding]; other site 940296000819 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 940296000820 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 940296000821 G1 box; other site 940296000822 putative GEF interaction site [polypeptide binding]; other site 940296000823 GTP/Mg2+ binding site [chemical binding]; other site 940296000824 Switch I region; other site 940296000825 G2 box; other site 940296000826 G3 box; other site 940296000827 Switch II region; other site 940296000828 G4 box; other site 940296000829 G5 box; other site 940296000830 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 940296000831 phosphoribosyl-AMP cyclohydrolase; Reviewed; Region: hisI; PRK00051 940296000832 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 940296000833 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 940296000834 substrate binding site [chemical binding]; other site 940296000835 glutamase interaction surface [polypeptide binding]; other site 940296000836 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 940296000837 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 940296000838 catalytic residues [active] 940296000839 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 940296000840 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 940296000841 ATP-binding cassette domain of the carbohydrate and solute transporters-like; Region: ABC_Carb_Solutes_like; cd03259 940296000842 Walker A/P-loop; other site 940296000843 ATP binding site [chemical binding]; other site 940296000844 Q-loop/lid; other site 940296000845 ABC transporter signature motif; other site 940296000846 Walker B; other site 940296000847 D-loop; other site 940296000848 H-loop/switch region; other site 940296000849 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 940296000850 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 940296000851 dimer interface [polypeptide binding]; other site 940296000852 conserved gate region; other site 940296000853 putative PBP binding loops; other site 940296000854 ABC-ATPase subunit interface; other site 940296000855 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 940296000856 dimer interface [polypeptide binding]; other site 940296000857 conserved gate region; other site 940296000858 ABC-ATPase subunit interface; other site 940296000859 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 940296000860 ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: AfuA; COG1840 940296000861 argininosuccinate lyase; Provisional; Region: PRK00855 940296000862 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 940296000863 active sites [active] 940296000864 tetramer interface [polypeptide binding]; other site 940296000865 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 940296000866 active site 940296000867 tetramer interface; other site 940296000868 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 940296000869 active site 940296000870 dimerization interface [polypeptide binding]; other site 940296000871 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 940296000872 dimer interface [polypeptide binding]; other site 940296000873 substrate binding site [chemical binding]; other site 940296000874 metal binding sites [ion binding]; metal-binding site 940296000875 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 940296000876 nudix motif; other site 940296000877 Protein of unknown function (DUF1020); Region: DUF1020; pfam06255 940296000878 Cation transport protein; Region: TrkH; cl17365 940296000879 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 940296000880 diadenosine tetraphosphatase; Reviewed; Region: apaH; PRK00166 940296000881 Escherichia coli ApaH and related proteins, metallophosphatase domain; Region: MPP_ApaH; cd07422 940296000882 active site 940296000883 metal binding site [ion binding]; metal-binding site 940296000884 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 940296000885 homotrimer interaction site [polypeptide binding]; other site 940296000886 putative active site [active] 940296000887 Opacity family porin protein; Region: Opacity; pfam02462 940296000888 coproporphyrinogen III oxidase; Provisional; Region: PRK08898 940296000889 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 940296000890 FeS/SAM binding site; other site 940296000891 HemN C-terminal domain; Region: HemN_C; pfam06969 940296000892 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 940296000893 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 940296000894 nucleotide binding pocket [chemical binding]; other site 940296000895 K-X-D-G motif; other site 940296000896 catalytic site [active] 940296000897 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 940296000898 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 940296000899 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 940296000900 Dimer interface [polypeptide binding]; other site 940296000901 BRCT sequence motif; other site 940296000902 ZipA, C-terminal domain (FtsZ-binding); Region: ZipA_C; smart00771 940296000903 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 940296000904 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 940296000905 amidase catalytic site [active] 940296000906 Zn binding residues [ion binding]; other site 940296000907 substrate binding site [chemical binding]; other site 940296000908 YceG-like family; Region: YceG; pfam02618 940296000909 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 940296000910 dimerization interface [polypeptide binding]; other site 940296000911 thymidylate kinase; Validated; Region: tmk; PRK00698 940296000912 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 940296000913 TMP-binding site; other site 940296000914 ATP-binding site [chemical binding]; other site 940296000915 Malic enzyme [Energy production and conversion]; Region: SfcA; COG0281 940296000916 Malic enzyme, N-terminal domain; Region: malic; pfam00390 940296000917 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 940296000918 putative NAD(P) binding site [chemical binding]; other site 940296000919 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 940296000920 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 940296000921 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3184 940296000922 Uncharacterized conserved protein [Function unknown]; Region: COG2835 940296000923 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 940296000924 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 940296000925 Ligand binding site; other site 940296000926 oligomer interface; other site 940296000927 tryptophan synthase alpha subunit; Provisional; Region: trpA; CHL00200 940296000928 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 940296000929 substrate binding site [chemical binding]; other site 940296000930 active site 940296000931 catalytic residues [active] 940296000932 heterodimer interface [polypeptide binding]; other site 940296000933 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 940296000934 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 940296000935 CNP1-like family; Region: CNP1; pfam08750 940296000936 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 940296000937 CPxP motif; other site 940296000938 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 940296000939 active site 940296000940 substrate binding pocket [chemical binding]; other site 940296000941 dimer interface [polypeptide binding]; other site 940296000942 transcription antitermination protein NusB; Reviewed; Region: nusB; PRK00202 940296000943 putative RNA binding site [nucleotide binding]; other site 940296000944 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 940296000945 homopentamer interface [polypeptide binding]; other site 940296000946 active site 940296000947 ribonuclease III; Reviewed; Region: rnc; PRK00102 940296000948 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 940296000949 dimerization interface [polypeptide binding]; other site 940296000950 active site 940296000951 metal binding site [ion binding]; metal-binding site 940296000952 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 940296000953 dsRNA binding site [nucleotide binding]; other site 940296000954 GTPase Era; Reviewed; Region: era; PRK00089 940296000955 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 940296000956 G1 box; other site 940296000957 GTP/Mg2+ binding site [chemical binding]; other site 940296000958 Switch I region; other site 940296000959 G2 box; other site 940296000960 Switch II region; other site 940296000961 G3 box; other site 940296000962 G4 box; other site 940296000963 G5 box; other site 940296000964 KH domain; Region: KH_2; pfam07650 940296000965 TonB-dependent lactoferrin and transferrin receptors; Region: TonB-tbp-lbp; TIGR01776 940296000966 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 940296000967 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 940296000968 active site 940296000969 transcription elongation factor GreB; Reviewed; Region: greB; PRK01885 940296000970 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 940296000971 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 940296000972 amidophosphoribosyltransferase; Provisional; Region: PRK09246 940296000973 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 940296000974 active site 940296000975 tetramer interface [polypeptide binding]; other site 940296000976 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 940296000977 active site 940296000978 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 940296000979 Colicin V production protein; Region: Colicin_V; pfam02674 940296000980 cell division protein FtsN; Region: ftsN; TIGR02223 940296000981 Sporulation related domain; Region: SPOR; pfam05036 940296000982 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 940296000983 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 940296000984 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 940296000985 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 940296000986 Walker A/P-loop; other site 940296000987 ATP binding site [chemical binding]; other site 940296000988 Q-loop/lid; other site 940296000989 ABC transporter signature motif; other site 940296000990 Walker B; other site 940296000991 D-loop; other site 940296000992 H-loop/switch region; other site 940296000993 Region found in RelA / SpoT proteins; Region: RelA_SpoT; smart00954 940296000994 metal binding triad [ion binding]; metal-binding site 940296000995 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 940296000996 Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]; Region: KsgA; COG0030 940296000997 MUG-like Uracil-DNA glycosylase enzyme family; Region: UDG_MUG_like; cd10032 940296000998 putative active site [active] 940296000999 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 940296001000 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 940296001001 pyridoxal 5'-phosphate binding site [chemical binding]; other site 940296001002 catalytic residue [active] 940296001003 Immunoglobulin A1 protease; Region: Peptidase_S6; pfam02395 940296001004 Pertactin-like passenger domains (virulence factors), C-terminal, subgroup 1, of autotransporter proteins of the type V secretion system of Gram-negative bacteria. This subgroup includes the passenger domains of Neisseria and Haemophilus IgA1 proteases; Region: PL1_Passenger_AT; cd01343 940296001005 TolA protein; Region: tolA_full; TIGR02794 940296001006 Autotransporter beta-domain; Region: Autotransporter; pfam03797 940296001007 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 940296001008 DNA internalization-related competence protein ComEC/Rec2; Region: ComEC_Rec2; TIGR00361 940296001009 Competence protein; Region: Competence; pfam03772 940296001010 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 940296001011 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 940296001012 Prokaryotic membrane lipoprotein lipid attachment site; Region: LPAM_1; pfam08139 940296001013 23S rRNA pseudouridine synthase D; Provisional; Region: rluD; PRK11180 940296001014 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 940296001015 RNA binding surface [nucleotide binding]; other site 940296001016 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 940296001017 active site 940296001018 bile acid transporter; Region: bass; TIGR00841 940296001019 Sodium Bile acid symporter family; Region: SBF; pfam01758 940296001020 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 940296001021 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 940296001022 Rare lipoprotein B [Cell envelope biogenesis, outer membrane]; Region: RlpB; COG2980 940296001023 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK05574 940296001024 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 940296001025 Predicted membrane protein/domain [Function unknown]; Region: COG1714 940296001026 hypothetical protein; Provisional; Region: PRK11820 940296001027 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 940296001028 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 940296001029 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 940296001030 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 940296001031 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 940296001032 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 940296001033 DNA binding residues [nucleotide binding] 940296001034 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 940296001035 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 940296001036 putative active site [active] 940296001037 catalytic triad [active] 940296001038 putative dimer interface [polypeptide binding]; other site 940296001039 Protein of unknown function (DUF808); Region: DUF808; cl01002 940296001040 potassium/proton antiporter; Reviewed; Region: PRK05326 940296001041 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 940296001042 Cytochrome c; Region: Cytochrom_C; pfam00034 940296001043 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 940296001044 ferrochelatase; Reviewed; Region: hemH; PRK00035 940296001045 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 940296001046 C-terminal domain interface [polypeptide binding]; other site 940296001047 active site 940296001048 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 940296001049 active site 940296001050 N-terminal domain interface [polypeptide binding]; other site 940296001051 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 940296001052 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 940296001053 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 940296001054 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 940296001055 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; pfam07973 940296001056 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 940296001057 active site 940296001058 dimer interface [polypeptide binding]; other site 940296001059 motif 1; other site 940296001060 motif 2; other site 940296001061 motif 3; other site 940296001062 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 940296001063 anticodon binding site; other site 940296001064 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 940296001065 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 940296001066 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 940296001067 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 940296001068 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 940296001069 23S rRNA binding site [nucleotide binding]; other site 940296001070 L21 binding site [polypeptide binding]; other site 940296001071 L13 binding site [polypeptide binding]; other site 940296001072 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 940296001073 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 940296001074 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 940296001075 dimer interface [polypeptide binding]; other site 940296001076 motif 1; other site 940296001077 active site 940296001078 motif 2; other site 940296001079 motif 3; other site 940296001080 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 940296001081 additional DNA contacts [nucleotide binding]; other site 940296001082 mismatch recognition site; other site 940296001083 active site 940296001084 zinc binding site [ion binding]; other site 940296001085 DNA intercalation site [nucleotide binding]; other site 940296001086 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 940296001087 cofactor binding site; other site 940296001088 HNH endonuclease; Region: HNH_2; pfam13391 940296001089 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 940296001090 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 940296001091 putative tRNA-binding site [nucleotide binding]; other site 940296001092 B3/4 domain; Region: B3_4; pfam03483 940296001093 tRNA synthetase B5 domain; Region: B5; smart00874 940296001094 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 940296001095 dimer interface [polypeptide binding]; other site 940296001096 motif 1; other site 940296001097 motif 3; other site 940296001098 motif 2; other site 940296001099 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 940296001100 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 940296001101 IHF - DNA interface [nucleotide binding]; other site 940296001102 IHF dimer interface [polypeptide binding]; other site 940296001103 Protein affecting phage T7 exclusion by the F plasmid [General function prediction only]; Region: FxsA; COG3030 940296001104 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK06173 940296001105 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 940296001106 inhibitor-cofactor binding pocket; inhibition site 940296001107 pyridoxal 5'-phosphate binding site [chemical binding]; other site 940296001108 catalytic residue [active] 940296001109 dithiobiotin synthetase; Reviewed; Region: bioD; PRK00090 940296001110 AAA domain; Region: AAA_26; pfam13500 940296001111 Chorismate lyase; Region: Chor_lyase; cl01230 940296001112 4-hydroxybenzoate octaprenyltransferase; Reviewed; Region: ubiA; PRK12848 940296001113 UbiA prenyltransferase family; Region: UbiA; pfam01040 940296001114 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 940296001115 active site 940296001116 phosphorylation site [posttranslational modification] 940296001117 HPr kinase/phosphorylase; Provisional; Region: PRK05428 940296001118 HPr Serine kinase N terminus; Region: Hpr_kinase_N; pfam02603 940296001119 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 940296001120 Hpr binding site; other site 940296001121 active site 940296001122 homohexamer subunit interaction site [polypeptide binding]; other site 940296001123 glmZ(sRNA)-inactivating NTPase; Provisional; Region: PRK05416 940296001124 ribosome biogenesis GTP-binding protein YlqF; Region: GTPase_YlqF; TIGR03596 940296001125 Circularly permuted YlqF GTPase; Region: YlqF; cd01856 940296001126 GTP/Mg2+ binding site [chemical binding]; other site 940296001127 G4 box; other site 940296001128 G5 box; other site 940296001129 G1 box; other site 940296001130 Switch I region; other site 940296001131 G2 box; other site 940296001132 G3 box; other site 940296001133 Switch II region; other site 940296001134 Chromosome segregation and condensation protein B [DNA replication, recombination and repair]; Region: scpB; COG1386 940296001135 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 940296001136 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 940296001137 Walker A/P-loop; other site 940296001138 ATP binding site [chemical binding]; other site 940296001139 Q-loop/lid; other site 940296001140 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 940296001141 ABC transporter signature motif; other site 940296001142 Walker B; other site 940296001143 D-loop; other site 940296001144 H-loop/switch region; other site 940296001145 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 940296001146 tRNA U-34 5-methylaminomethyl-2-thiouridine biosynthesis protein MnmC, C-terminal domain; Region: MnmC_Cterm; TIGR03197 940296001147 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3536 940296001148 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 940296001149 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 940296001150 S-adenosylmethionine binding site [chemical binding]; other site 940296001151 Predicted flavin-nucleotide-binding protein [General function prediction only]; Region: COG3467 940296001152 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 940296001153 catalytic center binding site [active] 940296001154 ATP binding site [chemical binding]; other site 940296001155 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3094 940296001156 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 940296001157 S-adenosylmethionine binding site [chemical binding]; other site 940296001158 bacterial Hfq-like; Region: Hfq; cd01716 940296001159 hexamer interface [polypeptide binding]; other site 940296001160 Sm1 motif; other site 940296001161 RNA binding site [nucleotide binding]; other site 940296001162 Sm2 motif; other site 940296001163 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 940296001164 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 940296001165 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 940296001166 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 940296001167 catalytic triad [active] 940296001168 XerD and XerC integrases, DNA breaking-rejoining enzymes, N- and C-terminal domains. XerD-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination...; Region: INT_XerDC; cd00798 940296001169 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 940296001170 active site 940296001171 Int/Topo IB signature motif; other site 940296001172 dTDP-4-dehydrorhamnose reductase; Region: rmlD; TIGR01214 940296001173 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 940296001174 NADP binding site [chemical binding]; other site 940296001175 active site 940296001176 putative substrate binding site [chemical binding]; other site 940296001177 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 940296001178 non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_Sc; cd01414 940296001179 ATP binding site [chemical binding]; other site 940296001180 active site 940296001181 substrate binding site [chemical binding]; other site 940296001182 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 940296001183 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 940296001184 RNase E interface [polypeptide binding]; other site 940296001185 trimer interface [polypeptide binding]; other site 940296001186 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 940296001187 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 940296001188 RNase E interface [polypeptide binding]; other site 940296001189 trimer interface [polypeptide binding]; other site 940296001190 active site 940296001191 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 940296001192 putative nucleic acid binding region [nucleotide binding]; other site 940296001193 G-X-X-G motif; other site 940296001194 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 940296001195 RNA binding site [nucleotide binding]; other site 940296001196 domain interface; other site 940296001197 Uncharacterized conserved protein [Function unknown]; Region: COG2836 940296001198 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 940296001199 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 940296001200 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 940296001201 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 940296001202 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 940296001203 dimer interface [polypeptide binding]; other site 940296001204 pyridoxal 5'-phosphate binding site [chemical binding]; other site 940296001205 catalytic residue [active] 940296001206 EamA-like transporter family; Region: EamA; pfam00892 940296001207 Signal peptidase I [Intracellular trafficking and secretion]; Region: LepB; COG0681 940296001208 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 940296001209 Catalytic site [active] 940296001210 conjugative transfer signal peptidase TraF; Region: TraF_Ti; TIGR02771 940296001211 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 940296001212 GTP-binding protein LepA; Provisional; Region: PRK05433 940296001213 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 940296001214 G1 box; other site 940296001215 putative GEF interaction site [polypeptide binding]; other site 940296001216 GTP/Mg2+ binding site [chemical binding]; other site 940296001217 Switch I region; other site 940296001218 G2 box; other site 940296001219 G3 box; other site 940296001220 Switch II region; other site 940296001221 G4 box; other site 940296001222 G5 box; other site 940296001223 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 940296001224 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 940296001225 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 940296001226 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Validated; Region: PRK05584 940296001227 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Region: MTA/SAH-Nsdase; TIGR01704 940296001228 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 940296001229 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 940296001230 Walker A motif; other site 940296001231 ATP binding site [chemical binding]; other site 940296001232 Walker B motif; other site 940296001233 DNA polymerase III subunit delta'; Validated; Region: PRK08699 940296001234 DNA polymerase III subunit delta'; Validated; Region: PRK08485 940296001235 Tfp pilus assembly protein PilZ [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilZ; COG3215 940296001236 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 940296001237 Predicted metal-dependent hydrolases with the TIM-barrel fold [General function prediction only]; Region: COG1099 940296001238 active site 940296001239 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 940296001240 putative GSH binding site [chemical binding]; other site 940296001241 catalytic residues [active] 940296001242 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 940296001243 active site 940296001244 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4390 940296001245 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3677 940296001246 InsA N-terminal domain; Region: Zn_Tnp_IS1; pfam03811 940296001247 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 940296001248 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 940296001249 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 940296001250 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 940296001251 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 940296001252 active site 940296001253 Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]; Region: HemX; COG2959 940296001254 putative uroporphyrinogen III C-methyltransferase; Provisional; Region: PRK10920 940296001255 Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]; Region: HemY; COG3071 940296001256 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 940296001257 substrate binding site [chemical binding]; other site 940296001258 active site 940296001259 DEAD-like helicases superfamily; Region: DEXDc; smart00487 940296001260 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 940296001261 ATP binding site [chemical binding]; other site 940296001262 putative Mg++ binding site [ion binding]; other site 940296001263 Z1 domain; Region: Z1; pfam10593 940296001264 Putative catalytic domain of type II restriction enzyme NgoFVII and similar proteins; Region: PLDc_RE_NgoFVII; cd09177 940296001265 PLD-like domain; Region: PLDc_2; pfam13091 940296001266 putative homodimer interface [polypeptide binding]; other site 940296001267 putative active site [active] 940296001268 catalytic site [active] 940296001269 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 940296001270 C-5 cytosine-specific DNA methylase; Region: DNA_methylase; pfam00145 940296001271 cofactor binding site; other site 940296001272 DNA binding site [nucleotide binding] 940296001273 substrate interaction site [chemical binding]; other site 940296001274 DNA repair protein RadA; Provisional; Region: PRK11823 940296001275 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 940296001276 Walker A motif/ATP binding site; other site 940296001277 ATP binding site [chemical binding]; other site 940296001278 Walker B motif; other site 940296001279 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 940296001280 Uncharacterized conserved protein [Function unknown]; Region: COG3439 940296001281 exodeoxyribonuclease V, beta subunit; Region: recB; TIGR00609 940296001282 Part of AAA domain; Region: AAA_19; pfam13245 940296001283 Family description; Region: UvrD_C_2; pfam13538 940296001284 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 940296001285 Dyp-type peroxidase family; Region: Dyp_perox; pfam04261 940296001286 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 940296001287 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 940296001288 substrate binding pocket [chemical binding]; other site 940296001289 membrane-bound complex binding site; other site 940296001290 hinge residues; other site 940296001291 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 940296001292 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 940296001293 dimer interface [polypeptide binding]; other site 940296001294 conserved gate region; other site 940296001295 putative PBP binding loops; other site 940296001296 ABC-ATPase subunit interface; other site 940296001297 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 940296001298 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 940296001299 Walker A/P-loop; other site 940296001300 ATP binding site [chemical binding]; other site 940296001301 Q-loop/lid; other site 940296001302 ABC transporter signature motif; other site 940296001303 Walker B; other site 940296001304 D-loop; other site 940296001305 H-loop/switch region; other site 940296001306 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 940296001307 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 940296001308 active site 940296001309 substrate binding site [chemical binding]; other site 940296001310 metal binding site [ion binding]; metal-binding site 940296001311 cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the...; Region: cyclophilin; cl00197 940296001312 active site 940296001313 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 940296001314 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 940296001315 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 940296001316 putative active site [active] 940296001317 catalytic residue [active] 940296001318 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2914 940296001319 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 940296001320 putative coenzyme Q binding site [chemical binding]; other site 940296001321 ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]; Region: HflB; COG0465 940296001322 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 940296001323 Walker A motif; other site 940296001324 ATP binding site [chemical binding]; other site 940296001325 Walker B motif; other site 940296001326 arginine finger; other site 940296001327 Peptidase family M41; Region: Peptidase_M41; pfam01434 940296001328 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 940296001329 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 940296001330 S-adenosylmethionine binding site [chemical binding]; other site 940296001331 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]; Region: COG1534 940296001332 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 940296001333 dimer interface [polypeptide binding]; other site 940296001334 active site 940296001335 aspartate-rich active site metal binding site; other site 940296001336 allosteric magnesium binding site [ion binding]; other site 940296001337 Schiff base residues; other site 940296001338 Cystathionine beta-lyases/cystathionine gamma-synthases [Amino acid transport and metabolism]; Region: MetC; COG0626 940296001339 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 940296001340 homodimer interface [polypeptide binding]; other site 940296001341 substrate-cofactor binding pocket; other site 940296001342 pyridoxal 5'-phosphate binding site [chemical binding]; other site 940296001343 catalytic residue [active] 940296001344 putative GTP cyclohydrolase; Provisional; Region: PRK13674 940296001345 NAD(P)H:FMN oxidoreductase family. This domain catalyzes the reduction of flavin, nitrocompound, quinones and azo compounds using NADH or NADPH as an electron donor. The enzyme is a homodimer, and each monomer binds a FMN as co-factor. This family...; Region: NfsB_like_nitroreductase; cd02149 940296001346 dimer interface [polypeptide binding]; other site 940296001347 FMN binding site [chemical binding]; other site 940296001348 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 940296001349 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 940296001350 RNA binding surface [nucleotide binding]; other site 940296001351 Pseudouridine synthase, a subgroup of the RsuA family; Region: PSSA_1; cd02555 940296001352 active site 940296001353 inorganic polyphosphate/ATP-NAD kinase; Provisional; Region: ppnK; PRK04539 940296001354 ATP-NAD kinase; Region: NAD_kinase; pfam01513 940296001355 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3165 940296001356 SCP-2 sterol transfer family; Region: SCP2; cl01225 940296001357 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 940296001358 atypical (a) SDRs, subgroup 4; Region: SDR_a4; cd05266 940296001359 putative NAD(P) binding site [chemical binding]; other site 940296001360 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 940296001361 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 940296001362 Bacterial transcriptional repressor; Region: TetR; pfam13972 940296001363 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK00046 940296001364 FAD binding domain; Region: FAD_binding_4; pfam01565 940296001365 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 940296001366 multidrug efflux protein; Reviewed; Region: PRK01766 940296001367 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Vibrio cholerae NorM; Region: MATE_NorM_like; cd13131 940296001368 cation binding site [ion binding]; other site 940296001369 ATP phosphoribosyltransferase regulatory subunit; Provisional; Region: hisZ; PRK12292 940296001370 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 940296001371 dimer interface [polypeptide binding]; other site 940296001372 motif 1; other site 940296001373 active site 940296001374 motif 2; other site 940296001375 motif 3; other site 940296001376 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 940296001377 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 940296001378 GDP-binding site [chemical binding]; other site 940296001379 ACT binding site; other site 940296001380 IMP binding site; other site 940296001381 heat shock protein HtpX; Provisional; Region: PRK05457 940296001382 adenylate kinase; Reviewed; Region: adk; PRK00279 940296001383 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 940296001384 AMP-binding site [chemical binding]; other site 940296001385 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 940296001386 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 940296001387 active site 940296001388 dimer interface [polypeptide binding]; other site 940296001389 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 940296001390 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 940296001391 putative ribose interaction site [chemical binding]; other site 940296001392 putative ADP binding site [chemical binding]; other site 940296001393 ADP-L-glycero-D-mannoheptose 6-epimerase (GME), extended (e) SDRs; Region: ADP_GME_SDR_e; cd05248 940296001394 ADP-L-glycero-D-manno-heptose-6-epimerase; Region: heptose_epim; TIGR02197 940296001395 NADP binding site [chemical binding]; other site 940296001396 homopentamer interface [polypeptide binding]; other site 940296001397 substrate binding site [chemical binding]; other site 940296001398 active site 940296001399 type I restriction system adenine methylase (hsdM); Region: hsdM; TIGR00497 940296001400 HsdM N-terminal domain; Region: HsdM_N; pfam12161 940296001401 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 940296001402 S-adenosylmethionine binding site [chemical binding]; other site 940296001403 DNA-damage-inducible protein D; Provisional; Region: dinD; PRK11525 940296001404 BRO family, N-terminal domain; Region: Bro-N; pfam02498 940296001405 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 940296001406 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 940296001407 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 940296001408 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 940296001409 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 940296001410 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 940296001411 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 940296001412 ATP binding site [chemical binding]; other site 940296001413 putative Mg++ binding site [ion binding]; other site 940296001414 ATP-dependent Clp protease ATP-binding subunit clpA; Region: ClpA; TIGR02639 940296001415 Clp amino terminal domain; Region: Clp_N; pfam02861 940296001416 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 940296001417 Walker A motif; other site 940296001418 ATP binding site [chemical binding]; other site 940296001419 Walker B motif; other site 940296001420 arginine finger; other site 940296001421 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 940296001422 Walker A motif; other site 940296001423 ATP binding site [chemical binding]; other site 940296001424 Walker B motif; other site 940296001425 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 940296001426 Uncharacterized conserved protein [Function unknown]; Region: COG2127 940296001427 peptidase PmbA; Provisional; Region: PRK11040 940296001428 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3028 940296001429 ssDNA exonuclease RecJ; Provisional; Region: PRK11070 940296001430 DHH family; Region: DHH; pfam01368 940296001431 DHHA1 domain; Region: DHHA1; pfam02272 940296001432 poly(A) polymerase; Region: pcnB; TIGR01942 940296001433 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 940296001434 active site 940296001435 NTP binding site [chemical binding]; other site 940296001436 metal binding triad [ion binding]; metal-binding site 940296001437 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 940296001438 Polymerase A arginine-rich C-terminus; Region: PolyA_pol_arg_C; pfam12626 940296001439 Protein of unknown function (DUF3247); Region: DUF3247; pfam11607 940296001440 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 940296001441 PhoH-like protein; Region: PhoH; pfam02562 940296001442 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 940296001443 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 940296001444 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 940296001445 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 940296001446 Predicted periplasmic/secreted protein [Function unknown]; Region: COG3471 940296001447 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 940296001448 trimer interface [polypeptide binding]; other site 940296001449 active site 940296001450 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4642 940296001451 DNA recombination-dependent growth factor C [DNA replication, recombination, and repair]; Region: RdgC; COG2974 940296001452 GTP-binding protein Der; Reviewed; Region: PRK00093 940296001453 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 940296001454 G1 box; other site 940296001455 GTP/Mg2+ binding site [chemical binding]; other site 940296001456 Switch I region; other site 940296001457 G2 box; other site 940296001458 Switch II region; other site 940296001459 G3 box; other site 940296001460 G4 box; other site 940296001461 G5 box; other site 940296001462 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 940296001463 G1 box; other site 940296001464 GTP/Mg2+ binding site [chemical binding]; other site 940296001465 Switch I region; other site 940296001466 G2 box; other site 940296001467 G3 box; other site 940296001468 Switch II region; other site 940296001469 G4 box; other site 940296001470 G5 box; other site 940296001471 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 940296001472 histidyl-tRNA synthetase; Region: hisS; TIGR00442 940296001473 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 940296001474 dimer interface [polypeptide binding]; other site 940296001475 motif 1; other site 940296001476 active site 940296001477 motif 2; other site 940296001478 motif 3; other site 940296001479 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 940296001480 anticodon binding site; other site 940296001481 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 940296001482 putative active site [active] 940296001483 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 940296001484 Pseudouridine synthase, a subgroup of the RluA family; Region: PSRA_1; cd02558 940296001485 probable active site [active] 940296001486 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 940296001487 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 940296001488 spermidine synthase; Provisional; Region: PRK04457 940296001489 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 940296001490 oligomerization interface [polypeptide binding]; other site 940296001491 active site 940296001492 metal binding site [ion binding]; metal-binding site 940296001493 pantoate--beta-alanine ligase; Region: panC; TIGR00018 940296001494 Pantoate-beta-alanine ligase; Region: PanC; cd00560 940296001495 active site 940296001496 ATP-binding site [chemical binding]; other site 940296001497 pantoate-binding site; other site 940296001498 HXXH motif; other site 940296001499 TPR repeat; Region: TPR_11; pfam13414 940296001500 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 940296001501 binding surface 940296001502 TPR motif; other site 940296001503 Outer membrane lipoprotein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: LolB; COG3017 940296001504 Outer membrane lipoprotein LolB; Region: LolB; pfam03550 940296001505 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: ipk; PRK00343 940296001506 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 940296001507 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 940296001508 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 940296001509 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 940296001510 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 940296001511 active site 940296001512 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 940296001513 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 940296001514 5S rRNA interface [nucleotide binding]; other site 940296001515 CTC domain interface [polypeptide binding]; other site 940296001516 L16 interface [polypeptide binding]; other site 940296001517 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 940296001518 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 940296001519 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; smart00936 940296001520 threonine dehydratase; Reviewed; Region: PRK09224 940296001521 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 940296001522 tetramer interface [polypeptide binding]; other site 940296001523 pyridoxal 5'-phosphate binding site [chemical binding]; other site 940296001524 catalytic residue [active] 940296001525 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_1; cd04906 940296001526 putative Ile/Val binding site [chemical binding]; other site 940296001527 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase); Region: ACT_ThrD-I_2; cd04907 940296001528 putative Ile/Val binding site [chemical binding]; other site 940296001529 ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: CysA; COG1118 940296001530 ATP-binding cassette domain of the sulfate transporter; Region: ABC_CysA_sulfate_importer; cd03296 940296001531 Walker A/P-loop; other site 940296001532 ATP binding site [chemical binding]; other site 940296001533 Q-loop/lid; other site 940296001534 ABC transporter signature motif; other site 940296001535 Walker B; other site 940296001536 D-loop; other site 940296001537 H-loop/switch region; other site 940296001538 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 940296001539 dimer interface [polypeptide binding]; other site 940296001540 conserved gate region; other site 940296001541 putative PBP binding loops; other site 940296001542 ABC-ATPase subunit interface; other site 940296001543 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 940296001544 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 940296001545 dimer interface [polypeptide binding]; other site 940296001546 conserved gate region; other site 940296001547 putative PBP binding loops; other site 940296001548 ABC-ATPase subunit interface; other site 940296001549 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1755 940296001550 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 940296001551 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 940296001552 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 940296001553 replicative DNA helicase; Region: DnaB; TIGR00665 940296001554 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 940296001555 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 940296001556 Walker A motif; other site 940296001557 ATP binding site [chemical binding]; other site 940296001558 Walker B motif; other site 940296001559 DNA binding loops [nucleotide binding] 940296001560 Tfp pilus assembly protein FimT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimT; COG4970 940296001561 Type II transport protein GspH; Region: GspH; pfam12019 940296001562 Tfp pilus assembly protein PilV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilV; COG4967 940296001563 Prokaryotic N-terminal methylation site; Region: N_methyl_3; pfam13633 940296001564 Tfp pilus assembly protein PilW [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilW; COG4966 940296001565 Tfp pilus assembly protein PilX [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilX; COG4726 940296001566 PilX N-terminal; Region: PilX_N; pfam14341 940296001567 Tfp pilus assembly protein, major pilin PilA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilA; COG4969 940296001568 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 940296001569 Minor type IV pilin, PilX; Region: Pilin_PilX; pfam11530 940296001570 AzlC protein; Region: AzlC; cl00570 940296001571 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 940296001572 trimer interface [polypeptide binding]; other site 940296001573 active site 940296001574 succinyldiaminopimelate transaminase; Provisional; Region: PRK09147 940296001575 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 940296001576 pyridoxal 5'-phosphate binding site [chemical binding]; other site 940296001577 homodimer interface [polypeptide binding]; other site 940296001578 catalytic residue [active] 940296001579 hypothetical protein; Validated; Region: PRK02101 940296001580 integrase; Provisional; Region: PRK09692 940296001581 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 940296001582 active site 940296001583 Int/Topo IB signature motif; other site 940296001584 Protein of unknown function (DUF2786); Region: DUF2786; pfam10979 940296001585 Siphovirus Gp157; Region: Sipho_Gp157; pfam05565 940296001586 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 940296001587 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 940296001588 non-specific DNA binding site [nucleotide binding]; other site 940296001589 salt bridge; other site 940296001590 sequence-specific DNA binding site [nucleotide binding]; other site 940296001591 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 940296001592 non-specific DNA binding site [nucleotide binding]; other site 940296001593 salt bridge; other site 940296001594 sequence-specific DNA binding site [nucleotide binding]; other site 940296001595 Predicted transcriptional regulator [Transcription]; Region: COG2932 940296001596 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 940296001597 Catalytic site [active] 940296001598 Helix-turn-helix domain; Region: HTH_39; pfam14090 940296001599 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 940296001600 putative DNA binding site [nucleotide binding]; other site 940296001601 putative Zn2+ binding site [ion binding]; other site 940296001602 Protein of unknwon function (DUF3310); Region: DUF3310; pfam11753 940296001603 Endodeoxyribonuclease RusA; Region: RusA; pfam05866 940296001604 Protein of unknown function (DUF1364); Region: DUF1364; pfam07102 940296001605 NinB protein; Region: NinB; pfam05772 940296001606 HNH endonuclease; Region: HNH_3; pfam13392 940296001607 AP2 domain; Region: AP2; pfam00847 940296001608 Phage terminase large subunit; Region: Terminase_3; cl12054 940296001609 Protein of unknown function (DUF4043); Region: DUF4043; pfam13252 940296001610 Prophage antirepressor [Transcription]; Region: COG3617 940296001611 BRO family, N-terminal domain; Region: Bro-N; smart01040 940296001612 Monomeric isocitrate dehydrogenase [Energy production and conversion]; Region: Icd; COG2838 940296001613 Monomeric isocitrate dehydrogenase; Region: IDH; cl15383 940296001614 Glycosyltransferase family 52; Region: Glyco_transf_52; pfam07922 940296001615 Cytochrome C' Region: Cytochrom_C_2; cl01610 940296001616 malonic semialdehyde reductase; Provisional; Region: PRK10538 940296001617 classical (c) SDR, subgroup 5; Region: SDR_c5; cd05346 940296001618 putative NAD(P) binding site [chemical binding]; other site 940296001619 homotetramer interface [polypeptide binding]; other site 940296001620 homodimer interface [polypeptide binding]; other site 940296001621 active site 940296001622 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 940296001623 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl17254 940296001624 Autotransporter beta-domain; Region: Autotransporter; pfam03797 940296001625 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 940296001626 catalytic residues [active] 940296001627 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 940296001628 Protein of unknown function (DUF1020); Region: DUF1020; pfam06255 940296001629 Protein of unknown function (DUF1020); Region: DUF1020; pfam06255 940296001630 Protein of unknown function (DUF1020); Region: DUF1020; pfam06255 940296001631 Uncharacterized virulence-associated protein D [Function unknown]; Region: VapD; COG3309 940296001632 Uncharacterized small protein [Function unknown]; Region: COG2879 940296001633 carbon starvation protein A; Provisional; Region: PRK15015 940296001634 Carbon starvation protein CstA; Region: CstA; pfam02554 940296001635 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 940296001636 Protein of unknown function (DUF1436); Region: DUF1436; pfam07262 940296001637 succinic semialdehyde dehydrogenase; Region: PLN02278 940296001638 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 940296001639 tetramerization interface [polypeptide binding]; other site 940296001640 NAD(P) binding site [chemical binding]; other site 940296001641 catalytic residues [active] 940296001642 Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]; Region: TerC; COG0861 940296001643 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 940296001644 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 940296001645 Transporter associated domain; Region: CorC_HlyC; smart01091 940296001646 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 940296001647 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 940296001648 Peptidase family M23; Region: Peptidase_M23; pfam01551 940296001649 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 940296001650 recombination regulator RecX; Reviewed; Region: recX; PRK00117 940296001651 phosphoglycolate phosphatase; Provisional; Region: PRK13222 940296001652 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 940296001653 motif II; other site 940296001654 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Region: ELFV_dehydrog; pfam00208 940296001655 NAD(P) binding domain of glutamate dehydrogenase, subgroup 1; Region: NAD_bind_1_Glu_DH; cd01076 940296001656 NAD(P) binding site [chemical binding]; other site 940296001657 ABC-type Co2+ transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: CbiK; COG5266 940296001658 Uncharacterized protein, 4-oxalocrotonate tautomerase homolog [General function prediction only]; Region: COG1942 940296001659 active site 1 [active] 940296001660 dimer interface [polypeptide binding]; other site 940296001661 hexamer interface [polypeptide binding]; other site 940296001662 active site 2 [active] 940296001663 aminotransferase AlaT; Validated; Region: PRK09265 940296001664 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 940296001665 pyridoxal 5'-phosphate binding site [chemical binding]; other site 940296001666 homodimer interface [polypeptide binding]; other site 940296001667 catalytic residue [active] 940296001668 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 940296001669 Clp amino terminal domain; Region: Clp_N; pfam02861 940296001670 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 940296001671 Walker A motif; other site 940296001672 ATP binding site [chemical binding]; other site 940296001673 Walker B motif; other site 940296001674 arginine finger; other site 940296001675 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 940296001676 Walker A motif; other site 940296001677 ATP binding site [chemical binding]; other site 940296001678 Walker B motif; other site 940296001679 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 940296001680 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 940296001681 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 940296001682 active site 940296001683 HIGH motif; other site 940296001684 dimer interface [polypeptide binding]; other site 940296001685 KMSKS motif; other site 940296001686 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 940296001687 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 940296001688 Protein of unknown function (DUF560); Region: DUF560; pfam04575 940296001689 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl17254 940296001690 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl17254 940296001691 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG1943 940296001692 Transposase and inactivated derivatives, IS5 family [DNA replication, recombination, and repair]; Region: COG3039 940296001693 DDE superfamily endonuclease; Region: DDE_4; cl17710 940296001694 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 940296001695 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 940296001696 N-acetyl-D-glucosamine binding site [chemical binding]; other site 940296001697 catalytic residue [active] 940296001698 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 940296001699 Major Facilitator Superfamily; Region: MFS_1; pfam07690 940296001700 putative substrate translocation pore; other site 940296001701 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 940296001702 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 940296001703 dimer interface [polypeptide binding]; other site 940296001704 ssDNA binding site [nucleotide binding]; other site 940296001705 tetramer (dimer of dimers) interface [polypeptide binding]; other site 940296001706 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 940296001707 EamA-like transporter family; Region: EamA; pfam00892 940296001708 fumarate hydratase; Reviewed; Region: fumC; PRK00485 940296001709 Class II fumarases; Region: Fumarase_classII; cd01362 940296001710 active site 940296001711 tetramer interface [polypeptide binding]; other site 940296001712 transketolase; Reviewed; Region: PRK12753 940296001713 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 940296001714 TPP-binding site [chemical binding]; other site 940296001715 dimer interface [polypeptide binding]; other site 940296001716 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 940296001717 PYR/PP interface [polypeptide binding]; other site 940296001718 dimer interface [polypeptide binding]; other site 940296001719 TPP binding site [chemical binding]; other site 940296001720 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 940296001721 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 940296001722 4Fe-4S binding domain; Region: Fer4_5; pfam12801 940296001723 4Fe-4S binding domain; Region: Fer4_3; pfam12798 940296001724 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 940296001725 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3198 940296001726 FixH; Region: FixH; pfam05751 940296001727 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 940296001728 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 940296001729 FMN binding site [chemical binding]; other site 940296001730 substrate binding site [chemical binding]; other site 940296001731 putative catalytic residue [active] 940296001732 DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]; Region: DnaQ; COG0847 940296001733 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 940296001734 active site 940296001735 catalytic site [active] 940296001736 substrate binding site [chemical binding]; other site 940296001737 Integrase core domain; Region: rve; pfam00665 940296001738 Putative DNA-binding protein N-terminus; Region: Put_DNA-bind_N; pfam06971 940296001739 phage-associated protein, BcepMu gp16 family; Region: BcepMu_gp16; TIGR04111 940296001740 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 940296001741 non-specific DNA binding site [nucleotide binding]; other site 940296001742 salt bridge; other site 940296001743 sequence-specific DNA binding site [nucleotide binding]; other site 940296001744 37-kD nucleoid-associated bacterial protein; Region: NA37; cl15473 940296001745 phage/conjugal plasmid C-4 type zinc finger protein, TraR family; Region: C4_traR_proteo; TIGR02419 940296001746 CRISPR/Cas system-associated protein Cas8c; Region: Cas8c_I-C; cl12004 940296001747 CRISPR/Cas system-associated protein Cas8c; Region: Cas8c_I-C; cl12004 940296001748 CRISPR/Cas system-associated RAMP superfamily protein Cas7; Region: Cas7_I-C; cl01465 940296001749 CRISPR/Cas system-associated RAMP superfamily protein Cas7; Region: Cas7_I-C; cl01465 940296001750 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cd09637 940296001751 CRISPR/Cas system-associated protein Cas1; Region: Cas1_I-II-III; cl00656 940296001752 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 940296001753 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 940296001754 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 940296001755 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 940296001756 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 940296001757 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 940296001758 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 940296001759 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 940296001760 DNA binding residues [nucleotide binding] 940296001761 DNA primase; Validated; Region: dnaG; PRK05667 940296001762 CHC2 zinc finger; Region: zf-CHC2; pfam01807 940296001763 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 940296001764 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 940296001765 active site 940296001766 metal binding site [ion binding]; metal-binding site 940296001767 interdomain interaction site; other site 940296001768 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 940296001769 DNA primase DnaG DnaB-binding; Region: DnaG_DnaB_bind; pfam08278 940296001770 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 940296001771 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 940296001772 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 940296001773 SEC-C motif; Region: SEC-C; pfam02810 940296001774 Protein of unknown function (DUF721); Region: DUF721; pfam05258 940296001775 Azurin [Energy production and conversion]; Region: COG3241 940296001776 Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49); Region: G6PD_bact; pfam10786 940296001777 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 940296001778 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 940296001779 metal binding site [ion binding]; metal-binding site 940296001780 dimer interface [polypeptide binding]; other site 940296001781 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 940296001782 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 940296001783 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 940296001784 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 940296001785 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 940296001786 DNA binding site [nucleotide binding] 940296001787 active site 940296001788 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 940296001789 Glycosyltransferase family 9 (heptosyltransferase); Region: Glyco_transf_9; pfam01075 940296001790 putative active site [active] 940296001791 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 940296001792 SmpB-tmRNA interface; other site 940296001793 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; cl00185 940296001794 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 940296001795 Autotransporter beta-domain; Region: Autotransporter; pfam03797 940296001796 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 940296001797 FAD binding domain; Region: FAD_binding_4; pfam01565 940296001798 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional; Region: PRK15095 940296001799 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 940296001800 active site lid residues [active] 940296001801 substrate binding pocket [chemical binding]; other site 940296001802 catalytic residues [active] 940296001803 substrate-Mg2+ binding site; other site 940296001804 aspartate-rich region 1; other site 940296001805 aspartate-rich region 2; other site 940296001806 Domain of unknown function (DUF1841); Region: DUF1841; pfam08897 940296001807 Thiol:disulfide interchange protein [Posttranslational modification, protein turnover, chaperones / Energy production and conversion]; Region: COG4232 940296001808 Disulphide bond corrector protein DsbC; Region: DsbC; pfam11412 940296001809 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 940296001810 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 940296001811 DsbD alpha interface [polypeptide binding]; other site 940296001812 catalytic residues [active] 940296001813 acetate kinase A/propionate kinase 2; Reviewed; Region: PRK00180 940296001814 propionate/acetate kinase; Provisional; Region: PRK12379 940296001815 Uncharacterized protein, possibly involved in nitrogen fixation [Inorganic ion transport and metabolism]; Region: FixS; COG3197 940296001816 acylglycerophosphoethanolamine acyltransferase; Provisional; Region: PRK06814 940296001817 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 940296001818 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 940296001819 active site 940296001820 catalytic site [active] 940296001821 substrate binding site [chemical binding]; other site 940296001822 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 940296001823 substrate binding site; other site 940296001824 dimer interface; other site 940296001825 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 940296001826 homotrimer interaction site [polypeptide binding]; other site 940296001827 zinc binding site [ion binding]; other site 940296001828 CDP-binding sites; other site 940296001829 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 940296001830 tetramer (dimer of dimers) interface [polypeptide binding]; other site 940296001831 active site 940296001832 dimer interface [polypeptide binding]; other site 940296001833 Staphylococcal nuclease homologues; Region: SNc; smart00318 940296001834 Catalytic site; other site 940296001835 Staphylococcal nuclease homologue; Region: SNase; pfam00565 940296001836 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 940296001837 dimer interface [polypeptide binding]; other site 940296001838 conserved gate region; other site 940296001839 putative PBP binding loops; other site 940296001840 ABC-ATPase subunit interface; other site 940296001841 Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]; Region: MdoB; COG1368 940296001842 Sulfatase; Region: Sulfatase; cl17466 940296001843 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 940296001844 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 940296001845 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 940296001846 active site 940296001847 HIGH motif; other site 940296001848 KMSK motif region; other site 940296001849 Anticodon-binding domain of arginyl tRNA synthetases; Region: Anticodon_Ia_Arg; cd07956 940296001850 tRNA binding surface [nucleotide binding]; other site 940296001851 anticodon binding site; other site 940296001852 nicotinate phosphoribosyltransferase; Region: NAPRTase; TIGR01514 940296001853 Nicotinate phosphoribosyltransferase (NAPRTase), related to PncB. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting; Region: PncB_like; cd01401 940296001854 active site 940296001855 Rec8/ScpA/Scc1-like protein (kleisin family) [Replication, recombination, and repair]; Region: scpA; COG1354 940296001856 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 940296001857 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 940296001858 putative ATP binding site [chemical binding]; other site 940296001859 putative substrate interface [chemical binding]; other site 940296001860 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 940296001861 Ligand Binding Site [chemical binding]; other site 940296001862 ribonuclease PH; Reviewed; Region: rph; PRK00173 940296001863 Ribonuclease PH; Region: RNase_PH_bact; cd11362 940296001864 hexamer interface [polypeptide binding]; other site 940296001865 active site 940296001866 aspartate kinase; Reviewed; Region: PRK06635 940296001867 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 940296001868 putative nucleotide binding site [chemical binding]; other site 940296001869 putative catalytic residues [active] 940296001870 putative Mg ion binding site [ion binding]; other site 940296001871 putative aspartate binding site [chemical binding]; other site 940296001872 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 940296001873 putative allosteric regulatory site; other site 940296001874 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 940296001875 TIGR02594 family protein; Region: TIGR02594 940296001876 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 940296001877 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 940296001878 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 940296001879 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl17254 940296001880 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl17254 940296001881 proline iminopeptidase, Neisseria-type subfamily; Region: pro_imino_pep_1; TIGR01249 940296001882 Serine carboxypeptidase; Region: Peptidase_S10; cl08270 940296001883 Uncharacterized lipoprotein [Cell envelope biogenesis, outer membrane]; Region: NlpB; COG3317 940296001884 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 940296001885 dihydrodipicolinate synthase; Region: dapA; TIGR00674 940296001886 dimer interface [polypeptide binding]; other site 940296001887 active site 940296001888 catalytic residue [active] 940296001889 Xanthine/uracil permeases [Nucleotide transport and metabolism]; Region: UraA; COG2233 940296001890 xanthine permease; Region: pbuX; TIGR03173 940296001891 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional; Region: PRK11181 940296001892 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 940296001893 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 940296001894 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2839 940296001895 Regulator of competence-specific genes [Transcription]; Region: TfoX; COG3070 940296001896 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 940296001897 nucleoside/Zn binding site; other site 940296001898 dimer interface [polypeptide binding]; other site 940296001899 catalytic motif [active] 940296001900 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 940296001901 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 940296001902 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4394 940296001903 Uncharacterized protein conserved in bacteria (DUF2331); Region: DUF2331; pfam10093 940296001904 elongation factor P; Validated; Region: PRK00529 940296001905 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 940296001906 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 940296001907 RNA binding site [nucleotide binding]; other site 940296001908 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 940296001909 RNA binding site [nucleotide binding]; other site 940296001910 Methyltransferase domain; Region: Methyltransf_23; pfam13489 940296001911 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 940296001912 S-adenosylmethionine binding site [chemical binding]; other site 940296001913 homoserine O-acetyltransferase; Provisional; Region: metX; PRK00175 940296001914 homoserine O-acetyltransferase; Region: homoserO_Ac_trn; TIGR01392 940296001915 50S ribosomal protein L31 type B; Reviewed; Region: rpmE2; PRK01678 940296001916 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 940296001917 FAD binding site [chemical binding]; other site 940296001918 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional; Region: PRK05222 940296001919 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 940296001920 THF binding site; other site 940296001921 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 940296001922 substrate binding site [chemical binding]; other site 940296001923 THF binding site; other site 940296001924 zinc-binding site [ion binding]; other site 940296001925 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 940296001926 catalytic triad [active] 940296001927 dimer interface [polypeptide binding]; other site 940296001928 Glutaredoxin (GRX) family, PRX5 hybrid subfamily; composed of hybrid proteins containing peroxiredoxin (PRX) and GRX domains, which is found in some pathogenic bacteria and cyanobacteria. PRXs are thiol-specific antioxidant (TSA) proteins that confer a...; Region: GRX_hybridPRX5; cd03029 940296001929 GSH binding site [chemical binding]; other site 940296001930 catalytic residues [active] 940296001931 dihydrolipoamide dehydrogenase; Validated; Region: PRK06292 940296001932 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 940296001933 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 940296001934 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 940296001935 Iron-sulfur protein interface; other site 940296001936 proximal quinone binding site [chemical binding]; other site 940296001937 SdhD (CybS) interface [polypeptide binding]; other site 940296001938 proximal heme binding site [chemical binding]; other site 940296001939 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 940296001940 SdhC subunit interface [polypeptide binding]; other site 940296001941 proximal heme binding site [chemical binding]; other site 940296001942 cardiolipin binding site; other site 940296001943 Iron-sulfur protein interface; other site 940296001944 proximal quinone binding site [chemical binding]; other site 940296001945 succinate dehydrogenase, flavoprotein subunit, E. coli/mitochondrial subgroup; Region: sdhA_forward; TIGR01816 940296001946 L-aspartate oxidase; Provisional; Region: PRK06175 940296001947 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 940296001948 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 940296001949 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 940296001950 Uncharacterized conserved protein [Function unknown]; Region: COG2938 940296001951 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 940296001952 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 940296001953 dimer interface [polypeptide binding]; other site 940296001954 active site 940296001955 citrylCoA binding site [chemical binding]; other site 940296001956 NADH binding [chemical binding]; other site 940296001957 cationic pore residues; other site 940296001958 oxalacetate/citrate binding site [chemical binding]; other site 940296001959 coenzyme A binding site [chemical binding]; other site 940296001960 catalytic triad [active] 940296001961 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 940296001962 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 940296001963 TPP-binding site [chemical binding]; other site 940296001964 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 940296001965 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 940296001966 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 940296001967 E3 interaction surface; other site 940296001968 lipoyl attachment site [posttranslational modification]; other site 940296001969 e3 binding domain; Region: E3_binding; pfam02817 940296001970 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 940296001971 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 940296001972 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 940296001973 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 940296001974 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 940296001975 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 940296001976 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 940296001977 CoA-ligase; Region: Ligase_CoA; pfam00549 940296001978 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 940296001979 CoA binding domain; Region: CoA_binding; smart00881 940296001980 CoA-ligase; Region: Ligase_CoA; pfam00549 940296001981 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 940296001982 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 940296001983 Plasmid stability protein [General function prediction only]; Region: StbC; COG4691 940296001984 PIN (PilT N terminus) domain: Superfamily; Region: PIN_SF; cl14812 940296001985 putative active site [active] 940296001986 Uncharacterized conserved protein containing a ferredoxin-like domain [Energy production and conversion]; Region: COG1139 940296001987 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 940296001988 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 940296001989 Domain of unknown function (DUF3390); Region: DUF3390; pfam11870 940296001990 Uncharacterized conserved protein [Function unknown]; Region: COG1556 940296001991 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 940296001992 Cysteine-rich domain; Region: CCG; pfam02754 940296001993 Cysteine-rich domain; Region: CCG; pfam02754 940296001994 putative transporter; Provisional; Region: PRK10504 940296001995 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 940296001996 putative substrate translocation pore; other site 940296001997 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 940296001998 Phosphatidylserine/phosphatidylglycerophosphate/car diolipin synthases and related enzymes [Lipid metabolism]; Region: Cls; COG1502 940296001999 Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_1; cd09111 940296002000 putative active site [active] 940296002001 catalytic site [active] 940296002002 Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_2; cd09113 940296002003 putative active site [active] 940296002004 catalytic site [active] 940296002005 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 940296002006 NlpC/P60 family; Region: NLPC_P60; pfam00877 940296002007 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 940296002008 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 940296002009 hinge; other site 940296002010 active site 940296002011 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 940296002012 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 940296002013 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 940296002014 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 940296002015 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 940296002016 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 940296002017 trimer interface [polypeptide binding]; other site 940296002018 eyelet of channel; other site 940296002019 tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; Region: COG0042 940296002020 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 940296002021 FMN binding site [chemical binding]; other site 940296002022 active site 940296002023 catalytic residues [active] 940296002024 substrate binding site [chemical binding]; other site 940296002025 Protein of unknown function (DUF3683); Region: DUF3683; pfam12447 940296002026 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 940296002027 FAD binding domain; Region: FAD_binding_4; pfam01565 940296002028 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 940296002029 4Fe-4S dicluster domain; Region: Fer4_8; pfam13183 940296002030 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 940296002031 Cysteine-rich domain; Region: CCG; pfam02754 940296002032 Cysteine-rich domain; Region: CCG; pfam02754 940296002033 Domain of unknown function (DUF3400); Region: DUF3400; pfam11880 940296002034 D-lactate dehydrogenase; Provisional; Region: PRK11183 940296002035 FAD binding domain; Region: FAD_binding_4; pfam01565 940296002036 D-lactate dehydrogenase, membrane binding; Region: Lact-deh-memb; pfam09330 940296002037 Protein of unknown function (DUF2628); Region: DUF2628; pfam10947 940296002038 Uncharacterized conserved protein [Function unknown]; Region: COG2128 940296002039 alkylhydroperoxidase AhpD family core domain; Region: ahpD_dom; TIGR00778 940296002040 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 940296002041 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 940296002042 active site 940296002043 DDE superfamily endonuclease; Region: DDE_3; pfam13358 940296002044 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3335 940296002045 Homeodomain-like domain; Region: HTH_23; cl17451 940296002046 HTH-like domain; Region: HTH_21; pfam13276 940296002047 Integrase core domain; Region: rve; pfam00665 940296002048 Integrase core domain; Region: rve; pfam00665 940296002049 Integrase core domain; Region: rve_2; pfam13333 940296002050 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 940296002051 Smr domain; Region: Smr; pfam01713 940296002052 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 940296002053 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 940296002054 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 940296002055 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 940296002056 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 940296002057 Coenzyme A binding pocket [chemical binding]; other site 940296002058 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 940296002059 XdhC Rossmann domain; Region: XdhC_C; pfam13478 940296002060 ATP-grasp domain; Region: ATP-grasp; pfam02222 940296002061 NgoMIV restriction enzyme; Region: NgoMIV_restric; pfam09015 940296002062 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 940296002063 C-5 cytosine-specific DNA methylase; Region: DNA_methylase; pfam00145 940296002064 cofactor binding site; other site 940296002065 DNA binding site [nucleotide binding] 940296002066 substrate interaction site [chemical binding]; other site 940296002067 anthranilate synthase component I; Provisional; Region: PRK13565 940296002068 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 940296002069 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 940296002070 ABC transporter ATPase component; Reviewed; Region: PRK11147 940296002071 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 940296002072 Walker A/P-loop; other site 940296002073 ATP binding site [chemical binding]; other site 940296002074 Q-loop/lid; other site 940296002075 ABC transporter signature motif; other site 940296002076 Walker B; other site 940296002077 D-loop; other site 940296002078 H-loop/switch region; other site 940296002079 ABC transporter; Region: ABC_tran_2; pfam12848 940296002080 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 940296002081 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 940296002082 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 940296002083 Outer membrane protein OpcA; Region: OpcA; pfam07239 940296002084 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 940296002085 sequence-specific DNA binding site [nucleotide binding]; other site 940296002086 salt bridge; other site 940296002087 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 940296002088 Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of hydroxymethyl...; Region: SHMT; cd00378 940296002089 dimer interface [polypeptide binding]; other site 940296002090 active site 940296002091 glycine-pyridoxal phosphate binding site [chemical binding]; other site 940296002092 folate binding site [chemical binding]; other site 940296002093 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 940296002094 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 940296002095 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 940296002096 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2841 940296002097 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 940296002098 AMP binding site [chemical binding]; other site 940296002099 metal binding site [ion binding]; metal-binding site 940296002100 active site 940296002101 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 940296002102 putative glycerol-3-phosphate acyltransferase PlsY; Provisional; Region: PRK00220 940296002103 Dihydroneopterin aldolase [Coenzyme metabolism]; Region: FolB; COG1539 940296002104 active site 940296002105 nudix-type nucleoside diphosphatase, YffH/AdpP family; Region: TIGR00052 940296002106 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 940296002107 dimer interface [polypeptide binding]; other site 940296002108 ADP-ribose binding site [chemical binding]; other site 940296002109 active site 940296002110 nudix motif; other site 940296002111 metal binding site [ion binding]; metal-binding site 940296002112 Predicted membrane protein [Function unknown]; Region: COG3235 940296002113 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 940296002114 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 940296002115 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 940296002116 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 940296002117 putative catalytic cysteine [active] 940296002118 glutamate 5-kinase; Region: proB; TIGR01027 940296002119 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 940296002120 nucleotide binding site [chemical binding]; other site 940296002121 homotetrameric interface [polypeptide binding]; other site 940296002122 putative phosphate binding site [ion binding]; other site 940296002123 putative allosteric binding site; other site 940296002124 PUA domain; Region: PUA; pfam01472 940296002125 2-isopropylmalate synthase; Validated; Region: PRK00915 940296002126 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 940296002127 active site 940296002128 catalytic residues [active] 940296002129 metal binding site [ion binding]; metal-binding site 940296002130 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; smart00917 940296002131 Predicted metal-binding protein related to the C-terminal domain of SecA [General function prediction only]; Region: COG3318 940296002132 yecA family protein; Region: ygfB_yecA; TIGR02292 940296002133 SEC-C motif; Region: SEC-C; pfam02810 940296002134 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 940296002135 Predicted carboxypeptidase [Amino acid transport and metabolism]; Region: COG2866 940296002136 Peptidase M14-like domain of ATP/GTP binding proteins and cytosolic carboxypeptidases; uncharacterized bacterial subgroup; Region: M14_Nna1_like_1; cd06234 940296002137 putative active site [active] 940296002138 Zn binding site [ion binding]; other site 940296002139 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 940296002140 feedback inhibition sensing region; other site 940296002141 homohexameric interface [polypeptide binding]; other site 940296002142 nucleotide binding site [chemical binding]; other site 940296002143 N-acetyl-L-glutamate binding site [chemical binding]; other site 940296002144 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 940296002145 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 940296002146 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 940296002147 DnaA regulatory inactivator Hda; Validated; Region: PRK08903 940296002148 ABC transporter transmembrane region 2; Region: ABC_membrane_2; cl00549 940296002149 ATP-binding cassette domain of peroxisomal transporter, subfamily D; Region: ABCD_peroxisomal_ALDP; cd03223 940296002150 ABC transporter; Region: ABC_tran; pfam00005 940296002151 ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]; Region: COG4178 940296002152 Putative bacterial lipoprotein (DUF799); Region: DUF799; pfam05643 940296002153 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4259 940296002154 Uncharacterized protein involved in formation of curli polymers [Cell envelope biogenesis, outer membrane]; Region: CsgG; COG1462 940296002155 short chain dehydrogenase; Provisional; Region: PRK08703 940296002156 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 940296002157 NAD(P) binding site [chemical binding]; other site 940296002158 active site 940296002159 Predicted NAD/FAD-binding protein [General function prediction only]; Region: COG2907 940296002160 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 940296002161 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 940296002162 active site lid residues [active] 940296002163 substrate binding pocket [chemical binding]; other site 940296002164 catalytic residues [active] 940296002165 substrate-Mg2+ binding site; other site 940296002166 aspartate-rich region 1; other site 940296002167 aspartate-rich region 2; other site 940296002168 chaperone protein HscA; Provisional; Region: hscA; PRK05183 940296002169 Nucleotide-binding domain of HscA and similar proteins; Region: HscA_like_NBD; cd10236 940296002170 nucleotide binding site [chemical binding]; other site 940296002171 putative NEF/HSP70 interaction site [polypeptide binding]; other site 940296002172 SBD interface [polypeptide binding]; other site 940296002173 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3779 940296002174 Uncharacterized protein conserved in bacteria (DUF2314); Region: DUF2314; pfam10077 940296002175 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 940296002176 Ankyrin repeats (many copies); Region: Ank_5; pfam13857 940296002177 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 940296002178 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 940296002179 catalytic loop [active] 940296002180 iron binding site [ion binding]; other site 940296002181 FeS assembly protein IscX; Region: iscX_yfhJ; TIGR03412 940296002182 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 940296002183 RNA binding surface [nucleotide binding]; other site 940296002184 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated; Region: PRK05724 940296002185 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 940296002186 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 940296002187 Ligand Binding Site [chemical binding]; other site 940296002188 TilS substrate binding domain; Region: TilS; pfam09179 940296002189 tRNA(Ile)-lysidine synthetase, C-terminal domain; Region: lysidine_TilS_C; TIGR02433 940296002190 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 940296002191 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 940296002192 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 940296002193 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase; Region: mpl; TIGR01081 940296002194 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 940296002195 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 940296002196 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 940296002197 biotin synthase; Region: bioB; TIGR00433 940296002198 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 940296002199 FeS/SAM binding site; other site 940296002200 Biotin and Thiamin Synthesis associated domain; Region: BATS; smart00876 940296002201 Bacterial capsule synthesis protein PGA_cap; Region: PGA_cap; smart00854 940296002202 CapA and related proteins, metallophosphatase domain; Region: MPP_CapA; cd07381 940296002203 putative active site [active] 940296002204 putative metal binding site [ion binding]; other site 940296002205 dihydroxy-acid dehydratase; Provisional; Region: PRK12448 940296002206 Nitrite and sulphite reductase 4Fe-4S domain; Region: NIR_SIR; pfam01077 940296002207 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 940296002208 Nitrite and sulphite reductase 4Fe-4S domain; Region: NIR_SIR; pfam01077 940296002209 sulfite reductase subunit beta; Provisional; Region: PRK13504 940296002210 Cytochrome p450- like alpha subunits of E. coli sulfite reductase (SiR) multimerize with beta subunits to catalyze the NADPH dependent reduction of sulfite to sulfide. Beta subunits have an Fe4S4 cluster and a siroheme, while the alpha subunits (cysJ...; Region: SiR; cd06199 940296002211 FAD binding pocket [chemical binding]; other site 940296002212 FAD binding motif [chemical binding]; other site 940296002213 catalytic residues [active] 940296002214 NAD binding pocket [chemical binding]; other site 940296002215 phosphate binding motif [ion binding]; other site 940296002216 beta-alpha-beta structure motif; other site 940296002217 Flavodoxin; Region: Flavodoxin_1; pfam00258 940296002218 Putative NAD(P)-binding; Region: NAD_binding_7; pfam13241 940296002219 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 940296002220 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 940296002221 Cytochrome b [Energy production and conversion]; Region: COG3658 940296002222 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 940296002223 putative substrate binding site [chemical binding]; other site 940296002224 putative ATP binding site [chemical binding]; other site 940296002225 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 940296002226 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 940296002227 G1 box; other site 940296002228 putative GEF interaction site [polypeptide binding]; other site 940296002229 GTP/Mg2+ binding site [chemical binding]; other site 940296002230 Switch I region; other site 940296002231 G2 box; other site 940296002232 G3 box; other site 940296002233 Switch II region; other site 940296002234 G4 box; other site 940296002235 G5 box; other site 940296002236 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 940296002237 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 940296002238 ribonuclease R; Region: RNase_R; TIGR02063 940296002239 Ribonuclease B OB domain; Region: OB_RNB; pfam08206 940296002240 RNB domain; Region: RNB; pfam00773 940296002241 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 940296002242 RNA binding site [nucleotide binding]; other site 940296002243 SPRY domain; Region: SPRY; cl02614 940296002244 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 940296002245 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 940296002246 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 940296002247 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 940296002248 active site 940296002249 UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: GlnD; COG2844 940296002250 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 940296002251 metal binding triad; other site 940296002252 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 940296002253 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 940296002254 Zn2+ binding site [ion binding]; other site 940296002255 Mg2+ binding site [ion binding]; other site 940296002256 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 940296002257 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 940296002258 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 940296002259 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 940296002260 non-specific DNA binding site [nucleotide binding]; other site 940296002261 salt bridge; other site 940296002262 sequence-specific DNA binding site [nucleotide binding]; other site 940296002263 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 940296002264 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 940296002265 heme binding site [chemical binding]; other site 940296002266 ferroxidase pore; other site 940296002267 ferroxidase diiron center [ion binding]; other site 940296002268 Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]; Region: Bfr; COG2193 940296002269 Bacterioferritin, ferritin-like diiron-binding domain; Region: Bacterioferritin; cd00907 940296002270 heme binding site [chemical binding]; other site 940296002271 ferroxidase pore; other site 940296002272 ferroxidase diiron center [ion binding]; other site 940296002273 lipoyl synthase; Provisional; Region: PRK05481 940296002274 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 940296002275 FeS/SAM binding site; other site 940296002276 lipoate-protein ligase B; Provisional; Region: PRK14342 940296002277 Uncharacterized conserved protein [Function unknown]; Region: COG2921 940296002278 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 940296002279 Domain of unknown function DUF20; Region: UPF0118; pfam01594 940296002280 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 940296002281 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 940296002282 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: COG1585 940296002283 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 940296002284 ligand binding site [chemical binding]; other site 940296002285 active site 940296002286 UGI interface [polypeptide binding]; other site 940296002287 catalytic site [active] 940296002288 putative ABC transporter ATP-binding protein; Provisional; Region: PRK10636 940296002289 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 940296002290 Walker A/P-loop; other site 940296002291 ATP binding site [chemical binding]; other site 940296002292 Q-loop/lid; other site 940296002293 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 940296002294 ABC transporter signature motif; other site 940296002295 Walker B; other site 940296002296 D-loop; other site 940296002297 ABC transporter; Region: ABC_tran_2; pfam12848 940296002298 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 940296002299 Mth938-like domain. The members of this family include: Mth938, 2P1, Xcr35, Rpa2829, and several uncharacterized sequences. Mth938 is a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. This protein crystallizes as a...; Region: Mth938-like; cd00248 940296002300 homoserine dehydrogenase; Provisional; Region: PRK06349 940296002301 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 940296002302 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 940296002303 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 940296002304 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 940296002305 Found in ATP-dependent protease La (LON); Region: LON; smart00464 940296002306 Protein of unknown function (DUF1357); Region: DUF1357; pfam07094 940296002307 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 940296002308 Walker A motif; other site 940296002309 ATP binding site [chemical binding]; other site 940296002310 Walker B motif; other site 940296002311 arginine finger; other site 940296002312 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 940296002313 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 940296002314 Transposase; Region: DEDD_Tnp_IS110; pfam01548 940296002315 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 940296002316 Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis]; Region: HemK; COG2890 940296002317 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 940296002318 S-adenosylmethionine binding site [chemical binding]; other site 940296002319 exodeoxyribonuclease V, alpha subunit; Region: recD; TIGR01447 940296002320 AAA domain; Region: AAA_30; pfam13604 940296002321 Family description; Region: UvrD_C_2; pfam13538 940296002322 lipoprotein releasing system, ATP-binding protein; Region: LolD_lipo_ex; TIGR02211 940296002323 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 940296002324 Walker A/P-loop; other site 940296002325 ATP binding site [chemical binding]; other site 940296002326 Q-loop/lid; other site 940296002327 ABC transporter signature motif; other site 940296002328 Walker B; other site 940296002329 D-loop; other site 940296002330 H-loop/switch region; other site 940296002331 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 940296002332 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 940296002333 FtsX-like permease family; Region: FtsX; pfam02687 940296002334 Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]; Region: RecR; COG0353 940296002335 RecR protein; Region: RecR; pfam02132 940296002336 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 940296002337 putative active site [active] 940296002338 putative metal-binding site [ion binding]; other site 940296002339 tetramer interface [polypeptide binding]; other site 940296002340 SurA N-terminal domain; Region: SurA_N_3; cl07813 940296002341 Parvulin-like peptidyl-prolyl isomerase [Posttranslational modification, protein turnover, chaperones]; Region: SurA; COG0760 940296002342 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 940296002343 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 940296002344 ArsC family; Region: ArsC; pfam03960 940296002345 putative catalytic residues [active] 940296002346 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 940296002347 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 940296002348 Walker A/P-loop; other site 940296002349 ATP binding site [chemical binding]; other site 940296002350 ABC transporter signature motif; other site 940296002351 Walker B; other site 940296002352 D-loop; other site 940296002353 H-loop/switch region; other site 940296002354 ABC transporter; Region: ABC_tran_2; pfam12848 940296002355 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 940296002356 multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed; Region: cca; PRK10885 940296002357 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 940296002358 active site 940296002359 NTP binding site [chemical binding]; other site 940296002360 metal binding triad [ion binding]; metal-binding site 940296002361 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 940296002362 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 940296002363 Zn2+ binding site [ion binding]; other site 940296002364 Mg2+ binding site [ion binding]; other site 940296002365 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 940296002366 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 940296002367 Walker A motif; other site 940296002368 ATP binding site [chemical binding]; other site 940296002369 Walker B motif; other site 940296002370 arginine finger; other site 940296002371 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 940296002372 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 940296002373 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 940296002374 substrate binding site [chemical binding]; other site 940296002375 hexamer interface [polypeptide binding]; other site 940296002376 metal binding site [ion binding]; metal-binding site 940296002377 P pilus assembly/Cpx signaling pathway, periplasmic inhibitor/zinc-resistance associated protein [Intracellular trafficking and secretion / Cell motility and secretio / Signal transduction mechanisms / Inorganic ion transport and metabolism]; Region: CpxP; COG3678 940296002378 dimer interface [polypeptide binding]; other site 940296002379 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG2607 940296002380 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 940296002381 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 940296002382 Walker A motif; other site 940296002383 ATP binding site [chemical binding]; other site 940296002384 Walker B motif; other site 940296002385 riboflavin synthase subunit alpha; Provisional; Region: PRK13020 940296002386 Lumazine binding domain; Region: Lum_binding; pfam00677 940296002387 Lumazine binding domain; Region: Lum_binding; pfam00677 940296002388 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 940296002389 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 940296002390 GTP binding site; other site 940296002391 Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]; Region: NarQ; COG3850 940296002392 Type IV pili methyl-accepting chemotaxis transducer N-term; Region: PilJ; pfam13675 940296002393 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 940296002394 dimerization interface [polypeptide binding]; other site 940296002395 GAF domain; Region: GAF_3; pfam13492 940296002396 Histidine kinase; Region: HisKA_3; pfam07730 940296002397 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 940296002398 ATP binding site [chemical binding]; other site 940296002399 Mg2+ binding site [ion binding]; other site 940296002400 G-X-G motif; other site 940296002401 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 940296002402 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 940296002403 active site 940296002404 phosphorylation site [posttranslational modification] 940296002405 intermolecular recognition site; other site 940296002406 dimerization interface [polypeptide binding]; other site 940296002407 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 940296002408 DNA binding residues [nucleotide binding] 940296002409 dimerization interface [polypeptide binding]; other site 940296002410 Pertactin-like passenger domains (virulence factors), C-terminal, subgroup 2, of autotransporter proteins of the type V secretion system of Gram-negative bacteria. This subgroup includes the passenger domains of the nonprotease autotransporters, Ag43; Region: PL2_Passenger_AT; cd01344 940296002411 Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase [Nucleotide transport and metabolism]; Region: PurE; COG0041 940296002412 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1729 940296002413 Tetratricopeptide repeat; Region: TPR_6; pfam13174 940296002414 Predicted O-methyltransferase [General function prediction only]; Region: COG4122 940296002415 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 940296002416 S-adenosylmethionine binding site [chemical binding]; other site 940296002417 Protein of unknown function (DUF3460); Region: DUF3460; pfam11943 940296002418 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 940296002419 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 940296002420 ATP binding site [chemical binding]; other site 940296002421 Mg2+ binding site [ion binding]; other site 940296002422 G-X-G motif; other site 940296002423 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 940296002424 ATP binding site [chemical binding]; other site 940296002425 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 940296002426 DNA polymerase III subunits gamma and tau; Validated; Region: PRK08691 940296002427 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 940296002428 Walker A motif; other site 940296002429 ATP binding site [chemical binding]; other site 940296002430 Walker B motif; other site 940296002431 arginine finger; other site 940296002432 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 940296002433 hypothetical protein; Validated; Region: PRK00153 940296002434 recombinase A; Provisional; Region: recA; PRK09354 940296002435 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 940296002436 hexamer interface [polypeptide binding]; other site 940296002437 Walker A motif; other site 940296002438 ATP binding site [chemical binding]; other site 940296002439 Walker B motif; other site 940296002440 3-dehydroquinate dehydratase [Amino acid transport and metabolism]; Region: AroD; COG0710 940296002441 Type I 3-dehydroquinase, (3-dehydroquinate dehydratase or DHQase); Region: DHQase_I; cd00502 940296002442 active site 940296002443 catalytic residue [active] 940296002444 dimer interface [polypeptide binding]; other site 940296002445 ATP-dependent DNA helicase Rep; Region: rep; TIGR01074 940296002446 Part of AAA domain; Region: AAA_19; pfam13245 940296002447 Family description; Region: UvrD_C_2; pfam13538 940296002448 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 940296002449 active site 940296002450 DNA polymerase IV; Validated; Region: PRK02406 940296002451 DNA binding site [nucleotide binding] 940296002452 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 940296002453 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 940296002454 FAD binding pocket [chemical binding]; other site 940296002455 FAD binding motif [chemical binding]; other site 940296002456 phosphate binding motif [ion binding]; other site 940296002457 beta-alpha-beta structure motif; other site 940296002458 NAD binding pocket [chemical binding]; other site 940296002459 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 940296002460 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl17200 940296002461 non-specific DNA binding site [nucleotide binding]; other site 940296002462 salt bridge; other site 940296002463 sequence-specific DNA binding site [nucleotide binding]; other site 940296002464 Phage-related baseplate assembly protein; Region: Phage_base_V; cl17812 940296002465 Gene 25-like lysozyme; Region: GPW_gp25; cl01403 940296002466 Baseplate J-like protein; Region: Baseplate_J; cl01294 940296002467 Plasmid maintenance system antidote protein [General function prediction only]; Region: VapI; COG3093 940296002468 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 940296002469 non-specific DNA binding site [nucleotide binding]; other site 940296002470 salt bridge; other site 940296002471 sequence-specific DNA binding site [nucleotide binding]; other site 940296002472 Plasmid maintenance system killer protein; Region: Plasmid_killer; cl01422 940296002473 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: COG1598 940296002474 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 940296002475 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 940296002476 active site 940296002477 dimer interface [polypeptide binding]; other site 940296002478 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 940296002479 dimer interface [polypeptide binding]; other site 940296002480 active site 940296002481 DNA-binding transcriptional regulator HexR; Provisional; Region: PRK11302 940296002482 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 940296002483 RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate...; Region: SIS_RpiR; cd05013 940296002484 putative active site [active] 940296002485 glucokinase; Provisional; Region: glk; PRK00292 940296002486 glucokinase, proteobacterial type; Region: glk; TIGR00749 940296002487 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 940296002488 6PGL: 6-Phosphogluconolactonase (6PGL) subfamily; 6PGL catalyzes the second step of the oxidative phase of the pentose phosphate pathway, the hydrolyzation of 6-phosphoglucono-1,5-lactone (delta form) to 6-phosphogluconate. 6PGL is thought to guard...; Region: 6PGL; cd01400 940296002489 putative active site [active] 940296002490 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 940296002491 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 940296002492 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 940296002493 phosphogluconate dehydratase; Validated; Region: PRK09054 940296002494 6-phosphogluconate dehydratase; Region: edd; TIGR01196 940296002495 keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase; Provisional; Region: PRK05718 940296002496 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 940296002497 active site 940296002498 intersubunit interface [polypeptide binding]; other site 940296002499 catalytic residue [active] 940296002500 formaldehyde dehydrogenase (FDH)-like; Region: FDH_like_ADH2; cd08286 940296002501 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 940296002502 catalytic Zn binding site [ion binding]; other site 940296002503 structural Zn binding site [ion binding]; other site 940296002504 NAD(P) binding site [chemical binding]; other site 940296002505 A/G-specific adenine glycosylase; Region: mutY; TIGR01084 940296002506 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 940296002507 minor groove reading motif; other site 940296002508 helix-hairpin-helix signature motif; other site 940296002509 substrate binding pocket [chemical binding]; other site 940296002510 active site 940296002511 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 940296002512 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 940296002513 DNA binding and oxoG recognition site [nucleotide binding] 940296002514 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 940296002515 Haemolysin secretion/activation protein ShlB/FhaC/HecB; Region: ShlB; pfam03865 940296002516 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 940296002517 POTRA domain, ShlB-type; Region: POTRA_2; pfam08479 940296002518 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 940296002519 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 940296002520 Large exoproteins involved in heme utilization or adhesion [Intracellular trafficking and secretion]; Region: FhaB; COG3210 940296002521 Haemagluttinin repeat; Region: Fil_haemagg_2; pfam13332 940296002522 Extended Signal Peptide of Type V secretion system; Region: ESPR; pfam13018 940296002523 haemagglutination activity domain; Region: Haemagg_act; pfam05860 940296002524 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II-like protein; Provisional; Region: PRK14019 940296002525 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 940296002526 GTP cyclohydrolase II; Region: GTP_cyclohydro2; pfam00925 940296002527 dimerization interface [polypeptide binding]; other site 940296002528 active site 940296002529 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 940296002530 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 940296002531 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 940296002532 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 940296002533 Virulence protein [General function prediction only]; Region: COG3943 940296002534 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 940296002535 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 940296002536 Type III restriction enzyme, res subunit; Region: ResIII; pfam04851 940296002537 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 940296002538 ATP binding site [chemical binding]; other site 940296002539 putative Mg++ binding site [ion binding]; other site 940296002540 recombination factor protein RarA; Reviewed; Region: PRK13342 940296002541 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 940296002542 Walker A motif; other site 940296002543 ATP binding site [chemical binding]; other site 940296002544 Walker B motif; other site 940296002545 arginine finger; other site 940296002546 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 940296002547 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; cl00185 940296002548 Autotransporter beta-domain; Region: Autotransporter; pfam03797 940296002549 Transcriptional regulator [Transcription]; Region: LysR; COG0583 940296002550 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 940296002551 Protein of unknown function (DUF3360); Region: DUF3360; pfam11840 940296002552 Protein of unknown function (DUF3360); Region: DUF3360; pfam11840 940296002553 Protein of unknown function (DUF3360); Region: DUF3360; pfam11840 940296002554 Protein of unknown function (DUF3360); Region: DUF3360; pfam11840 940296002555 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 940296002556 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 940296002557 pyridoxal 5'-phosphate binding site [chemical binding]; other site 940296002558 catalytic residue [active] 940296002559 Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]; Region: Hmp; COG1018 940296002560 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 940296002561 FAD binding pocket [chemical binding]; other site 940296002562 FAD binding motif [chemical binding]; other site 940296002563 phosphate binding motif [ion binding]; other site 940296002564 beta-alpha-beta structure motif; other site 940296002565 NAD binding pocket [chemical binding]; other site 940296002566 Putative metal-binding domain of cation transport ATPase; Region: ATPase-cat_bd; pfam12156 940296002567 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 940296002568 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 940296002569 metal-binding site [ion binding] 940296002570 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 940296002571 Soluble P-type ATPase [General function prediction only]; Region: COG4087 940296002572 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 940296002573 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 940296002574 HflX GTPase family; Region: HflX; cd01878 940296002575 G1 box; other site 940296002576 GTP/Mg2+ binding site [chemical binding]; other site 940296002577 Switch I region; other site 940296002578 G2 box; other site 940296002579 G3 box; other site 940296002580 Switch II region; other site 940296002581 G4 box; other site 940296002582 G5 box; other site 940296002583 SCP_bacterial: SCP-like extracellular protein domain, as found in bacteria and archaea. The wider family of SCP containing proteins includes plant pathogenesis-related protein 1 (PR-1), CRISPs, mammalian cysteine-rich secretory proteins, and allergen 5...; Region: SCP_bacterial; cd05379 940296002584 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1636 940296002585 hypothetical protein; Reviewed; Region: PRK00024 940296002586 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 940296002587 MPN+ (JAMM) motif; other site 940296002588 Zinc-binding site [ion binding]; other site 940296002589 Glutamate-cysteine ligase; Region: GshA; pfam08886 940296002590 glutamate--cysteine ligase, T. ferrooxidans family; Region: gshA_ferroox; TIGR02049 940296002591 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 940296002592 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 940296002593 substrate binding site [chemical binding]; other site 940296002594 ligand binding site [chemical binding]; other site 940296002595 isopropylmalate isomerase small subunit; Provisional; Region: leuD; PRK01641 940296002596 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 940296002597 substrate binding site [chemical binding]; other site 940296002598 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 940296002599 DNA-methyltransferase (dcm); Region: dcm; TIGR00675 940296002600 cofactor binding site; other site 940296002601 DNA binding site [nucleotide binding] 940296002602 substrate interaction site [chemical binding]; other site 940296002603 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 940296002604 NgoBV restriction endonuclease; Region: RE_NgoBV; pfam09564 940296002605 3-isopropylmalate dehydrogenase; Provisional; Region: PRK00772 940296002606 tartrate dehydrogenase; Region: TTC; TIGR02089 940296002607 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 940296002608 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 940296002609 active site 940296002610 dimerization interface [polypeptide binding]; other site 940296002611 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 940296002612 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 940296002613 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3782 940296002614 16S rRNA methyltransferase B; Provisional; Region: PRK14904 940296002615 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 940296002616 S-adenosylmethionine binding site [chemical binding]; other site 940296002617 Domain of unknown function (DUF4124); Region: DUF4124; pfam13511 940296002618 NAD-dependent aldehyde dehydrogenases [Energy production and conversion]; Region: PutA; COG1012 940296002619 Mycobacterium tuberculosis succinate-semialdehyde dehydrogenase 1-like; Region: ALDH_SSADH1_GabD1; cd07100 940296002620 NAD(P) binding site [chemical binding]; other site 940296002621 catalytic residues [active] 940296002622 Multiple antibiotic transporter [Intracellular trafficking and secretion]; Region: MarC; COG2095 940296002623 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 940296002624 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 940296002625 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 940296002626 Uncharacterized protein conserved in bacteria [Function unknown]; Region: VirK; COG2990 940296002627 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 940296002628 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 940296002629 GatB domain; Region: GatB_Yqey; smart00845 940296002630 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated; Region: PRK07609 940296002631 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 940296002632 catalytic loop [active] 940296002633 iron binding site [ion binding]; other site 940296002634 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 940296002635 FAD binding pocket [chemical binding]; other site 940296002636 FAD binding motif [chemical binding]; other site 940296002637 phosphate binding motif [ion binding]; other site 940296002638 beta-alpha-beta structure motif; other site 940296002639 NAD binding pocket [chemical binding]; other site 940296002640 Pyridoxamine-phosphate oxidase [Coenzyme metabolism]; Region: PdxH; COG0259 940296002641 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 940296002642 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 940296002643 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 940296002644 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 940296002645 RNA binding surface [nucleotide binding]; other site 940296002646 Pseudouridine synthase, Escherichia coli RluB like; Region: PseudoU_synth_RluB; cd02556 940296002647 probable active site [active] 940296002648 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 940296002649 Major Facilitator Superfamily; Region: MFS_1; pfam07690 940296002650 putative substrate translocation pore; other site 940296002651 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 940296002652 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 940296002653 generic binding surface II; other site 940296002654 generic binding surface I; other site 940296002655 NAD synthase [Coenzyme metabolism]; Region: NadE; COG0171 940296002656 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 940296002657 homodimer interface [polypeptide binding]; other site 940296002658 NAD binding pocket [chemical binding]; other site 940296002659 ATP binding pocket [chemical binding]; other site 940296002660 Mg binding site [ion binding]; other site 940296002661 active-site loop [active] 940296002662 Hemerythrin-like domain; Region: Hr-like; cd12108 940296002663 Fe binding site [ion binding]; other site 940296002664 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 940296002665 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 940296002666 catalytic residues [active] 940296002667 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 940296002668 S-adenosylmethionine binding site [chemical binding]; other site 940296002669 helicase 45; Provisional; Region: PTZ00424 940296002670 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 940296002671 ATP binding site [chemical binding]; other site 940296002672 Mg++ binding site [ion binding]; other site 940296002673 motif III; other site 940296002674 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 940296002675 nucleotide binding region [chemical binding]; other site 940296002676 ATP-binding site [chemical binding]; other site 940296002677 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein; Reviewed; Region: argD; PRK05093 940296002678 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 940296002679 inhibitor-cofactor binding pocket; inhibition site 940296002680 pyridoxal 5'-phosphate binding site [chemical binding]; other site 940296002681 catalytic residue [active] 940296002682 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 940296002683 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 940296002684 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 940296002685 Walker A motif; other site 940296002686 ATP binding site [chemical binding]; other site 940296002687 Walker B motif; other site 940296002688 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 940296002689 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 940296002690 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK01851 940296002691 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 940296002692 RNA binding site [nucleotide binding]; other site 940296002693 active site 940296002694 Pseudouridine synthase II TruB, C-terminal; Region: TruB-C_2; pfam09157 940296002695 Type III restriction/modification enzyme methylation subunit; Region: TypeIII_RM_meth; pfam12564 940296002696 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 940296002697 DNA methylase; Region: N6_N4_Mtase; pfam01555 940296002698 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 940296002699 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3421 940296002700 ATP binding site [chemical binding]; other site 940296002701 putative Mg++ binding site [ion binding]; other site 940296002702 Isopentenyl diphosphate isomerase (BS_ypgA, MTH48 and related proteins) [Coenzyme transport and metabolism]; Region: idi; COG1304 940296002703 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 940296002704 phosphate binding site [ion binding]; other site 940296002705 iron-sulfur cluster assembly transcription factor IscR; Region: IscR; TIGR02010 940296002706 Rrf2 family protein; Region: rrf2_super; TIGR00738 940296002707 cysteine desulfurase; Provisional; Region: PRK14012 940296002708 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 940296002709 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 940296002710 catalytic residue [active] 940296002711 Fic/DOC family; Region: Fic; cl00960 940296002712 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 940296002713 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 940296002714 trimerization site [polypeptide binding]; other site 940296002715 active site 940296002716 iron-sulfur cluster assembly protein IscA; Region: IscA; TIGR02011 940296002717 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3036 940296002718 co-chaperone HscB; Provisional; Region: hscB; PRK03578 940296002719 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 940296002720 HSP70 interaction site [polypeptide binding]; other site 940296002721 HSCB C-terminal oligomerisation domain; Region: HSCB_C; pfam07743 940296002722 DNA gyrase subunit A; Validated; Region: PRK05560 940296002723 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 940296002724 CAP-like domain; other site 940296002725 active site 940296002726 primary dimer interface [polypeptide binding]; other site 940296002727 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 940296002728 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 940296002729 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 940296002730 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 940296002731 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 940296002732 Site-specific recombinase [DNA replication, recombination, and repair]; Region: COG4389 940296002733 Membrane-bound lytic murein transglycosylase B [Cell envelope biogenesis, outer membrane]; Region: MltB; COG2951 940296002734 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 940296002735 N-acetyl-D-glucosamine binding site [chemical binding]; other site 940296002736 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 940296002737 Acyl-CoA dehydrogenase, N-terminal domain; Region: Acyl-CoA_dh_N; pfam02771 940296002738 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 940296002739 active site 940296002740 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 940296002741 DEAD-like helicases superfamily; Region: DEXDc; smart00487 940296002742 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 940296002743 ATP binding site [chemical binding]; other site 940296002744 putative Mg++ binding site [ion binding]; other site 940296002745 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 940296002746 nucleotide binding region [chemical binding]; other site 940296002747 ATP-binding site [chemical binding]; other site 940296002748 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 940296002749 Protein of unknown function (DUF2004); Region: DUF2004; pfam09406 940296002750 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 940296002751 tetramerization interface [polypeptide binding]; other site 940296002752 active site 940296002753 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK12457 940296002754 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 940296002755 Domain of unknown function (DUF4149); Region: DUF4149; pfam13664 940296002756 enolase; Provisional; Region: eno; PRK00077 940296002757 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 940296002758 dimer interface [polypeptide binding]; other site 940296002759 metal binding site [ion binding]; metal-binding site 940296002760 substrate binding pocket [chemical binding]; other site 940296002761 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 940296002762 cell division protein FtsB; Reviewed; Region: ftsB; PRK00888 940296002763 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 940296002764 ribonucleotide-diphosphate reductase subunit beta; Provisional; Region: nrdF2; PRK13966 940296002765 dimer interface [polypeptide binding]; other site 940296002766 putative radical transfer pathway; other site 940296002767 diiron center [ion binding]; other site 940296002768 tyrosyl radical; other site 940296002769 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09103 940296002770 ATP cone domain; Region: ATP-cone; pfam03477 940296002771 Class I ribonucleotide reductase; Region: RNR_I; cd01679 940296002772 active site 940296002773 dimer interface [polypeptide binding]; other site 940296002774 catalytic residues [active] 940296002775 effector binding site; other site 940296002776 R2 peptide binding site; other site 940296002777 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 940296002778 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 940296002779 putative acyl-acceptor binding pocket; other site 940296002780 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 940296002781 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 940296002782 DNA binding site [nucleotide binding] 940296002783 catalytic residue [active] 940296002784 H2TH interface [polypeptide binding]; other site 940296002785 putative catalytic residues [active] 940296002786 turnover-facilitating residue; other site 940296002787 intercalation triad [nucleotide binding]; other site 940296002788 8OG recognition residue [nucleotide binding]; other site 940296002789 putative reading head residues; other site 940296002790 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 940296002791 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 940296002792 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 940296002793 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 940296002794 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 940296002795 N-acetyl-D-glucosamine binding site [chemical binding]; other site 940296002796 catalytic residue [active] 940296002797 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 940296002798 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 940296002799 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 940296002800 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 940296002801 Pseudouridine synthase, Escherichia coli RsuA like; Region: PseudoU_synth_RsuA; cd02553 940296002802 active site 940296002803 uracil binding [chemical binding]; other site 940296002804 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 940296002805 Na2 binding site [ion binding]; other site 940296002806 putative substrate binding site 1 [chemical binding]; other site 940296002807 Na binding site 1 [ion binding]; other site 940296002808 putative substrate binding site 2 [chemical binding]; other site 940296002809 Cytidylate kinase [Nucleotide transport and metabolism]; Region: Cmk; COG0283 940296002810 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 940296002811 CMP-binding site; other site 940296002812 The sites determining sugar specificity; other site 940296002813 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 940296002814 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 940296002815 RNA binding site [nucleotide binding]; other site 940296002816 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 940296002817 RNA binding site [nucleotide binding]; other site 940296002818 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 940296002819 RNA binding site [nucleotide binding]; other site 940296002820 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 940296002821 RNA binding site [nucleotide binding]; other site 940296002822 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 940296002823 RNA binding site [nucleotide binding]; other site 940296002824 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 940296002825 RNA binding site [nucleotide binding]; other site 940296002826 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 940296002827 IHF dimer interface [polypeptide binding]; other site 940296002828 IHF - DNA interface [nucleotide binding]; other site 940296002829 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 940296002830 Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB; Region: HTH_YyaN; cd01109 940296002831 DNA binding residues [nucleotide binding] 940296002832 putative dimer interface [polypeptide binding]; other site 940296002833 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 940296002834 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 940296002835 S-formylglutathione hydrolase; Region: fghA_ester_D; TIGR02821 940296002836 S-formylglutathione hydrolase; Region: PLN02442 940296002837 Predicted ATPase [General function prediction only]; Region: COG1485 940296002838 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 940296002839 active site 940296002840 multimer interface [polypeptide binding]; other site 940296002841 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK11194 940296002842 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 940296002843 FeS/SAM binding site; other site 940296002844 Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilF; COG3063 940296002845 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 940296002846 binding surface 940296002847 TPR motif; other site 940296002848 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 940296002849 TPR motif; other site 940296002850 binding surface 940296002851 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 940296002852 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 940296002853 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 940296002854 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 940296002855 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 940296002856 oligomer interface [polypeptide binding]; other site 940296002857 active site residues [active] 940296002858 trigger factor; Provisional; Region: tig; PRK01490 940296002859 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 940296002860 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 940296002861 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 940296002862 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 940296002863 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 940296002864 Xanthine/uracil permeases [Nucleotide transport and metabolism]; Region: UraA; COG2233 940296002865 Domain of unknown function (DUF4189); Region: DUF4189; pfam13827 940296002866 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 940296002867 CDP-diacylglycerol--serine O-phosphatidyltransferase; Region: pssA; TIGR00473 940296002868 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 940296002869 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 940296002870 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 940296002871 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 940296002872 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 940296002873 Primosomal replication protein N [DNA replication, recombination, and repair]; Region: PriB; COG2965 940296002874 generic binding surface I; other site 940296002875 generic binding surface II; other site 940296002876 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 940296002877 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 940296002878 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 940296002879 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 940296002880 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 940296002881 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 940296002882 metal-binding site [ion binding] 940296002883 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 940296002884 Soluble P-type ATPase [General function prediction only]; Region: COG4087 940296002885 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 940296002886 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 940296002887 GIY-YIG motif/motif A; other site 940296002888 active site 940296002889 catalytic site [active] 940296002890 putative DNA binding site [nucleotide binding]; other site 940296002891 metal binding site [ion binding]; metal-binding site 940296002892 UvrB/uvrC motif; Region: UVR; pfam02151 940296002893 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 940296002894 Helix-hairpin-helix motif; Region: HHH; pfam00633 940296002895 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 940296002896 Sel1-like repeats; Region: SEL1; smart00671 940296002897 Sel1-like repeats; Region: SEL1; smart00671 940296002898 Sel1-like repeats; Region: SEL1; smart00671 940296002899 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 940296002900 S-adenosylmethionine binding site [chemical binding]; other site 940296002901 Carbonic anhydrase [Inorganic ion transport and metabolism]; Region: Cah; COG3338 940296002902 Carbonic anhydrase alpha, prokaryotic-like subfamily. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon...; Region: alpha_CA_prokaryotic_like; cd03124 940296002903 active site 940296002904 zinc binding site [ion binding]; other site 940296002905 Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes; Region: Motor_domain; cl00286 940296002906 excinuclease ABC subunit B; Provisional; Region: PRK05298 940296002907 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 940296002908 ATP-binding site [chemical binding]; other site 940296002909 ATP binding site [chemical binding]; other site 940296002910 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 940296002911 nucleotide binding region [chemical binding]; other site 940296002912 ATP-binding site [chemical binding]; other site 940296002913 Ultra-violet resistance protein B; Region: UvrB; pfam12344 940296002914 UvrB/uvrC motif; Region: UVR; pfam02151 940296002915 Transposase domain (DUF772); Region: DUF772; pfam05598 940296002916 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]; Region: COG4942 940296002917 Peptidase family M23; Region: Peptidase_M23; pfam01551 940296002918 Uncharacterized protein conserved in bacteria [Function unknown]; Region: CreA; COG3045 940296002919 CreA protein; Region: CreA; pfam05981 940296002920 Putative transcriptional regulator [Transcription]; Region: COG1678 940296002921 Holliday junction resolvase-like protein; Reviewed; Region: PRK00109 940296002922 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 940296002923 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 940296002924 prolyl-tRNA synthetase; Provisional; Region: PRK09194 940296002925 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 940296002926 dimer interface [polypeptide binding]; other site 940296002927 motif 1; other site 940296002928 active site 940296002929 motif 2; other site 940296002930 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 940296002931 putative deacylase active site [active] 940296002932 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 940296002933 active site 940296002934 motif 3; other site 940296002935 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 940296002936 anticodon binding site; other site 940296002937 pyruvate dehydrogenase subunit E1; Reviewed; Region: aceE; PRK09405 940296002938 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 940296002939 dimer interface [polypeptide binding]; other site 940296002940 TPP-binding site [chemical binding]; other site 940296002941 dihydrolipoamide acetyltransferase; Reviewed; Region: PRK11855 940296002942 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 940296002943 E3 interaction surface; other site 940296002944 lipoyl attachment site [posttranslational modification]; other site 940296002945 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 940296002946 E3 interaction surface; other site 940296002947 lipoyl attachment site [posttranslational modification]; other site 940296002948 e3 binding domain; Region: E3_binding; pfam02817 940296002949 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 940296002950 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 940296002951 E3 interaction surface; other site 940296002952 lipoyl attachment site [posttranslational modification]; other site 940296002953 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06467 940296002954 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 940296002955 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 940296002956 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 940296002957 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5339 940296002958 Bacterial protein of unknown function (DUF945); Region: DUF945; pfam06097 940296002959 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 940296002960 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 940296002961 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 940296002962 Uncharacterized conserved protein [Function unknown]; Region: COG2353 940296002963 aspartate ammonia-lyase; Provisional; Region: aspA; PRK12273 940296002964 Aspartase; Region: Aspartase; cd01357 940296002965 active sites [active] 940296002966 tetramer interface [polypeptide binding]; other site 940296002967 TPR repeat; Region: TPR_11; pfam13414 940296002968 Protein of unknown function (DUF560); Region: DUF560; pfam04575 940296002969 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 940296002970 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 940296002971 DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]; Region: DnaJ; COG0484 940296002972 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 940296002973 HSP70 interaction site [polypeptide binding]; other site 940296002974 Predicted membrane protein [Function unknown]; Region: COG3671 940296002975 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 940296002976 putative deacylase active site [active] 940296002977 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 940296002978 homotrimer interaction site [polypeptide binding]; other site 940296002979 putative active site [active] 940296002980 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 940296002981 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 940296002982 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 940296002983 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 940296002984 Ligand Binding Site [chemical binding]; other site 940296002985 type III restriction-modification system StyLTI enzyme res; Provisional; Region: PRK15483 940296002986 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 940296002987 DNA methylase; Region: N6_N4_Mtase; pfam01555 940296002988 DNA methylase; Region: N6_N4_Mtase; pfam01555 940296002989 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 940296002990 substrate binding site [chemical binding]; other site 940296002991 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 940296002992 CobW/HypB/UreG, nucleotide-binding domain; Region: cobW; pfam02492 940296002993 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; smart00833 940296002994 Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]; Region: Fur; COG0735 940296002995 metal binding site 2 [ion binding]; metal-binding site 940296002996 putative DNA binding helix; other site 940296002997 metal binding site 1 [ion binding]; metal-binding site 940296002998 dimer interface [polypeptide binding]; other site 940296002999 structural Zn2+ binding site [ion binding]; other site 940296003000 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 940296003001 Low molecular weight phosphatase family; Region: LMWPc; cd00115 940296003002 active site 940296003003 glycerate kinase; Region: TIGR00045 940296003004 Methyltransferase domain; Region: Methyltransf_31; pfam13847 940296003005 Predicted regulatory domain of a methyltransferase [General function prediction only]; Region: COG4797 940296003006 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 940296003007 metal-binding site [ion binding] 940296003008 putative arabinose transporter; Provisional; Region: PRK03545 940296003009 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cl17904 940296003010 Predicted membrane protein involved in D-alanine export [Cell envelope biogenesis, outer membrane]; Region: DltB; COG1696 940296003011 SGNH_peri2; putative periplasmic member of the SGNH-family of hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known...; Region: SGNH_hydrolase_peri2; cd01829 940296003012 active site 940296003013 catalytic triad [active] 940296003014 oxyanion hole [active] 940296003015 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 940296003016 SGNH_peri1; putative periplasmic member of the SGNH-family of hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known...; Region: SGNH_hydrolase_peri1; cd01825 940296003017 active site 940296003018 oxyanion hole [active] 940296003019 catalytic triad [active] 940296003020 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK06187 940296003021 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 940296003022 acyl-activating enzyme (AAE) consensus motif; other site 940296003023 putative AMP binding site [chemical binding]; other site 940296003024 putative active site [active] 940296003025 putative CoA binding site [chemical binding]; other site 940296003026 Choline-glycine betaine transporter [Cell envelope biogenesis, outer membrane]; Region: BetT; COG1292 940296003027 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 940296003028 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 940296003029 dimerization interface [polypeptide binding]; other site 940296003030 putative ATP binding site [chemical binding]; other site 940296003031 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 940296003032 active site 940296003033 DNA binding site [nucleotide binding] 940296003034 Int/Topo IB signature motif; other site 940296003035 Phage-related minor tail protein [Function unknown]; Region: COG5281 940296003036 tape measure domain; Region: tape_meas_nterm; TIGR02675 940296003037 TIGR02594 family protein; Region: TIGR02594 940296003038 PemK-like protein; Region: PemK; cl00995 940296003039 Putative phage tail protein; Region: Phage-tail_3; pfam13550 940296003040 Domain of unknown function (DUF1983); Region: DUF1983; pfam09327 940296003041 Fibronectin type III protein; Region: DUF3672; pfam12421 940296003042 Phage derived protein Gp49-like (DUF891); Region: Gp49; cl01470 940296003043 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 940296003044 non-specific DNA binding site [nucleotide binding]; other site 940296003045 sequence-specific DNA binding site [nucleotide binding]; other site 940296003046 salt bridge; other site 940296003047 NlpC/P60 family; Region: NLPC_P60; cl17555 940296003048 Uncharacterized conserved protein (DUF2163); Region: DUF2163; pfam09931 940296003049 phage conserved hypothetical protein BR0599; Region: phg_TIGR02218 940296003050 Phage conserved hypothetical protein BR0599; Region: Phage_BR0599; pfam09356 940296003051 Conserved hypothetical protein 2217 (DUF2460); Region: DUF2460; pfam09343 940296003052 phage conserved hypothetical protein, phiE125 gp8 family; Region: phage_chp_gp8; TIGR02215 940296003053 Head-Tail Connector Protein gp6 of Bacteriophage HK97 and similar proteins; Region: gp6; cd08054 940296003054 Caudovirus prohead protease; Region: Peptidase_U35; cl01521 940296003055 phage portal protein, HK97 family; Region: portal_HK97; TIGR01537 940296003056 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5410 940296003057 Terminase-like family; Region: Terminase_6; pfam03237 940296003058 Phage-related terminase [General function prediction only]; Region: COG5362; cl02216 940296003059 Prophage antirepressor [Transcription]; Region: COG3617 940296003060 BRO family, N-terminal domain; Region: Bro-N; smart01040 940296003061 Uncharacterized conserved protein [Function unknown]; Region: COG4748 940296003062 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 940296003063 Endodeoxyribonuclease RusA; Region: RusA; pfam05866 940296003064 Protein of unknwon function (DUF3310); Region: DUF3310; pfam11753 940296003065 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 940296003066 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 940296003067 Walker A motif; other site 940296003068 ATP binding site [chemical binding]; other site 940296003069 Walker B motif; other site 940296003070 arginine finger; other site 940296003071 Bacteriophage replication protein O; Region: Phage_rep_O; cl04545 940296003072 Uncharacterized protein conserved in bacteria, prophage-related [Function unknown]; Region: COG4197 940296003073 Predicted transcriptional regulator [Transcription]; Region: COG2932 940296003074 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 940296003075 Catalytic site [active] 940296003076 Siphovirus Gp157; Region: Sipho_Gp157; pfam05565 940296003077 GTP cyclohydrolase II (RibA). GTP cyclohydrolase II catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5' phosphate, formate, pyrophosphate (APy), and GMP in the biosynthetic pathway of riboflavin. Riboflavin is the...; Region: GTP_cyclohydro2; cd00641 940296003078 dimerization interface [polypeptide binding]; other site 940296003079 active site 940296003080 Glycosyl transferase family 2; Region: Glycos_transf_2; pfam00535 940296003081 active site 940296003082 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 940296003083 Transposase; Region: DEDD_Tnp_IS110; pfam01548 940296003084 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 940296003085 Zonular occludens toxin (Zot); Region: Zot; pfam05707 940296003086 Protein of unknown function (DUF2523); Region: DUF2523; pfam10734 940296003087 Neisseria meningitidis TspB protein; Region: Neisseria_TspB; pfam05616 940296003088 Protein of unknown function (DUF1132); Region: DUF1132; pfam06575 940296003089 Putative phage replication protein RstA [DNA replication, recombination, and repair]; Region: COG2946 940296003090 Replication initiation factor; Region: Rep_trans; pfam02486 940296003091 HIT domain; Region: HIT; pfam01230 940296003092 HIT family signature motif; other site 940296003093 catalytic residue [active] 940296003094 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 940296003095 dimer interface [polypeptide binding]; other site 940296003096 catalytic triad [active] 940296003097 Nitric oxide reductase large subunit [Inorganic ion transport and metabolism]; Region: NorB; COG3256 940296003098 nitrite reductase, copper-containing; Region: Cu_nitrite_red; TIGR02376 940296003099 Multicopper oxidase; Region: Cu-oxidase_3; pfam07732 940296003100 Multicopper oxidase; Region: Cu-oxidase; pfam00394 940296003101 Uncharacterized conserved protein [Function unknown]; Region: COG1262 940296003102 Formylglycine-generating sulfatase enzyme; Region: FGE-sulfatase; pfam03781 940296003103 Pilin (bacterial filament); Region: Pilin; pfam00114 940296003104 Tfp pilus assembly protein, major pilin PilA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilA; COG4969 940296003105 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl17254 940296003106 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl17254 940296003107 Nitroreductase-like family which includes NADH oxidase and arsenite oxidiase. NADH oxidase catalyses the oxidation of NAD(P)H and accepts a wide broad range of compounds as electron acceptors, such as nitrocompound. Arsenite oxidase in a...; Region: Arsenite_oxidase; cd02135 940296003108 putative FMN binding site [chemical binding]; other site 940296003109 putative metal dependent hydrolase; Provisional; Region: PRK11598 940296003110 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 940296003111 Sulfatase; Region: Sulfatase; pfam00884 940296003112 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 940296003113 homodimer interface [polypeptide binding]; other site 940296003114 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 940296003115 substrate-cofactor binding pocket; other site 940296003116 pyridoxal 5'-phosphate binding site [chemical binding]; other site 940296003117 catalytic residue [active] 940296003118 ribosome maturation protein RimP; Reviewed; Region: PRK00092 940296003119 Sm and related proteins; Region: Sm_like; cl00259 940296003120 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 940296003121 putative oligomer interface [polypeptide binding]; other site 940296003122 putative RNA binding site [nucleotide binding]; other site 940296003123 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 940296003124 NusA N-terminal domain; Region: NusA_N; pfam08529 940296003125 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 940296003126 RNA binding site [nucleotide binding]; other site 940296003127 homodimer interface [polypeptide binding]; other site 940296003128 NusA-like KH domain; Region: KH_5; pfam13184 940296003129 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 940296003130 G-X-X-G motif; other site 940296003131 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 940296003132 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 940296003133 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 940296003134 translation initiation factor IF-2; Region: IF-2; TIGR00487 940296003135 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 940296003136 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 940296003137 G1 box; other site 940296003138 putative GEF interaction site [polypeptide binding]; other site 940296003139 GTP/Mg2+ binding site [chemical binding]; other site 940296003140 Switch I region; other site 940296003141 G2 box; other site 940296003142 G3 box; other site 940296003143 Switch II region; other site 940296003144 G4 box; other site 940296003145 G5 box; other site 940296003146 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 940296003147 Translation-initiation factor 2; Region: IF-2; pfam11987 940296003148 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 940296003149 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cd00882 940296003150 G1 box; other site 940296003151 GTP/Mg2+ binding site [chemical binding]; other site 940296003152 G2 box; other site 940296003153 Switch I region; other site 940296003154 G3 box; other site 940296003155 Switch II region; other site 940296003156 Domain of unknown function (DUF3482); Region: DUF3482; pfam11981 940296003157 Protein of unknown function (DUF2868); Region: DUF2868; pfam11067 940296003158 Predicted membrane protein, hemolysin III homolog [General function prediction only]; Region: COG1272 940296003159 channel protein, hemolysin III family; Region: hlyIII; TIGR01065 940296003160 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 940296003161 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 940296003162 hypothetical protein; Validated; Region: PRK00110 940296003163 Disulfide bond formation protein DsbB; Region: DsbB; pfam02600 940296003164 leucine-responsive transcriptional regulator; Provisional; Region: PRK11169 940296003165 AsnC-type helix-turn-helix domain; Region: HTH_AsnC-type; pfam13404 940296003166 putative DNA binding site [nucleotide binding]; other site 940296003167 putative Zn2+ binding site [ion binding]; other site 940296003168 AsnC family; Region: AsnC_trans_reg; pfam01037 940296003169 Alanine racemase [Cell envelope biogenesis, outer membrane]; Region: Alr; COG0787 940296003170 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases; Region: PLPDE_III_AR_proteobact; cd06827 940296003171 active site 940296003172 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 940296003173 substrate binding site [chemical binding]; other site 940296003174 catalytic residues [active] 940296003175 dimer interface [polypeptide binding]; other site 940296003176 Uncharacterized proteins with similarity to Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL_like_DUF711; cd08025 940296003177 ACT domain proteins similar to the yet uncharacterized Streptococcus pneumoniae ACT domain protein; Region: ACT_1ZPV; cd04872 940296003178 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 940296003179 Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis]; Region: HemK; COG2890 940296003180 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 940296003181 S-adenosylmethionine binding site [chemical binding]; other site 940296003182 Phage Mu protein F like protein; Region: Phage_Mu_F; cl10072 940296003183 comEA protein; Region: comE; TIGR01259 940296003184 Helix-hairpin-helix motif; Region: HHH; pfam00633 940296003185 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 940296003186 Flavoprotein; Region: Flavoprotein; pfam02441 940296003187 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 940296003188 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 940296003189 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 940296003190 Zn2+ binding site [ion binding]; other site 940296003191 Mg2+ binding site [ion binding]; other site 940296003192 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 940296003193 synthetase active site [active] 940296003194 NTP binding site [chemical binding]; other site 940296003195 metal binding site [ion binding]; metal-binding site 940296003196 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 940296003197 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 940296003198 DNA-directed RNA polymerase subunit omega; Reviewed; Region: rpoZ; PRK00392 940296003199 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 940296003200 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 940296003201 catalytic site [active] 940296003202 G-X2-G-X-G-K; other site 940296003203 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 940296003204 active site 940296003205 Cof subfamily of IIB subfamily of haloacid dehalogenase superfamily; Region: Cof-subfamily; TIGR00099 940296003206 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 940296003207 active site 940296003208 motif I; other site 940296003209 motif II; other site 940296003210 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 940296003211 putative protease; Provisional; Region: PRK15452 940296003212 Peptidase family U32; Region: Peptidase_U32; pfam01136 940296003213 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 940296003214 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 940296003215 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 940296003216 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; cd00232 940296003217 heme binding pocket [chemical binding]; other site 940296003218 heme ligand [chemical binding]; other site 940296003219 Uncharacterized paraquat-inducible protein A [Function unknown]; Region: PqiA; COG2995 940296003220 zinc-ribbon domain; Region: zf-ribbon_3; pfam13248 940296003221 Paraquat-inducible protein A; Region: PqiA; pfam04403 940296003222 Paraquat-inducible protein A; Region: PqiA; pfam04403 940296003223 Paraquat-inducible protein B [General function prediction only]; Region: PqiB; COG3008 940296003224 mce related protein; Region: MCE; pfam02470 940296003225 mce related protein; Region: MCE; pfam02470 940296003226 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3009 940296003227 Protein of unknown function (DUF330); Region: DUF330; pfam03886 940296003228 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair]; Region: Tag; COG2818 940296003229 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 940296003230 active site 940296003231 catalytic triad [active] 940296003232 oxyanion hole [active] 940296003233 switch loop; other site 940296003234 glycine dehydrogenase; Provisional; Region: PRK05367 940296003235 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 940296003236 tetramer interface [polypeptide binding]; other site 940296003237 pyridoxal 5'-phosphate binding site [chemical binding]; other site 940296003238 catalytic residue [active] 940296003239 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 940296003240 tetramer interface [polypeptide binding]; other site 940296003241 pyridoxal 5'-phosphate binding site [chemical binding]; other site 940296003242 catalytic residue [active] 940296003243 Cytochrome c5 [Energy production and conversion]; Region: CycB; COG3245 940296003244 Cytochrome c5 [Energy production and conversion]; Region: CycB; COG3245 940296003245 aromatic amino acid aminotransferase; Provisional; Region: PRK09257 940296003246 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 940296003247 pyridoxal 5'-phosphate binding site [chemical binding]; other site 940296003248 homodimer interface [polypeptide binding]; other site 940296003249 catalytic residue [active] 940296003250 tRNA (uracil-5-)-methyltransferase; Validated; Region: PRK05031 940296003251 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 940296003252 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 940296003253 Tetramer interface [polypeptide binding]; other site 940296003254 active site 940296003255 FMN-binding site [chemical binding]; other site 940296003256 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 940296003257 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 940296003258 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 940296003259 ATP binding site [chemical binding]; other site 940296003260 Mg2+ binding site [ion binding]; other site 940296003261 G-X-G motif; other site 940296003262 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 940296003263 anchoring element; other site 940296003264 dimer interface [polypeptide binding]; other site 940296003265 ATP binding site [chemical binding]; other site 940296003266 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 940296003267 active site 940296003268 metal binding site [ion binding]; metal-binding site 940296003269 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 940296003270 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 940296003271 putative active site [active] 940296003272 Ap4A binding site [chemical binding]; other site 940296003273 nudix motif; other site 940296003274 putative metal binding site [ion binding]; other site 940296003275 seryl-tRNA synthetase; Provisional; Region: PRK05431 940296003276 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 940296003277 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 940296003278 dimer interface [polypeptide binding]; other site 940296003279 active site 940296003280 motif 1; other site 940296003281 motif 2; other site 940296003282 motif 3; other site 940296003283 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 940296003284 D-Lactate and related Dehydrogenases, NAD-binding and catalytic domains; Region: LDH_like_2; cd12183 940296003285 putative ligand binding site [chemical binding]; other site 940296003286 putative NAD binding site [chemical binding]; other site 940296003287 catalytic site [active] 940296003288 peptide chain release factor 1; Validated; Region: prfA; PRK00591 940296003289 This domain is found in peptide chain release factors; Region: PCRF; smart00937 940296003290 RF-1 domain; Region: RF-1; pfam00472 940296003291 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 940296003292 active site 940296003293 Type I (cytosolic) bacterial L-asparaginase; Region: L-asparaginase_I; cd08963 940296003294 active site 940296003295 homodimer interface [polypeptide binding]; other site 940296003296 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 940296003297 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 940296003298 phosphoglucosamine mutase; Provisional; Region: glmM; PRK10887 940296003299 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 940296003300 active site 940296003301 substrate binding site [chemical binding]; other site 940296003302 metal binding site [ion binding]; metal-binding site 940296003303 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 940296003304 dihydropteroate synthase; Region: DHPS; TIGR01496 940296003305 substrate binding pocket [chemical binding]; other site 940296003306 dimer interface [polypeptide binding]; other site 940296003307 inhibitor binding site; inhibition site 940296003308 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase [Cell envelope biogenesis, outer membrane]; Region: KdsA; cl17225 940296003309 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 940296003310 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 940296003311 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 940296003312 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4899 940296003313 Beta-ketoacyl synthase, N-terminal domain; Region: Ketoacyl-synt_2; pfam13723 940296003314 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 940296003315 active site 2 [active] 940296003316 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 940296003317 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 940296003318 active site 940296003319 Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the...; Region: cond_enzymes; cl09938 940296003320 active site 940296003321 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 940296003322 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 940296003323 putative metal binding site; other site 940296003324 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 940296003325 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 940296003326 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 940296003327 Na2 binding site [ion binding]; other site 940296003328 putative substrate binding site 1 [chemical binding]; other site 940296003329 Na binding site 1 [ion binding]; other site 940296003330 putative substrate binding site 2 [chemical binding]; other site 940296003331 ApbE family; Region: ApbE; pfam02424 940296003332 ApbE family; Region: ApbE; pfam02424 940296003333 thymidylate synthase; Reviewed; Region: thyA; PRK01827 940296003334 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 940296003335 dimerization interface [polypeptide binding]; other site 940296003336 active site 940296003337 glutamate dehydrogenase; Provisional; Region: PRK09414 940296003338 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 940296003339 NAD(P) binding domain of glutamate dehydrogenase, subgroup 2; Region: NAD_bind_2_Glu_DH; cd05313 940296003340 NAD(P) binding site [chemical binding]; other site 940296003341 Transcriptional regulators [Transcription]; Region: FadR; COG2186 940296003342 Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; Region: WHTH_GntR; cd07377 940296003343 DNA-binding site [nucleotide binding]; DNA binding site 940296003344 FCD domain; Region: FCD; pfam07729 940296003345 L-lactate permease; Region: Lactate_perm; cl00701 940296003346 copper/silver efflux system outer membrane protein CusC; Provisional; Region: PRK09837 940296003347 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 940296003348 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 940296003349 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 940296003350 HlyD family secretion protein; Region: HlyD_3; pfam13437 940296003351 DNA-binding transcriptional repressor AcrR; Provisional; Region: PRK10668 940296003352 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 940296003353 MAATS-type transcriptional repressor, C-terminal region; Region: TetR_C_2; pfam08361 940296003354 p-Aminobenzoyl-glutamate transporter family; Region: ydaH; TIGR00819 940296003355 AbgT putative transporter family; Region: ABG_transport; pfam03806 940296003356 exonuclease V subunit gamma; Provisional; Region: recC; PRK11069 940296003357 exodeoxyribonuclease V, gamma subunit; Region: recC; TIGR01450 940296003358 Uncharacterized iron-regulated membrane protein [Function unknown]; Region: PiuB; COG3182 940296003359 PepSY-associated TM helix; Region: PepSY_TM_1; pfam13172 940296003360 PepSY-associated TM helix; Region: PepSY_TM_2; pfam13703 940296003361 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 940296003362 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 940296003363 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 940296003364 Cytochrome c5 [Energy production and conversion]; Region: CycB; COG3245 940296003365 Cbb3-type cytochrome oxidase, subunit 3 [Posttranslational modification, protein turnover, chaperones]; Region: CcoQ; COG4736 940296003366 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 940296003367 cbb3-type cytochrome c oxidase subunit II; Provisional; Region: PRK14487 940296003368 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 940296003369 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 940296003370 Low-spin heme binding site [chemical binding]; other site 940296003371 Putative water exit pathway; other site 940296003372 Binuclear center (active site) [active] 940296003373 Putative proton exit pathway; other site 940296003374 Predicted protease with the C-terminal PDZ domain [General function prediction only]; Region: COG3975 940296003375 M61 glycyl aminopeptidase; Region: Peptidase_M61; pfam05299 940296003376 PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated; Region: PDZ; cl00117 940296003377 protein binding site [polypeptide binding]; other site 940296003378 TIGR01244 family protein; Region: TIGR01244 940296003379 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 940296003380 TolR protein; Region: tolR; TIGR02801 940296003381 Biopolymer transport proteins [Intracellular trafficking and secretion]; Region: TolQ; COG0811 940296003382 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 940296003383 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 940296003384 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 940296003385 Peptidase family M50; Region: Peptidase_M50; pfam02163 940296003386 active site 940296003387 putative substrate binding region [chemical binding]; other site 940296003388 Glutaredoxin 2 [Posttranslational modification, protein turnover, chaperones]; Region: GrxB; COG2999 940296003389 GST_N family, Glutaredoxin 2 (GRX2) subfamily; composed of bacterial proteins similar to E. coli GRX2, an atypical GRX with a molecular mass of about 24kD, compared with other GRXs which are 9-12kD in size. GRX2 adopts a GST fold containing an N-terminal...; Region: GST_N_GRX2; cd03037 940296003390 C-terminal domain interface [polypeptide binding]; other site 940296003391 GSH binding site (G-site) [chemical binding]; other site 940296003392 catalytic residues [active] 940296003393 putative dimer interface [polypeptide binding]; other site 940296003394 C-terminal, alpha helical domain of Glutaredoxin 2; Region: GST_C_GRX2; cd03199 940296003395 N-terminal domain interface [polypeptide binding]; other site 940296003396 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 940296003397 HD domain; Region: HD_4; pfam13328 940296003398 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 940296003399 synthetase active site [active] 940296003400 NTP binding site [chemical binding]; other site 940296003401 metal binding site [ion binding]; metal-binding site 940296003402 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 940296003403 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 940296003404 Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein; Region: Hint; cl17442 940296003405 Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein; Region: Hint; cl17442 940296003406 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 940296003407 Pretoxin HINT domain; Region: PT-HINT; pfam07591 940296003408 Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein; Region: Hint; cd00081 940296003409 thioester formation/cholesterol transfer; other site 940296003410 protein-splicing catalytic site; other site 940296003411 Suppressor of fused protein (SUFU); Region: SUFU; pfam05076 940296003412 Protein of unknown function (DUF1260); Region: DUF1260; pfam06877 940296003413 Suppressor of fused protein (SUFU); Region: SUFU; pfam05076 940296003414 Protein of unknown function (DUF1020); Region: DUF1020; pfam06255 940296003415 Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein; Region: Hint; cd00081 940296003416 protein-splicing catalytic site; other site 940296003417 thioester formation/cholesterol transfer; other site 940296003418 Pretoxin HINT domain; Region: PT-HINT; pfam07591 940296003419 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 940296003420 putative active site [active] 940296003421 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 940296003422 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 940296003423 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 940296003424 Ferredoxin-like protein [Energy production and conversion]; Region: FixX; COG2440 940296003425 Predicted lipoprotein involved in nitrous oxide reduction [Energy production and conversion]; Region: NosL; COG4314 940296003426 ABC-2 family transporter protein; Region: ABC2_membrane_2; pfam12679 940296003427 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: COG4152 940296003428 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 940296003429 Walker A/P-loop; other site 940296003430 ATP binding site [chemical binding]; other site 940296003431 Q-loop/lid; other site 940296003432 ABC transporter signature motif; other site 940296003433 Walker B; other site 940296003434 D-loop; other site 940296003435 H-loop/switch region; other site 940296003436 Right handed beta helix region; Region: Beta_helix; pfam13229 940296003437 nitrous-oxide reductase; Validated; Region: PRK02888 940296003438 FMN-binding domain; Region: FMN_bind; cl01081 940296003439 Polyferredoxin [Energy production and conversion]; Region: NapH; COG0348 940296003440 4Fe-4S binding domain; Region: Fer4_5; pfam12801 940296003441 4Fe-4S binding domain; Region: Fer4_5; pfam12801 940296003442 Regulator of nitric oxide reductase transcription [Transcription]; Region: NosR; COG3901 940296003443 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 940296003444 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 940296003445 tRNA; other site 940296003446 putative tRNA binding site [nucleotide binding]; other site 940296003447 putative NADP binding site [chemical binding]; other site 940296003448 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 940296003449 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 940296003450 lipoyl attachment site [posttranslational modification]; other site 940296003451 glycine cleavage system aminomethyltransferase T; Reviewed; Region: gcvT; PRK00389 940296003452 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 940296003453 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 940296003454 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 940296003455 putative DNA binding site [nucleotide binding]; other site 940296003456 putative Zn2+ binding site [ion binding]; other site 940296003457 AsnC family; Region: AsnC_trans_reg; pfam01037 940296003458 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3310 940296003459 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2832 940296003460 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 940296003461 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 940296003462 transmembrane helices; other site 940296003463 Na(+)-translocating NADH-quinone reductase subunit A; Provisional; Region: PRK05352 940296003464 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 940296003465 E3 interaction surface; other site 940296003466 lipoyl attachment site [posttranslational modification]; other site 940296003467 NQRA C-terminal domain; Region: NQRA_SLBB; pfam11973 940296003468 Na(+)-translocating NADH-quinone reductase subunit B; Provisional; Region: PRK05349 940296003469 Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrC [Energy production and conversion]; Region: NqrC; COG2869 940296003470 NADH:ubiquinone oxidoreductase, Na(+)-translocating, C subunit; Region: nqrC; TIGR01938 940296003471 Na(+)-translocating NADH-quinone reductase subunit D; Validated; Region: PRK09292 940296003472 Na(+)-translocating NADH-quinone reductase subunit E; Provisional; Region: PRK02830 940296003473 Na(+)-translocating NADH-quinone reductase subunit F; Provisional; Region: PRK05464 940296003474 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 940296003475 catalytic loop [active] 940296003476 iron binding site [ion binding]; other site 940296003477 Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) FAD/NADH binding domain. (Na+-NQR) provides a means of storing redox reaction energy via the transmembrane translocation of Na2+ ions. The C-terminal domain resembles ferredoxin:NADP+ oxidoreductase; Region: NADH_quinone_reductase; cd06188 940296003478 FAD binding pocket [chemical binding]; other site 940296003479 FAD binding motif [chemical binding]; other site 940296003480 phosphate binding motif [ion binding]; other site 940296003481 beta-alpha-beta structure motif; other site 940296003482 NAD binding pocket [chemical binding]; other site 940296003483 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 940296003484 ApbE family; Region: ApbE; pfam02424 940296003485 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2991 940296003486 GrpE; Region: GrpE; pfam01025 940296003487 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 940296003488 dimer interface [polypeptide binding]; other site 940296003489 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 940296003490 serine acetyltransferase; Provisional; Region: cysE; PRK11132 940296003491 Serine acetyltransferase, N-terminal; Region: SATase_N; pfam06426 940296003492 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 940296003493 trimer interface [polypeptide binding]; other site 940296003494 active site 940296003495 substrate binding site [chemical binding]; other site 940296003496 CoA binding site [chemical binding]; other site 940296003497 putative ubiquinone biosynthesis protein UbiB; Reviewed; Region: ubiB; PRK04750 940296003498 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 940296003499 iron-sulfur cluster insertion protein ErpA; Provisional; Region: PRK13623 940296003500 Predicted transcriptional regulator [Transcription]; Region: COG2932 940296003501 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 940296003502 Catalytic site [active] 940296003503 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 940296003504 Nucleotide-binding domain of human HSPA9, Escherichia coli DnaK, and similar proteins; Region: HSPA9-like_NBD; cd11733 940296003505 nucleotide binding site [chemical binding]; other site 940296003506 NEF interaction site [polypeptide binding]; other site 940296003507 SBD interface [polypeptide binding]; other site 940296003508 ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]; Region: TauA; COG0715 940296003509 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 940296003510 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 940296003511 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: TauB; COG1116 940296003512 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 940296003513 Walker A/P-loop; other site 940296003514 ATP binding site [chemical binding]; other site 940296003515 Q-loop/lid; other site 940296003516 ABC transporter signature motif; other site 940296003517 Walker B; other site 940296003518 D-loop; other site 940296003519 H-loop/switch region; other site 940296003520 Predicted permease, cadmium resistance protein [Inorganic ion transport and metabolism]; Region: CadD; COG4300 940296003521 Cadmium resistance transporter; Region: Cad; pfam03596 940296003522 NnrS protein; Region: NnrS; cl01258 940296003523 primosome assembly protein PriA; Validated; Region: PRK05580 940296003524 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 940296003525 ATP binding site [chemical binding]; other site 940296003526 putative Mg++ binding site [ion binding]; other site 940296003527 helicase superfamily c-terminal domain; Region: HELICc; smart00490 940296003528 ATP-binding site [chemical binding]; other site 940296003529 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 940296003530 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 940296003531 dimerization domain [polypeptide binding]; other site 940296003532 dimer interface [polypeptide binding]; other site 940296003533 catalytic residues [active] 940296003534 macrolide transporter ATP-binding /permease protein; Provisional; Region: PRK10535 940296003535 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 940296003536 Walker A/P-loop; other site 940296003537 ATP binding site [chemical binding]; other site 940296003538 Q-loop/lid; other site 940296003539 ABC transporter signature motif; other site 940296003540 Walker B; other site 940296003541 D-loop; other site 940296003542 H-loop/switch region; other site 940296003543 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 940296003544 FtsX-like permease family; Region: FtsX; pfam02687 940296003545 macrolide transporter subunit MacA; Provisional; Region: PRK11578 940296003546 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 940296003547 HlyD family secretion protein; Region: HlyD_3; pfam13437 940296003548 Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilE; COG4968 940296003549 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 940296003550 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 940296003551 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 940296003552 Walker A/P-loop; other site 940296003553 ATP binding site [chemical binding]; other site 940296003554 Q-loop/lid; other site 940296003555 SMC proteins Flexible Hinge Domain; Region: SMC_hinge; smart00968 940296003556 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 940296003557 ABC transporter signature motif; other site 940296003558 Walker B; other site 940296003559 D-loop; other site 940296003560 H-loop/switch region; other site 940296003561 potential frameshift: common BLAST hit: gi|319775205|ref|YP_004137693.1| trimeric autotransporter adhesin 940296003562 Left-handed beta-roll, including virulence factors and various other proteins; Region: LbR-like; cl17507 940296003563 trimer interface [polypeptide binding]; other site 940296003564 YadA-like C-terminal region; Region: YadA; pfam03895 940296003565 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 940296003566 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 940296003567 putative active site [active] 940296003568 putative metal binding site [ion binding]; other site 940296003569 L-lactate permease [Energy production and conversion]; Region: LldP; COG1620 940296003570 L-lactate permease; Region: Lactate_perm; cl00701 940296003571 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4391 940296003572 Domain of unknown function (DUF4375); Region: DUF4375; pfam14300 940296003573 aromatic amino acid aminotransferase; Provisional; Region: PRK09257 940296003574 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 940296003575 pyridoxal 5'-phosphate binding site [chemical binding]; other site 940296003576 homodimer interface [polypeptide binding]; other site 940296003577 catalytic residue [active] 940296003578 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 940296003579 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 940296003580 dimer interface [polypeptide binding]; other site 940296003581 putative anticodon binding site; other site 940296003582 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 940296003583 motif 1; other site 940296003584 active site 940296003585 motif 2; other site 940296003586 motif 3; other site 940296003587 Mn2+ and Fe2+ transporters of the NRAMP family [Inorganic ion transport and metabolism]; Region: MntH; COG1914 940296003588 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 940296003589 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 940296003590 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 940296003591 X-Prolyl Aminopeptidase 2. E.C. 3.4.11.9. Also known as X-Pro aminopeptidase, proline aminopeptidase, aminopeptidase P, and aminoacylproline aminopeptidase. Catalyses release of any N-terminal amino acid, including proline, that is linked with proline; Region: APP; cd01085 940296003592 active site 940296003593 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 940296003594 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 940296003595 purine monophosphate binding site [chemical binding]; other site 940296003596 dimer interface [polypeptide binding]; other site 940296003597 putative catalytic residues [active] 940296003598 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; smart00798 940296003599 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 940296003600 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 940296003601 Putative ClC chloride channel. Clc proteins are putative halogen ion (Cl-, Br- and I-) transporters found in eubacteria. They belong to the ClC superfamily of halogen ion channels, which share a unique double-barreled architecture and voltage-dependent...; Region: ClC_like; cd01033 940296003602 putative ion selectivity filter; other site 940296003603 putative pore gating glutamate residue; other site 940296003604 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 940296003605 haloacid dehalogenase-like hydrolase; Region: HAD; cl17202 940296003606 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 940296003607 motif II; other site 940296003608 NAD(P) transhydrogenase subunit alpha; Provisional; Region: pntA; PRK09424 940296003609 Rubrum transdehydrogenase NAD-binding and catalytic domains; Region: Rubrum_tdh; cd05304 940296003610 ligand binding site [chemical binding]; other site 940296003611 homodimer interface [polypeptide binding]; other site 940296003612 NAD(P) binding site [chemical binding]; other site 940296003613 trimer interface B [polypeptide binding]; other site 940296003614 trimer interface A [polypeptide binding]; other site 940296003615 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 940296003616 MAPEG family; Region: MAPEG; cl09190 940296003617 pyridine nucleotide transhydrogenase; Provisional; Region: pntB; PRK09444 940296003618 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 940296003619 Putative NADPH-quinone reductase (modulator of drug activity B) [General function prediction only]; Region: MdaB; COG2249 940296003620 Transcriptional regulator [Transcription]; Region: LysR; COG0583 940296003621 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 940296003622 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA; cd08478 940296003623 putative effector binding pocket; other site 940296003624 dimerization interface [polypeptide binding]; other site 940296003625 Uncharacterized distant relative of homeotic protein bithoraxoid [General function prediction only]; Region: COG2018 940296003626 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 940296003627 G4 box; other site 940296003628 G5 box; other site 940296003629 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 940296003630 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 940296003631 S-adenosylmethionine binding site [chemical binding]; other site 940296003632 Protein of unknown function (DUF452); Region: DUF452; cl01062 940296003633 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 940296003634 KBL_like; this family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to serine palmitoyltransferase (SPT), 5-aminolevulinate synthase (ALAS); Region: KBL_like; cd06454 940296003635 substrate-cofactor binding pocket; other site 940296003636 pyridoxal 5'-phosphate binding site [chemical binding]; other site 940296003637 catalytic residue [active] 940296003638 23S rRNA m(5)U1939 methyltransferase; Reviewed; Region: rumA; PRK13168 940296003639 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 940296003640 Uncharacterized protein conserved in bacteria [Function unknown]; Region: ErfK; COG1376 940296003641 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 940296003642 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 940296003643 transmembrane helices; other site 940296003644 Agmatinase-like family includes proclavaminic acid amidinohydrolase; Region: Agmatinase_PAH; cd11592 940296003645 agmatinase; Region: agmatinase; TIGR01230 940296003646 oligomer interface [polypeptide binding]; other site 940296003647 putative active site [active] 940296003648 Mn binding site [ion binding]; other site 940296003649 Arginine decarboxylase (spermidine biosynthesis) [Amino acid transport and metabolism]; Region: SpeA; COG1166 940296003650 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase; Region: PLPDE_III_ADC; cd06830 940296003651 dimer interface [polypeptide binding]; other site 940296003652 active site 940296003653 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 940296003654 catalytic residues [active] 940296003655 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 940296003656 Peptidase propeptide and YPEB domain; Region: PepSY_2; pfam13670 940296003657 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 940296003658 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 940296003659 dimer interface [polypeptide binding]; other site 940296003660 anticodon binding site; other site 940296003661 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 940296003662 homodimer interface [polypeptide binding]; other site 940296003663 motif 1; other site 940296003664 active site 940296003665 motif 2; other site 940296003666 GAD domain; Region: GAD; pfam02938 940296003667 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 940296003668 motif 3; other site 940296003669 Uncharacterized conserved protein [Function unknown]; Region: COG2928 940296003670 Protein of unknown function (DUF3121); Region: DUF3121; cl11879 940296003671 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 940296003672 dimerization interface [polypeptide binding]; other site 940296003673 substrate binding site [chemical binding]; other site 940296003674 active site 940296003675 calcium binding site [ion binding]; other site 940296003676 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 940296003677 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 940296003678 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 940296003679 TonB-dependent lactoferrin and transferrin receptors; Region: TonB-tbp-lbp; TIGR01776 940296003680 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 940296003681 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 940296003682 Transferrin binding protein-like solute binding protein; Region: Lipoprotein_5; pfam01298 940296003683 Fic family protein [Function unknown]; Region: COG3177 940296003684 Fic/DOC family N-terminal; Region: Fic_N; pfam13784 940296003685 Fic/DOC family; Region: Fic; pfam02661 940296003686 glutamate racemase; Provisional; Region: PRK00865 940296003687 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 940296003688 AMIN domain; Region: AMIN; pfam11741 940296003689 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 940296003690 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 940296003691 active site 940296003692 metal binding site [ion binding]; metal-binding site 940296003693 Fic family protein [Function unknown]; Region: COG3177 940296003694 Fic/DOC family; Region: Fic; pfam02661 940296003695 Predicted N6-adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0116 940296003696 THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Region: THUMP_AdoMetMT; cd11715 940296003697 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 940296003698 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 940296003699 active site 940296003700 8-oxo-dGMP binding site [chemical binding]; other site 940296003701 nudix motif; other site 940296003702 metal binding site [ion binding]; metal-binding site 940296003703 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 940296003704 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 940296003705 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 940296003706 active site 940296003707 hydrophilic channel; other site 940296003708 dimerization interface [polypeptide binding]; other site 940296003709 catalytic residues [active] 940296003710 active site lid [active] 940296003711 Recombination protein O N terminal; Region: RecO_N; pfam11967 940296003712 Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]; Region: RecO; COG1381 940296003713 Recombination protein O C terminal; Region: RecO_C; pfam02565 940296003714 chorismate mutase domain of proteobacterial P-protein, clade 2; Region: CM_P2; TIGR01807 940296003715 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 940296003716 Prephenate dehydratase; Region: PDT; pfam00800 940296003717 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 940296003718 putative L-Phe binding site [chemical binding]; other site 940296003719 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 940296003720 putative substrate translocation pore; other site 940296003721 EamA-like transporter family; Region: EamA; pfam00892 940296003722 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 940296003723 EamA-like transporter family; Region: EamA; pfam00892 940296003724 Predicted amidohydrolase [General function prediction only]; Region: COG0388 940296003725 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 940296003726 putative active site [active] 940296003727 catalytic triad [active] 940296003728 dimer interface [polypeptide binding]; other site 940296003729 Prephenate dehydrogenase [Amino acid transport and metabolism]; Region: TyrA; COG0287 940296003730 prephenate dehydrogenase; Validated; Region: PRK08507 940296003731 Uncharacterized protein involved in response to NO [Inorganic ion transport and metabolism]; Region: NnrS; COG3213 940296003732 Predicted transcriptional regulator [Transcription]; Region: COG1959 940296003733 Transcriptional regulator; Region: Rrf2; cl17282 940296003734 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 940296003735 propionate/acetate kinase; Provisional; Region: PRK12379 940296003736 acetate kinase A/propionate kinase 2; Reviewed; Region: PRK00180 940296003737 probable AcnD-accessory protein PrpF; Region: prpF; TIGR02334 940296003738 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 940296003739 active site 940296003740 dimer interface [polypeptide binding]; other site 940296003741 metal binding site [ion binding]; metal-binding site 940296003742 shikimate kinase; Reviewed; Region: aroK; PRK00131 940296003743 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 940296003744 ADP binding site [chemical binding]; other site 940296003745 magnesium binding site [ion binding]; other site 940296003746 putative shikimate binding site; other site 940296003747 Aconitase catalytic domain; Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle; Region: Aconitase; cl00285 940296003748 ligand binding site [chemical binding]; other site 940296003749 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 940296003750 substrate binding site [chemical binding]; other site 940296003751 Aconitase catalytic domain; Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle; Region: Aconitase; cl00285 940296003752 substrate binding site [chemical binding]; other site 940296003753 hypothetical protein; Provisional; Region: PRK10621 940296003754 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 940296003755 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 940296003756 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 940296003757 dimer interface [polypeptide binding]; other site 940296003758 active site 940296003759 citrylCoA binding site [chemical binding]; other site 940296003760 oxalacetate/citrate binding site [chemical binding]; other site 940296003761 coenzyme A binding site [chemical binding]; other site 940296003762 catalytic triad [active] 940296003763 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 940296003764 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 940296003765 tetramer interface [polypeptide binding]; other site 940296003766 active site 940296003767 Mg2+/Mn2+ binding site [ion binding]; other site 940296003768 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 940296003769 cell division protein FtsZ; Validated; Region: PRK09330 940296003770 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 940296003771 nucleotide binding site [chemical binding]; other site 940296003772 SulA interaction site; other site 940296003773 cell division protein FtsA; Region: ftsA; TIGR01174 940296003774 Cell division protein FtsA; Region: FtsA; smart00842 940296003775 Cell division protein FtsA; Region: FtsA; pfam14450 940296003776 Cell division septal protein [Cell envelope biogenesis, outer membrane]; Region: FtsQ; COG1589 940296003777 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 940296003778 Cell division protein FtsQ; Region: FtsQ; pfam03799 940296003779 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 940296003780 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 940296003781 ATP-grasp domain; Region: ATP-grasp_4; cl17255 940296003782 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 940296003783 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 940296003784 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 940296003785 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 940296003786 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 940296003787 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 940296003788 active site 940296003789 homodimer interface [polypeptide binding]; other site 940296003790 cell division protein FtsW; Region: ftsW; TIGR02614 940296003791 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK04308 940296003792 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 940296003793 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 940296003794 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 940296003795 Sel1-like repeats; Region: SEL1; smart00671 940296003796 Sel1-like repeats; Region: SEL1; smart00671 940296003797 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 940296003798 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 940296003799 Mg++ binding site [ion binding]; other site 940296003800 putative catalytic motif [active] 940296003801 putative substrate binding site [chemical binding]; other site 940296003802 bifunctional preprotein translocase subunit SecD/SecF; Reviewed; Region: PRK13024 940296003803 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 940296003804 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Region: murF; TIGR01143 940296003805 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 940296003806 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 940296003807 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 940296003808 Sulfatase; Region: Sulfatase; pfam00884 940296003809 UDP-N-acetylmuramyl-tripeptide synthetase; Region: murE; TIGR01085 940296003810 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 940296003811 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 940296003812 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 940296003813 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 940296003814 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 940296003815 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 940296003816 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 940296003817 MraW methylase family; Region: Methyltransf_5; cl17771 940296003818 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2001 940296003819 MraZ protein; Region: MraZ; pfam02381 940296003820 MraZ protein; Region: MraZ; pfam02381 940296003821 Uncharacterized conserved protein [Function unknown]; Region: COG1565 940296003822 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 940296003823 undecaprenyl pyrophosphate phosphatase; Reviewed; Region: PRK00281 940296003824 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 940296003825 catalytic residues [active] 940296003826 hinge region; other site 940296003827 alpha helical domain; other site 940296003828 cell division protein FtsN; Region: ftsN; TIGR02223 940296003829 Sporulation related domain; Region: SPOR; pfam05036 940296003830 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 940296003831 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 940296003832 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 940296003833 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 940296003834 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2960 940296003835 Na(+)/proline cotransporter PutP and related proteins; solute binding domain; Region: SLC5sbd_PutP; cd11475 940296003836 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 940296003837 Na binding site [ion binding]; other site 940296003838 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed; Region: PRK11905 940296003839 Proline dehydrogenase [Amino acid transport and metabolism]; Region: PutA; COG0506 940296003840 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 940296003841 Glutamate binding site [chemical binding]; other site 940296003842 NAD binding site [chemical binding]; other site 940296003843 catalytic residues [active] 940296003844 putative outer membrane lipoprotein; Provisional; Region: PRK10510 940296003845 Glycine zipper 2TM domain; Region: Rick_17kDa_Anti; cl10470 940296003846 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 940296003847 ligand binding site [chemical binding]; other site 940296003848 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 940296003849 putative catalytic site [active] 940296003850 putative phosphate binding site [ion binding]; other site 940296003851 active site 940296003852 metal binding site A [ion binding]; metal-binding site 940296003853 DNA binding site [nucleotide binding] 940296003854 putative AP binding site [nucleotide binding]; other site 940296003855 putative metal binding site B [ion binding]; other site 940296003856 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 940296003857 dimerization interface [polypeptide binding]; other site 940296003858 putative DNA binding site [nucleotide binding]; other site 940296003859 putative Zn2+ binding site [ion binding]; other site 940296003860 Nicotinate-nucleotide pyrophosphorylase [Coenzyme metabolism]; Region: NadC; COG0157 940296003861 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 940296003862 dimerization interface [polypeptide binding]; other site 940296003863 active site 940296003864 Uncharacterized conserved protein [General function prediction only]; Region: COG4111 940296003865 quinolinate synthetase; Provisional; Region: PRK09375 940296003866 L-aspartate oxidase; Provisional; Region: PRK06175 940296003867 Aspartate oxidase [Coenzyme metabolism]; Region: NadB; COG0029 940296003868 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 940296003869 Transposase domain (DUF772); Region: DUF772; pfam05598 940296003870 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 940296003871 motif II; other site 940296003872 Glycosyl hydrolase family 65 central catalytic domain; Region: Glyco_hydro_65m; pfam03632 940296003873 Glycosyl hydrolase family 65, C-terminal domain; Region: Glyco_hydro_65C; pfam03633 940296003874 Glycosyl hydrolase family 65, N-terminal domain; Region: Glyco_hydro_65N; pfam03636 940296003875 Glycosyl hydrolase family 65 central catalytic domain; Region: Glyco_hydro_65m; pfam03632 940296003876 aldose 1-epimerase superfamily; Region: Aldose_epim; cl14648 940296003877 catalytic residues [active] 940296003878 GPH family sucrose/H+ symporter; Region: GPH_sucrose; TIGR01301 940296003879 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 940296003880 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 940296003881 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 940296003882 ABC transporter; Region: ABC_tran_2; pfam12848 940296003883 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 940296003884 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 940296003885 tetramer interfaces [polypeptide binding]; other site 940296003886 binuclear metal-binding site [ion binding]; other site 940296003887 thiamine-monophosphate kinase; Region: thiL; TIGR01379 940296003888 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 940296003889 ATP binding site [chemical binding]; other site 940296003890 dimerization interface [polypeptide binding]; other site 940296003891 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 940296003892 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 940296003893 ligand binding site [chemical binding]; other site 940296003894 transcriptional regulator CysB-like protein; Reviewed; Region: PRK12682 940296003895 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 940296003896 The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold; Region: PBP2_CysB_like; cd08413 940296003897 substrate binding site [chemical binding]; other site 940296003898 dimerization interface [polypeptide binding]; other site 940296003899 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 940296003900 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 940296003901 ligand binding site [chemical binding]; other site 940296003902 flexible hinge region; other site 940296003903 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 940296003904 putative switch regulator; other site 940296003905 non-specific DNA interactions [nucleotide binding]; other site 940296003906 DNA binding site [nucleotide binding] 940296003907 sequence specific DNA binding site [nucleotide binding]; other site 940296003908 putative cAMP binding site [chemical binding]; other site 940296003909 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 940296003910 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 940296003911 FeS/SAM binding site; other site 940296003912 HemN C-terminal domain; Region: HemN_C; pfam06969 940296003913 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 940296003914 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 940296003915 Uncharacterized protein family (UPF0075); Region: UPF0075; pfam03702 940296003916 Hint (Hedgehog/Intein) domain N-terminal region; Region: HintN; smart00306 940296003917 thioester formation/cholesterol transfer; other site 940296003918 Pretoxin HINT domain; Region: PT-HINT; pfam07591 940296003919 MafB19-like deaminase; Region: MafB19-deam; pfam14437 940296003920 Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein; Region: Hint; cl17442 940296003921 Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein; Region: Hint; cl17442 940296003922 Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein; Region: Hint; cl17442 940296003923 Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein; Region: Hint; cl17442 940296003924 Domain of unknown function (DUF4265); Region: DUF4265; pfam14085 940296003925 Suppressor of fused protein (SUFU); Region: SUFU; pfam05076 940296003926 The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific endonuclease SLX1; Region: GIY-YIG_UPF0213; cd10456 940296003927 GIY-YIG motif/motif A; other site 940296003928 putative active site [active] 940296003929 putative metal binding site [ion binding]; other site 940296003930 muropeptide transporter; Reviewed; Region: ampG; PRK11902 940296003931 AmpG-like permease; Region: 2A0125; TIGR00901 940296003932 glutamine synthetase; Provisional; Region: glnA; PRK09469 940296003933 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 940296003934 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 940296003935 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 940296003936 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 940296003937 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 940296003938 shikimate binding site; other site 940296003939 NAD(P) binding site [chemical binding]; other site 940296003940 monofunctional biosynthetic peptidoglycan transglycosylase; Provisional; Region: mtgA; PRK00056 940296003941 Transglycosylase; Region: Transgly; cl17702 940296003942 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 940296003943 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 940296003944 Walker A/P-loop; other site 940296003945 ATP binding site [chemical binding]; other site 940296003946 Q-loop/lid; other site 940296003947 ABC transporter signature motif; other site 940296003948 Walker B; other site 940296003949 D-loop; other site 940296003950 H-loop/switch region; other site 940296003951 lipopolysaccharide transport periplasmic protein LptA; Region: outer_YhbN_LptA; TIGR03002 940296003952 OstA-like protein; Region: OstA; pfam03968 940296003953 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3117 940296003954 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 940296003955 HAD-superfamily hydrolase, subfamily IIIA; Region: HAD-SF-IIIA; TIGR01662 940296003956 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 940296003957 active site 940296003958 motif I; other site 940296003959 motif II; other site 940296003960 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 940296003961 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 940296003962 putative active site [active] 940296003963 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 940296003964 Transaldolase-like proteins from plants and bacteria; Region: Transaldolase_like; cd00955 940296003965 putative active site [active] 940296003966 transaldolase; Provisional; Region: PRK03903 940296003967 catalytic residue [active] 940296003968 Glutamyl- and glutaminyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]; Region: GlnS; COG0008 940296003969 glutamyl-queuosine tRNA(Asp) synthetase; Region: queuosine_YadB; TIGR03838 940296003970 active site 940296003971 HIGH motif; other site 940296003972 nucleotide binding site [chemical binding]; other site 940296003973 active site 940296003974 KMSKS motif; other site 940296003975 tRNA-dihydrouridine synthase A; Provisional; Region: PRK11815 940296003976 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 940296003977 FMN binding site [chemical binding]; other site 940296003978 active site 940296003979 catalytic residues [active] 940296003980 substrate binding site [chemical binding]; other site 940296003981 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 940296003982 active site 940296003983 DNA binding site [nucleotide binding] 940296003984 Int/Topo IB signature motif; other site 940296003985 Pyocin activator protein PrtN; Region: PyocinActivator; pfam11112 940296003986 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 940296003987 Methyltransferase domain; Region: Methyltransf_26; pfam13659 940296003988 Siphovirus Gp157; Region: Sipho_Gp157; pfam05565 940296003989 Uncharacterized phage-associated protein [Function unknown]; Region: GepA; COG3600 940296003990 Predicted transcriptional regulator [Transcription]; Region: COG2932 940296003991 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 940296003992 Catalytic site [active] 940296003993 Helix-turn-helix domain; Region: HTH_39; pfam14090 940296003994 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 940296003995 putative DNA binding site [nucleotide binding]; other site 940296003996 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 940296003997 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 940296003998 Walker A motif; other site 940296003999 ATP binding site [chemical binding]; other site 940296004000 Walker B motif; other site 940296004001 arginine finger; other site 940296004002 Protein of unknwon function (DUF3310); Region: DUF3310; pfam11753 940296004003 Endodeoxyribonuclease RusA; Region: RusA; pfam05866 940296004004 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 940296004005 Transposase; Region: DEDD_Tnp_IS110; pfam01548 940296004006 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 940296004007 Zonular occludens toxin (Zot); Region: Zot; pfam05707 940296004008 Protein of unknown function (DUF2523); Region: DUF2523; pfam10734 940296004009 Neisseria meningitidis TspB protein; Region: Neisseria_TspB; pfam05616 940296004010 Protein of unknown function (DUF1132); Region: DUF1132; pfam06575 940296004011 Putative phage replication protein RstA [DNA replication, recombination, and repair]; Region: COG2946 940296004012 Replication initiation factor; Region: Rep_trans; pfam02486 940296004013 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 940296004014 additional DNA contacts [nucleotide binding]; other site 940296004015 mismatch recognition site; other site 940296004016 active site 940296004017 zinc binding site [ion binding]; other site 940296004018 DNA intercalation site [nucleotide binding]; other site 940296004019 TIGR02391 family protein; Region: hypoth_ymh 940296004020 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 940296004021 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 940296004022 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 940296004023 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 940296004024 DNA binding site [nucleotide binding] 940296004025 substrate interaction site [chemical binding]; other site 940296004026 comEA protein; Region: comE; TIGR01259 940296004027 Helix-hairpin-helix motif; Region: HHH; pfam00633 940296004028 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 940296004029 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 940296004030 active site 940296004031 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 940296004032 Nitrogen regulatory protein P-II; Region: P-II; smart00938 940296004033 phosphoribosylformylglycinamidine synthase; Provisional; Region: PRK05297 940296004034 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 940296004035 dimerization interface [polypeptide binding]; other site 940296004036 ATP binding site [chemical binding]; other site 940296004037 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 940296004038 dimerization interface [polypeptide binding]; other site 940296004039 ATP binding site [chemical binding]; other site 940296004040 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 940296004041 putative active site [active] 940296004042 catalytic triad [active] 940296004043 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 940296004044 Old yellow enzyme (OYE)-related FMN binding domain, group 2. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as...; Region: OYE_like_2_FMN; cd04733 940296004045 putative active site [active] 940296004046 putative FMN binding site [chemical binding]; other site 940296004047 putative substrate binding site [chemical binding]; other site 940296004048 putative catalytic residue [active] 940296004049 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 940296004050 dimerization interface [polypeptide binding]; other site 940296004051 putative DNA binding site [nucleotide binding]; other site 940296004052 putative Zn2+ binding site [ion binding]; other site 940296004053 hydroxyacylglutathione hydrolase; Region: GSH_gloB; TIGR03413 940296004054 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 940296004055 MgtE intracellular N domain; Region: MgtE_N; smart00924 940296004056 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 940296004057 Divalent cation transporter; Region: MgtE; cl00786 940296004058 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 940296004059 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 940296004060 dimerization interface [polypeptide binding]; other site 940296004061 domain crossover interface; other site 940296004062 redox-dependent activation switch; other site 940296004063 NlpC/P60 family; Region: NLPC_P60; pfam00877 940296004064 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 940296004065 Putative effector of murein hydrolase [Cell envelope biogenesis, outer membrane]; Region: LrgB; COG1346 940296004066 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 940296004067 heterotetramer interface [polypeptide binding]; other site 940296004068 active site pocket [active] 940296004069 cleavage site 940296004070 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 940296004071 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 940296004072 putative ion selectivity filter; other site 940296004073 putative pore gating glutamate residue; other site 940296004074 putative H+/Cl- coupling transport residue; other site 940296004075 DEAD-like helicases superfamily; Region: DEXDc; smart00487 940296004076 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 940296004077 ATP binding site [chemical binding]; other site 940296004078 putative Mg++ binding site [ion binding]; other site 940296004079 nucleotide binding region [chemical binding]; other site 940296004080 helicase superfamily c-terminal domain; Region: HELICc; smart00490 940296004081 ATP-binding site [chemical binding]; other site 940296004082 SIR2-like domain; Region: SIR2_2; pfam13289 940296004083 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 940296004084 Sulfatase; Region: Sulfatase; pfam00884 940296004085 HrpA-like helicases [DNA replication, recombination, and repair]; Region: HrpA; COG1643 940296004086 Helicase associated domain (HA2); Region: HA2; pfam04408 940296004087 Oligonucleotide/oligosaccharide-binding (OB)-fold; Region: OB_NTP_bind; pfam07717 940296004088 Domain of unknown function (DUF3418); Region: DUF3418; pfam11898 940296004089 Domain of unknown function (DUF3418); Region: DUF3418; pfam11898 940296004090 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 940296004091 Transposase; Region: DEDD_Tnp_IS110; pfam01548 940296004092 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 940296004093 Zonular occludens toxin (Zot); Region: Zot; pfam05707 940296004094 Protein of unknown function (DUF2523); Region: DUF2523; pfam10734 940296004095 Neisseria meningitidis TspB protein; Region: Neisseria_TspB; pfam05616 940296004096 Protein of unknown function (DUF1132); Region: DUF1132; pfam06575 940296004097 Putative phage replication protein RstA [DNA replication, recombination, and repair]; Region: COG2946 940296004098 Replication initiation factor; Region: Rep_trans; pfam02486 940296004099 Protein of unknown function (DUF2788); Region: DUF2788; pfam10981 940296004100 O-succinylhomoserine sulfhydrylase; Region: O_suc_HS_sulf; TIGR01325 940296004101 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 940296004102 homodimer interface [polypeptide binding]; other site 940296004103 substrate-cofactor binding pocket; other site 940296004104 pyridoxal 5'-phosphate binding site [chemical binding]; other site 940296004105 catalytic residue [active] 940296004106 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 940296004107 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 940296004108 substrate binding pocket [chemical binding]; other site 940296004109 membrane-bound complex binding site; other site 940296004110 hinge residues; other site 940296004111 Tartrate dehydratase alpha subunit/Fumarate hydratase class I, N-terminal domain [Energy production and conversion]; Region: TtdA; COG1951 940296004112 Fumarase C-terminus; Region: Fumerase_C; pfam05683 940296004113 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 940296004114 TrkA-N domain; Region: TrkA_N; pfam02254 940296004115 TrkA-C domain; Region: TrkA_C; pfam02080 940296004116 TrkA-N domain; Region: TrkA_N; pfam02254 940296004117 TrkA-C domain; Region: TrkA_C; pfam02080 940296004118 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; cl00185 940296004119 Autotransporter beta-domain; Region: Autotransporter; cl17461 940296004120 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 940296004121 dimer interface [polypeptide binding]; other site 940296004122 substrate binding site [chemical binding]; other site 940296004123 ATP binding site [chemical binding]; other site 940296004124 Uncharacterized protein/domain, possibly involved in tellurite resistance [Inorganic ion transport and metabolism]; Region: TehB; COG3615 940296004125 tellurite resistance protein TehB; Provisional; Region: PRK12335 940296004126 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 940296004127 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 940296004128 RNA/DNA hybrid binding site [nucleotide binding]; other site 940296004129 active site 940296004130 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 940296004131 Transposase; Region: DEDD_Tnp_IS110; pfam01548 940296004132 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 940296004133 Zonular occludens toxin (Zot); Region: Zot; pfam05707 940296004134 Protein of unknown function (DUF2523); Region: DUF2523; pfam10734 940296004135 Neisseria meningitidis TspB protein; Region: Neisseria_TspB; pfam05616 940296004136 Protein of unknown function (DUF2523); Region: DUF2523; pfam10734 940296004137 Zonular occludens toxin (Zot); Region: Zot; cl17485 940296004138 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 940296004139 Transposase; Region: DEDD_Tnp_IS110; pfam01548 940296004140 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 940296004141 TIGR02594 family protein; Region: TIGR02594 940296004142 PemK-like protein; Region: PemK; cl00995 940296004143 Prophage antirepressor [Transcription]; Region: COG3617 940296004144 BRO family, N-terminal domain; Region: Bro-N; smart01040 940296004145 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 940296004146 putative active site [active] 940296004147 dimerization interface [polypeptide binding]; other site 940296004148 putative tRNAtyr binding site [nucleotide binding]; other site 940296004149 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 940296004150 YciI-like protein; Reviewed; Region: PRK11370 940296004151 intracellular septation protein A; Reviewed; Region: PRK00259 940296004152 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 940296004153 Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimV; COG3170 940296004154 FimV C-terminal domain; Region: FimV_Cterm; TIGR03504 940296004155 Glyoxalase I catalyzes the isomerization of the hemithioacetal, formed by a 2-oxoaldehyde and glutathione, to S-D-lactoylglutathione; Region: Glyoxalase_I; cd07233 940296004156 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 940296004157 dimer interface [polypeptide binding]; other site 940296004158 active site 940296004159 glutathione binding site [chemical binding]; other site 940296004160 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]; Region: COG2956 940296004161 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 940296004162 TPR motif; other site 940296004163 binding surface 940296004164 Uncharacterized integral membrane protein [Function unknown]; Region: COG5416 940296004165 branched-chain amino acid aminotransferase; Provisional; Region: PRK13357 940296004166 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 940296004167 homodimer interface [polypeptide binding]; other site 940296004168 substrate-cofactor binding pocket; other site 940296004169 catalytic residue [active] 940296004170 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK08690 940296004171 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 940296004172 NAD binding site [chemical binding]; other site 940296004173 homotetramer interface [polypeptide binding]; other site 940296004174 homodimer interface [polypeptide binding]; other site 940296004175 substrate binding site [chemical binding]; other site 940296004176 active site 940296004177 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 940296004178 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 940296004179 trimer interface [polypeptide binding]; other site 940296004180 active site 940296004181 substrate binding site [chemical binding]; other site 940296004182 CoA binding site [chemical binding]; other site 940296004183 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 940296004184 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 940296004185 active site 940296004186 dimer interface [polypeptide binding]; other site 940296004187 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 940296004188 dimer interface [polypeptide binding]; other site 940296004189 active site 940296004190 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 940296004191 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 940296004192 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 940296004193 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 940296004194 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 940296004195 Type IV leader peptidase family; Region: Peptidase_A24; pfam01478 940296004196 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 940296004197 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 940296004198 CoA-binding site [chemical binding]; other site 940296004199 ATP-binding [chemical binding]; other site 940296004200 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 940296004201 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 940296004202 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 940296004203 Walker A motif; other site 940296004204 ATP binding site [chemical binding]; other site 940296004205 Walker B motif; other site 940296004206 Predicted membrane protein [Function unknown]; Region: COG2707 940296004207 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 940296004208 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 940296004209 substrate binding pocket [chemical binding]; other site 940296004210 chain length determination region; other site 940296004211 substrate-Mg2+ binding site; other site 940296004212 catalytic residues [active] 940296004213 aspartate-rich region 1; other site 940296004214 active site lid residues [active] 940296004215 aspartate-rich region 2; other site 940296004216 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 940296004217 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 940296004218 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 940296004219 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 940296004220 hypothetical protein; Provisional; Region: PRK09126 940296004221 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 940296004222 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 940296004223 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 940296004224 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 940296004225 putative substrate translocation pore; other site 940296004226 efflux pump membrane protein (multidrug resistance protein A); Region: 8a0101; TIGR00998 940296004227 HlyD family secretion protein; Region: HlyD_3; pfam13437 940296004228 Enzyme related to GTP cyclohydrolase I [General function prediction only]; Region: COG0780 940296004229 hypothetical protein; Provisional; Region: PRK11212 940296004230 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 940296004231 Peptidase family M23; Region: Peptidase_M23; pfam01551 940296004232 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4255 940296004233 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 940296004234 binding surface 940296004235 Tetratricopeptide repeat; Region: TPR_16; pfam13432 940296004236 TPR motif; other site 940296004237 Protein of unknown function (DUF560); Region: DUF560; pfam04575 940296004238 Predicted membrane protein [Function unknown]; Region: COG1981 940296004239 CYTH-like Clostridium thermocellum TTM-like subgroup 1; Region: CYTH-like_CthTTM-like_1; cd07891 940296004240 putative active site [active] 940296004241 putative metal binding residues [ion binding]; other site 940296004242 signature motif; other site 940296004243 putative dimer interface [polypeptide binding]; other site 940296004244 putative phosphate binding site [ion binding]; other site 940296004245 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 940296004246 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 940296004247 folate binding site [chemical binding]; other site 940296004248 NADP+ binding site [chemical binding]; other site 940296004249 phospho-2-dehydro-3-deoxyheptonate aldolase; Validated; Region: PRK09261 940296004250 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 940296004251 Outer membrane protein OpcA; Region: OpcA; pfam07239 940296004252 comEA protein; Region: comE; TIGR01259 940296004253 Helix-hairpin-helix motif; Region: HHH; pfam00633 940296004254 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4137 940296004255 signal recognition particle protein; Provisional; Region: PRK10867 940296004256 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 940296004257 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 940296004258 P loop; other site 940296004259 GTP binding site [chemical binding]; other site 940296004260 Signal peptide binding domain; Region: SRP_SPB; pfam02978 940296004261 Cysteine-rich 4 helical bundle widely conserved in bacteria; Region: DUF326; cd08026 940296004262 dimerization interface [polypeptide binding]; other site 940296004263 Nitroreductase-like family 4. 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_4; cd02140 940296004264 FMN binding site [chemical binding]; other site 940296004265 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 940296004266 Transposase; Region: DEDD_Tnp_IS110; pfam01548 940296004267 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 940296004268 Proteins of this family catalyze the reduction of flavin or nitrocompounds using NAD(P)H as electron donor in a obligatory two-electron transfer, utilizing FMN or FAD as cofactor. They are often found to be homodimers. Enzymes of this family are...; Region: Nitro_FMN_reductase; cl00514 940296004269 FMN binding site [chemical binding]; other site 940296004270 Predicted membrane protein [Function unknown]; Region: COG2259 940296004271 Transcriptional regulator [Transcription]; Region: LysR; COG0583 940296004272 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 940296004273 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 940296004274 putative effector binding pocket; other site 940296004275 dimerization interface [polypeptide binding]; other site 940296004276 Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]; Region: PhrB; COG0415 940296004277 DNA photolyase; Region: DNA_photolyase; pfam00875 940296004278 ATP-dependent DNA helicase DinG; Provisional; Region: dinG; PRK11747 940296004279 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 940296004280 DEAD_2; Region: DEAD_2; pfam06733 940296004281 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 940296004282 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2979 940296004283 tellurium resistance terB-like protein, subgroup 3; Region: terB_like_YebE; cd07178 940296004284 putative metal binding site [ion binding]; other site 940296004285 potential frameshift: common BLAST hit: gi|194099602|ref|YP_002002733.1| putative trans-acylase protein 940296004286 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 940296004287 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 940296004288 adenylosuccinate lyase; Provisional; Region: PRK09285 940296004289 PurB_like adenylosuccinases (adenylsuccinate lyase, ASL); Region: PurB; cd01598 940296004290 tetramer interface [polypeptide binding]; other site 940296004291 active site 940296004292 Predicted Rossmann fold nucleotide-binding protein [General function prediction only]; Region: COG1611 940296004293 Exoribonuclease R [Transcription]; Region: VacB; COG0557 940296004294 RNB domain; Region: RNB; pfam00773 940296004295 SurA N-terminal domain; Region: SurA_N; pfam09312 940296004296 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 940296004297 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 940296004298 Organic solvent tolerance protein; Region: OstA_C; pfam04453 940296004299 Predicted phosphotransferase related to Ser/Thr protein kinases [General function prediction only]; Region: COG3178 940296004300 Phosphotransferase enzyme family; Region: APH; pfam01636 940296004301 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 940296004302 catalytic residues [active] 940296004303 hinge region; other site 940296004304 alpha helical domain; other site 940296004305 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 940296004306 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 940296004307 Predicted hydrolase of the alpha/beta-hydrolase fold [General function prediction only]; Region: COG0429 940296004308 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 940296004309 active site 940296004310 ribulose/triose binding site [chemical binding]; other site 940296004311 phosphate binding site [ion binding]; other site 940296004312 substrate (anthranilate) binding pocket [chemical binding]; other site 940296004313 product (indole) binding pocket [chemical binding]; other site 940296004314 ATP-dependent DNA helicase RecQ; Region: recQ; TIGR01389 940296004315 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 940296004316 ATP binding site [chemical binding]; other site 940296004317 putative Mg++ binding site [ion binding]; other site 940296004318 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 940296004319 nucleotide binding region [chemical binding]; other site 940296004320 ATP-binding site [chemical binding]; other site 940296004321 This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure; Region: RQC; smart00956 940296004322 Helicase and RNase D C-terminal; Region: HRDC; smart00341 940296004323 Helicase and RNase D C-terminal; Region: HRDC; smart00341 940296004324 Helicase and RNase D C-terminal; Region: HRDC; smart00341 940296004325 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 940296004326 pimelyl-[acyl-carrier protein] methyl ester esterase; Region: bioH; TIGR01738 940296004327 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 940296004328 Serine hydrolase (FSH1); Region: FSH1; pfam03959 940296004329 comF family protein; Region: comF; TIGR00201 940296004330 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 940296004331 active site 940296004332 Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]; Region: CspR; COG0219 940296004333 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 940296004334 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 940296004335 Predicted membrane protein [Function unknown]; Region: COG3212 940296004336 Peptidase propeptide and YPEB domain; Region: PepSY; pfam03413 940296004337 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 940296004338 RuvA N terminal domain; Region: RuvA_N; pfam01330 940296004339 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 940296004340 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 940296004341 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 940296004342 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 940296004343 Walker A/P-loop; other site 940296004344 ATP binding site [chemical binding]; other site 940296004345 Q-loop/lid; other site 940296004346 ABC transporter signature motif; other site 940296004347 Walker B; other site 940296004348 D-loop; other site 940296004349 H-loop/switch region; other site 940296004350 GTPase RsgA; Reviewed; Region: PRK00098 940296004351 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 940296004352 RNA binding site [nucleotide binding]; other site 940296004353 homodimer interface [polypeptide binding]; other site 940296004354 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 940296004355 GTPase/Zn-binding domain interface [polypeptide binding]; other site 940296004356 GTP/Mg2+ binding site [chemical binding]; other site 940296004357 G4 box; other site 940296004358 G5 box; other site 940296004359 G1 box; other site 940296004360 Switch I region; other site 940296004361 G2 box; other site 940296004362 G3 box; other site 940296004363 Switch II region; other site 940296004364 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 940296004365 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 940296004366 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 940296004367 substrate binding pocket [chemical binding]; other site 940296004368 chain length determination region; other site 940296004369 substrate-Mg2+ binding site; other site 940296004370 catalytic residues [active] 940296004371 aspartate-rich region 1; other site 940296004372 active site lid residues [active] 940296004373 aspartate-rich region 2; other site 940296004374 Protein of unknown function (DUF2818); Region: DUF2818; pfam10993 940296004375 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 940296004376 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 940296004377 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 940296004378 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 940296004379 Catalytic domain of type II restriction endonucleases BfiI and NgoFVII, and uncharacterized proteins with a DEAD domain; Region: PLDc_Bfil_DEXD_like; cd09117 940296004380 PLD-like domain; Region: PLDc_2; pfam13091 940296004381 homodimer interface [polypeptide binding]; other site 940296004382 putative active site [active] 940296004383 catalytic site [active] 940296004384 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 940296004385 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 940296004386 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 940296004387 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 940296004388 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 940296004389 NADH dehydrogenase subunit J; Provisional; Region: PRK06433 940296004390 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 940296004391 4Fe-4S binding domain; Region: Fer4; cl02805 940296004392 4Fe-4S binding domain; Region: Fer4; pfam00037 940296004393 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 940296004394 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 940296004395 NADH dehydrogenase subunit G; Validated; Region: PRK09129 940296004396 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 940296004397 catalytic loop [active] 940296004398 iron binding site [ion binding]; other site 940296004399 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 940296004400 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 940296004401 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 940296004402 NADH-quinone oxidoreductase, F subunit; Region: nuoF_fam; TIGR01959 940296004403 SLBB domain; Region: SLBB; pfam10531 940296004404 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 940296004405 NADH dehydrogenase subunit E; Validated; Region: PRK07539 940296004406 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 940296004407 putative dimer interface [polypeptide binding]; other site 940296004408 [2Fe-2S] cluster binding site [ion binding]; other site 940296004409 NADH dehydrogenase subunit D; Validated; Region: PRK06075 940296004410 NADH dehydrogenase I, D subunit; Region: NuoD; TIGR01962 940296004411 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 940296004412 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 940296004413 NADH dehydrogenase subunit B; Validated; Region: PRK06411 940296004414 NADH:ubiquinone oxidoreductase subunit A; Validated; Region: PRK06602 940296004415 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 940296004416 S-adenosylmethionine binding site [chemical binding]; other site 940296004417 spermidine synthase; Provisional; Region: PRK03612 940296004418 Pilin (bacterial filament); Region: Pilin; pfam00114 940296004419 Tfp pilus assembly protein, major pilin PilA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilA; COG4969 940296004420 Pilin (bacterial filament); Region: Pilin; pfam00114 940296004421 Tfp pilus assembly protein, major pilin PilA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilA; COG4969 940296004422 Pilin (bacterial filament); Region: Pilin; pfam00114 940296004423 Tfp pilus assembly protein, major pilin PilA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilA; COG4969 940296004424 Pilin (bacterial filament); Region: Pilin; pfam00114 940296004425 Tfp pilus assembly protein, major pilin PilA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilA; COG4969 940296004426 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 940296004427 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 940296004428 Pilin (bacterial filament); Region: Pilin; pfam00114 940296004429 Tfp pilus assembly protein, major pilin PilA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilA; COG4969 940296004430 Tfp pilus assembly protein, major pilin PilA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilA; COG4969 940296004431 Pilin (bacterial filament); Region: Pilin; pfam00114 940296004432 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 940296004433 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 940296004434 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 940296004435 P loop; other site 940296004436 GTP binding site [chemical binding]; other site 940296004437 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional; Region: PRK14018 940296004438 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 940296004439 catalytic residues [active] 940296004440 Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: MsrA; COG0225 940296004441 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: COG0229 940296004442 Competence-damaged protein; Region: CinA; pfam02464 940296004443 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 940296004444 Conserved TM helix; Region: TM_helix; pfam05552 940296004445 Mechanosensitive ion channel; Region: MS_channel; pfam00924 940296004446 ABC-type thiamine transport system, periplasmic component [Coenzyme metabolism]; Region: TbpA; COG4143 940296004447 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 940296004448 pyrimidine 5'-nucleotidase; Region: Pyr-5-nucltdase; TIGR01993 940296004449 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 940296004450 motif II; other site 940296004451 UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase; Region: glmU; TIGR01173 940296004452 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 940296004453 Substrate binding site; other site 940296004454 Mg++ binding site; other site 940296004455 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 940296004456 active site 940296004457 substrate binding site [chemical binding]; other site 940296004458 CoA binding site [chemical binding]; other site 940296004459 Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnA; COG2824 940296004460 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; pfam08274 940296004461 PhnA protein; Region: PhnA; pfam03831 940296004462 Tat-translocated enzyme; Region: tat_substr_1; TIGR01412 940296004463 Predicted iron-dependent peroxidase [Inorganic ion transport and metabolism]; Region: COG2837 940296004464 inactive ferrous ion transporter periplasmic protein EfeO; Provisional; Region: PRK10378 940296004465 Cupredoxin-like domain; Region: Cupredoxin_1; pfam13473 940296004466 Imelysin; Region: Peptidase_M75; pfam09375 940296004467 High-affinity Fe2+/Pb2+ permease [Inorganic ion transport and metabolism]; Region: FTR1; COG0672 940296004468 Membrane-bound lytic murein transglycosylase [Cell envelope biogenesis, outer membrane]; Region: MltA; COG2821 940296004469 MltA specific insert domain; Region: MltA; pfam03562 940296004470 3D domain; Region: 3D; pfam06725 940296004471 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 940296004472 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 940296004473 glutaminase active site [active] 940296004474 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 940296004475 dimer interface [polypeptide binding]; other site 940296004476 active site 940296004477 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 940296004478 dimer interface [polypeptide binding]; other site 940296004479 active site 940296004480 methionyl-tRNA synthetase; Reviewed; Region: metG; PRK00133 940296004481 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 940296004482 active site 940296004483 HIGH motif; other site 940296004484 KMSKS motif; other site 940296004485 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 940296004486 tRNA binding surface [nucleotide binding]; other site 940296004487 anticodon binding site; other site 940296004488 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 940296004489 dimer interface [polypeptide binding]; other site 940296004490 putative tRNA-binding site [nucleotide binding]; other site 940296004491 Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; Region: FDH_GDH_like; cl17240 940296004492 Pilin (bacterial filament); Region: Pilin; pfam00114 940296004493 Tfp pilus assembly protein, major pilin PilA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilA; COG4969 940296004494 Pilin (bacterial filament); Region: Pilin; pfam00114 940296004495 Tfp pilus assembly protein, major pilin PilA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilA; COG4969 940296004496 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 940296004497 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 940296004498 Pilin (bacterial filament); Region: Pilin; pfam00114 940296004499 Tfp pilus assembly protein, major pilin PilA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilA; COG4969 940296004500 Pilin (bacterial filament); Region: Pilin; pfam00114 940296004501 Tfp pilus assembly protein, major pilin PilA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilA; COG4969 940296004502 Pilin (bacterial filament); Region: Pilin; pfam00114 940296004503 Tfp pilus assembly protein, major pilin PilA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilA; COG4969 940296004504 Pilin (bacterial filament); Region: Pilin; pfam00114 940296004505 Tfp pilus assembly protein, major pilin PilA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilA; COG4969 940296004506 Pilin (bacterial filament); Region: Pilin; pfam00114 940296004507 Tfp pilus assembly protein, major pilin PilA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilA; COG4969 940296004508 Pilin (bacterial filament); Region: Pilin; pfam00114 940296004509 Tfp pilus assembly protein, major pilin PilA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilA; COG4969 940296004510 thiamine biosynthesis protein ThiC; Provisional; Region: PRK09284 940296004511 ThiC-associated domain; Region: ThiC-associated; pfam13667 940296004512 Thiamine biosynthesis protein ThiC [Coenzyme metabolism]; Region: ThiC; COG0422 940296004513 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belong to this superfamily requires a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly...; Region: Nudix_hydrolase_3; cd03676 940296004514 nudix motif; other site 940296004515 sulfate ABC transporter, ATP-binding protein; Region: 3a0106s01; TIGR00968 940296004516 ATP-binding cassette domain of the carbohydrate and solute transporters-like; Region: ABC_Carb_Solutes_like; cd03259 940296004517 Walker A/P-loop; other site 940296004518 ATP binding site [chemical binding]; other site 940296004519 Q-loop/lid; other site 940296004520 ABC transporter signature motif; other site 940296004521 Walker B; other site 940296004522 D-loop; other site 940296004523 H-loop/switch region; other site 940296004524 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 940296004525 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 940296004526 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 940296004527 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 940296004528 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 940296004529 dimerization domain swap beta strand [polypeptide binding]; other site 940296004530 regulatory protein interface [polypeptide binding]; other site 940296004531 active site 940296004532 regulatory phosphorylation site [posttranslational modification]; other site 940296004533 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 940296004534 active pocket/dimerization site; other site 940296004535 active site 940296004536 phosphorylation site [posttranslational modification] 940296004537 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 940296004538 active site 940296004539 DNA ligase; Provisional; Region: PRK09125 940296004540 Adenylation domain of kDNA ligases and similar proteins; Region: Adenylation_kDNA_ligase_like; cd07896 940296004541 DNA binding site [nucleotide binding] 940296004542 active site 940296004543 The Oligonucleotide/oligosaccharide binding (OB)-fold domain of kDNA ligase-like ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit; Region: OBF_kDNA_ligase_like; cd08041 940296004544 DNA binding site [nucleotide binding] 940296004545 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 940296004546 Predicted nuclease of restriction endonuclease-like fold, RmuC family [General function prediction only]; Region: COG1322 940296004547 RmuC family; Region: RmuC; pfam02646 940296004548 Cytochrome c1 [Energy production and conversion]; Region: CYT1; COG2857 940296004549 Cytochrome b subunit of the bc complex [Energy production and conversion]; Region: QcrB; COG1290 940296004550 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 940296004551 Qi binding site; other site 940296004552 intrachain domain interface; other site 940296004553 interchain domain interface [polypeptide binding]; other site 940296004554 heme bH binding site [chemical binding]; other site 940296004555 heme bL binding site [chemical binding]; other site 940296004556 Qo binding site; other site 940296004557 interchain domain interface [polypeptide binding]; other site 940296004558 intrachain domain interface; other site 940296004559 Qi binding site; other site 940296004560 Cytochrome b(C-terminal)/b6/petD; Region: Cytochrom_B_C; pfam00032 940296004561 Qo binding site; other site 940296004562 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 940296004563 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 940296004564 [2Fe-2S] cluster binding site [ion binding]; other site 940296004565 Uncharacterized conserved protein [Function unknown]; Region: COG0327 940296004566 NIF3 (NGG1p interacting factor 3); Region: NIF3; cl15371 940296004567 DNA-binding transcriptional regulator MetR; Provisional; Region: PRK15421 940296004568 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 940296004569 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 940296004570 putative dimerization interface [polypeptide binding]; other site 940296004571 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 940296004572 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 940296004573 23S rRNA interface [nucleotide binding]; other site 940296004574 L3 interface [polypeptide binding]; other site 940296004575 Cell division protein ZapA (stimulator of FtsZ polymerization and Z-ring component) [Cell cycle control, cell division, chromosome partitioning]; Region: zapA; COG3027 940296004576 Protein of unknown function (DUF3584); Region: DUF3584; pfam12128 940296004577 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 940296004578 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 940296004579 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 940296004580 Phosphoenolpyruvate carboxylase [Energy production and conversion]; Region: Ppc; COG2352 940296004581 phosphoenolpyruvate carboxylase; Reviewed; Region: PRK00009 940296004582 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 940296004583 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 940296004584 ATP binding site [chemical binding]; other site 940296004585 substrate interface [chemical binding]; other site 940296004586 Predicted permease [General function prediction only]; Region: COG2056 940296004587 Na+-H+ antiporter family; Region: Na_H_antiport_2; pfam13726 940296004588 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 940296004589 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 940296004590 S-adenosylmethionine binding site [chemical binding]; other site 940296004591 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 940296004592 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 940296004593 substrate binding pocket [chemical binding]; other site 940296004594 membrane-bound complex binding site; other site 940296004595 hinge residues; other site 940296004596 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 940296004597 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 940296004598 Walker A/P-loop; other site 940296004599 ATP binding site [chemical binding]; other site 940296004600 Q-loop/lid; other site 940296004601 ABC transporter signature motif; other site 940296004602 Walker B; other site 940296004603 D-loop; other site 940296004604 H-loop/switch region; other site 940296004605 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 940296004606 dimer interface [polypeptide binding]; other site 940296004607 conserved gate region; other site 940296004608 putative PBP binding loops; other site 940296004609 ABC-ATPase subunit interface; other site 940296004610 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 940296004611 dimer interface [polypeptide binding]; other site 940296004612 conserved gate region; other site 940296004613 putative PBP binding loops; other site 940296004614 ABC-ATPase subunit interface; other site 940296004615 protease TldD; Provisional; Region: tldD; PRK10735 940296004616 putative hydroxymethylpyrimidine transporter CytX; Region: thia_cytX; TIGR02358 940296004617 Na binding site [ion binding]; other site 940296004618 tRNA (uracil-5-)-methyltransferase Gid; Reviewed; Region: PRK05335 940296004619 glycine oxidase ThiO; Region: thiamin_ThiO; TIGR02352 940296004620 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 940296004621 thiamine phosphate binding site [chemical binding]; other site 940296004622 active site 940296004623 pyrophosphate binding site [ion binding]; other site 940296004624 Protein of unknown function (DUF1020); Region: DUF1020; pfam06255 940296004625 Protein of unknown function (DUF1020); Region: DUF1020; pfam06255 940296004626 Protein of unknown function (DUF1020); Region: DUF1020; pfam06255 940296004627 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 940296004628 thiS-thiF/thiG interaction site; other site 940296004629 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 940296004630 ThiS interaction site; other site 940296004631 putative active site [active] 940296004632 tetramer interface [polypeptide binding]; other site 940296004633 Sporulation related domain; Region: SPOR; pfam05036 940296004634 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/pantothenate kinase; Reviewed; Region: PRK13325 940296004635 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 940296004636 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 940296004637 Pantothenate kinase type III (Bvg accessory factor family protein) [Transcription]; Region: COG1521 940296004638 rfaE bifunctional protein, domain II; Region: rfaE_dom_II; TIGR02199 940296004639 Cytidylyltransferase; Region: CTP_transf_2; pfam01467 940296004640 active site 940296004641 HIGH motif; other site 940296004642 nucleotide binding site [chemical binding]; other site 940296004643 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK10792 940296004644 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 940296004645 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 940296004646 homodimer interface [polypeptide binding]; other site 940296004647 NADP binding site [chemical binding]; other site 940296004648 substrate binding site [chemical binding]; other site 940296004649 RDD family; Region: RDD; pfam06271 940296004650 aspartate-semialdehyde dehydrogenase; Reviewed; Region: PRK06598 940296004651 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 940296004652 Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Nape_like_AP-endo; cd10281 940296004653 putative active site [active] 940296004654 putative catalytic site [active] 940296004655 putative DNA binding site [nucleotide binding]; other site 940296004656 putative phosphate binding site [ion binding]; other site 940296004657 metal binding site A [ion binding]; metal-binding site 940296004658 putative AP binding site [nucleotide binding]; other site 940296004659 putative metal binding site B [ion binding]; other site 940296004660 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 940296004661 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 940296004662 active site 940296004663 HIGH motif; other site 940296004664 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 940296004665 KMSKS motif; other site 940296004666 Anticodon-binding domain of cysteinyl tRNA synthetases; Region: Anticodon_Ia_Cys; cd07963 940296004667 tRNA binding surface [nucleotide binding]; other site 940296004668 anticodon binding site; other site 940296004669 HaeII restriction endonuclease; Region: RE_HaeII; pfam09554 940296004670 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 940296004671 DNA-methyltransferase (dcm); Region: dcm; TIGR00675 940296004672 cofactor binding site; other site 940296004673 DNA binding site [nucleotide binding] 940296004674 substrate interaction site [chemical binding]; other site 940296004675 GTPase CgtA; Reviewed; Region: obgE; PRK12299 940296004676 GTP1/OBG; Region: GTP1_OBG; pfam01018 940296004677 Obg GTPase; Region: Obg; cd01898 940296004678 G1 box; other site 940296004679 GTP/Mg2+ binding site [chemical binding]; other site 940296004680 Switch I region; other site 940296004681 G2 box; other site 940296004682 G3 box; other site 940296004683 Switch II region; other site 940296004684 G4 box; other site 940296004685 G5 box; other site 940296004686 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 940296004687 Predicted methyltransferases [General function prediction only]; Region: COG0313 940296004688 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 940296004689 putative SAM binding site [chemical binding]; other site 940296004690 putative homodimer interface [polypeptide binding]; other site 940296004691 Predicted endonuclease distantly related to archaeal Holliday junction resolvase [DNA replication, recombination, and repair]; Region: COG0792 940296004692 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 940296004693 dimer interface [polypeptide binding]; other site 940296004694 active site 940296004695 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 940296004696 active site 940296004697 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 940296004698 non-specific DNA binding site [nucleotide binding]; other site 940296004699 salt bridge; other site 940296004700 sequence-specific DNA binding site [nucleotide binding]; other site 940296004701 malate:quinone-oxidoreductase; Region: mal_quin_oxido; TIGR01320 940296004702 malate:quinone oxidoreductase; Validated; Region: PRK05257 940296004703 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 940296004704 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 940296004705 rRNA interaction site [nucleotide binding]; other site 940296004706 S8 interaction site; other site 940296004707 putative laminin-1 binding site; other site 940296004708 elongation factor Ts; Provisional; Region: tsf; PRK09377 940296004709 UBA/TS-N domain; Region: UBA; pfam00627 940296004710 Elongation factor TS; Region: EF_TS; pfam00889 940296004711 Elongation factor TS; Region: EF_TS; pfam00889 940296004712 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 940296004713 putative nucleotide binding site [chemical binding]; other site 940296004714 uridine monophosphate binding site [chemical binding]; other site 940296004715 homohexameric interface [polypeptide binding]; other site 940296004716 Protein of unknown function (DUF1020); Region: DUF1020; pfam06255 940296004717 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; pfam09346 940296004718 Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: SppA; COG0616 940296004719 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 940296004720 tandem repeat interface [polypeptide binding]; other site 940296004721 oligomer interface [polypeptide binding]; other site 940296004722 active site residues [active] 940296004723 Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]; Region: CinA; COG1058 940296004724 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 940296004725 putative MPT binding site; other site 940296004726 argininosuccinate synthase; Validated; Region: PRK05370 940296004727 argininosuccinate synthase; Provisional; Region: PRK13820 940296004728 Domain of unknown function (DUF4177); Region: DUF4177; pfam13783 940296004729 Transferrin binding protein-like solute binding protein; Region: Lipoprotein_5; pfam01298 940296004730 serine/threonine transporter SstT; Provisional; Region: PRK13628 940296004731 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 940296004732 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 940296004733 Surface antigen; Region: Bac_surface_Ag; pfam01103 940296004734 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2911 940296004735 Family of unknown function (DUF490); Region: DUF490; pfam04357 940296004736 Family of unknown function (DUF490); Region: DUF490; pfam04357 940296004737 Family of unknown function (DUF490); Region: DUF490; pfam04357 940296004738 POT family; Region: PTR2; cl17359 940296004739 amino acid/peptide transporter (Peptide:H+ symporter), bacterial; Region: yjdL_sub1_fam; TIGR00924 940296004740 peptide chain release factor 2; Validated; Region: prfB; PRK00578 940296004741 This domain is found in peptide chain release factors; Region: PCRF; smart00937 940296004742 RF-1 domain; Region: RF-1; pfam00472 940296004743 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 940296004744 Patatin-like phospholipase domain containing protein 6, protein 7, and fungal NTE1; Region: Pat_PNPLA6_PNPLA7_NTE1_like; cd07205 940296004745 active site 940296004746 nucleophile elbow; other site 940296004747 Predicted membrane protein [Function unknown]; Region: COG2259 940296004748 Protein of unknown function (DUF692); Region: DUF692; pfam05114 940296004749 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3219 940296004750 RNA polymerase sigma factor; Provisional; Region: PRK12532 940296004751 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 940296004752 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 940296004753 DNA binding residues [nucleotide binding] 940296004754 Putative zinc-finger; Region: zf-HC2; pfam13490 940296004755 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 940296004756 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 940296004757 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 940296004758 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 940296004759 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 940296004760 Domain of unknown function (DUF4298); Region: DUF4298; pfam14131 940296004761 Uncharacterized conserved protein [Function unknown]; Region: COG1739 940296004762 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 940296004763 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 940296004764 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 940296004765 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 940296004766 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 940296004767 Ligand binding site [chemical binding]; other site 940296004768 Electron transfer flavoprotein domain; Region: ETF; pfam01012 940296004769 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 940296004770 Glycosyltransferase family 9 (heptosyltransferase); Region: Glyco_transf_9; pfam01075 940296004771 putative active site [active] 940296004772 Nicotinamidase/pyrazinamidase (PZase). Nicotinamidase, a ubiquitous enzyme in prokaryotes, converts nicotinamide to nicotinic acid (niacin) and ammonia, which in turn can be recycled to make nicotinamide adenine dinucleotide (NAD). The same enzyme is...; Region: nicotinamidase; cd01011 940296004773 Isochorismatase family; Region: Isochorismatase; pfam00857 940296004774 catalytic triad [active] 940296004775 metal binding site [ion binding]; metal-binding site 940296004776 conserved cis-peptide bond; other site 940296004777 Escherichia coli YaeB and related proteins; Region: UPF0066; cd09281 940296004778 homodimer interaction site [polypeptide binding]; other site 940296004779 cofactor binding site; other site 940296004780 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 940296004781 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 940296004782 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 940296004783 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 940296004784 MutS domain I; Region: MutS_I; pfam01624 940296004785 MutS domain II; Region: MutS_II; pfam05188 940296004786 MutS domain III; Region: MutS_III; pfam05192 940296004787 MutS domain V; Region: MutS_V; pfam00488 940296004788 Walker A/P-loop; other site 940296004789 ATP binding site [chemical binding]; other site 940296004790 Q-loop/lid; other site 940296004791 ABC transporter signature motif; other site 940296004792 Walker B; other site 940296004793 D-loop; other site 940296004794 H-loop/switch region; other site 940296004795 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 940296004796 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 940296004797 Coenzyme A binding pocket [chemical binding]; other site 940296004798 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 940296004799 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 940296004800 active site 940296004801 HIGH motif; other site 940296004802 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 940296004803 active site 940296004804 KMSKS motif; other site 940296004805 Uncharacterized conserved protein [Function unknown]; Region: COG1434 940296004806 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 940296004807 putative active site [active] 940296004808 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 940296004809 ArsC family; Region: ArsC; pfam03960 940296004810 catalytic residues [active] 940296004811 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 940296004812 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 940296004813 catalytic residues [active] 940296004814 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 940296004815 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 940296004816 Walker A/P-loop; other site 940296004817 ATP binding site [chemical binding]; other site 940296004818 Q-loop/lid; other site 940296004819 ABC transporter signature motif; other site 940296004820 Walker B; other site 940296004821 D-loop; other site 940296004822 H-loop/switch region; other site 940296004823 putative protein insertion permease FtsX; Region: ftsX; TIGR00439 940296004824 cell division ABC transporter subunit FtsX; Provisional; Region: ftsX; PRK11026 940296004825 Predicted transcriptional regulator, BolA superfamily [Transcription]; Region: COG5007 940296004826 phosphoglycerate kinase; Provisional; Region: pgk; PRK00073 940296004827 Phosphoglycerate kinase; Region: PGK; pfam00162 940296004828 substrate binding site [chemical binding]; other site 940296004829 hinge regions; other site 940296004830 ADP binding site [chemical binding]; other site 940296004831 catalytic site [active] 940296004832 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 940296004833 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 940296004834 hinge; other site 940296004835 active site 940296004836 integral membrane protein, TerC family; Region: R_switched_Alx; TIGR03718 940296004837 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3399 940296004838 3-deoxy-D-manno-octulosonic-acid transferase [Cell envelope biogenesis, outer membrane]; Region: KdtA; COG1519 940296004839 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 940296004840 6-phosphogluconate dehydrogenase [Carbohydrate transport and metabolism]; Region: Gnd; COG0362 940296004841 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 940296004842 6-phosphogluconate dehydrogenase, C-terminal domain; Region: 6PGD; pfam00393 940296004843 Tfp pilus assembly protein, tip-associated adhesin PilY1 [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilY1; COG3419 940296004844 Tfp pilus assembly protein, tip-associated adhesin PilY1 [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilY1; COG3419 940296004845 Neisseria PilC beta-propeller domain; Region: Neisseria_PilC; pfam05567 940296004846 Neisseria PilC beta-propeller domain; Region: Neisseria_PilC; pfam05567 940296004847 Tfp pilus assembly protein, tip-associated adhesin PilY1 [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilY1; COG3419 940296004848 Neisseria PilC beta-propeller domain; Region: Neisseria_PilC; pfam05567 940296004849 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; Region: GIY-YIG_unchar_3; cd10448 940296004850 putative active site [active] 940296004851 putative metal binding site [ion binding]; other site 940296004852 TIGR01666 family membrane protein; Region: YCCS 940296004853 FUSC-like inner membrane protein yccS; Region: FUSC-like; pfam12805 940296004854 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 940296004855 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 940296004856 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 940296004857 Walker A motif; other site 940296004858 ATP binding site [chemical binding]; other site 940296004859 Walker B motif; other site 940296004860 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 940296004861 SPOC domain; Region: SPOC; pfam07744 940296004862 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 940296004863 Walker A motif; other site 940296004864 ATP binding site [chemical binding]; other site 940296004865 Walker B motif; other site 940296004866 Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins; Region: PLPDE_III_Yggs_like; cd06824 940296004867 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 940296004868 catalytic residue [active] 940296004869 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 940296004870 pyrroline-5-carboxylate reductase; Region: proC; TIGR00112 940296004871 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 940296004872 comEA protein; Region: comE; TIGR01259 940296004873 Helix-hairpin-helix motif; Region: HHH; pfam00633 940296004874 Transposase domain (DUF772); Region: DUF772; pfam05598 940296004875 chaperone protein DnaJ; Provisional; Region: PRK10767 940296004876 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 940296004877 HSP70 interaction site [polypeptide binding]; other site 940296004878 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 940296004879 substrate binding site [polypeptide binding]; other site 940296004880 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 940296004881 Zn binding sites [ion binding]; other site 940296004882 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 940296004883 dimer interface [polypeptide binding]; other site 940296004884 Predicted membrane protein [Function unknown]; Region: COG1297 940296004885 putative oligopeptide transporter, OPT family; Region: TIGR00733 940296004886 dTDP-4-dehydrorhamnose 3,5-epimerase; Region: rmlC; TIGR01221 940296004887 G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase; Region: G1P_TT_short; cd02538 940296004888 glucose-1-phosphate thymidylyltransferase, short form; Region: rmlA; TIGR01207 940296004889 substrate binding site; other site 940296004890 tetramer interface; other site 940296004891 dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: dTDP_GD_SDR_e; cd05246 940296004892 dTDP-glucose 4,6 dehydratase; Provisional; Region: PRK10084 940296004893 NAD binding site [chemical binding]; other site 940296004894 substrate binding site [chemical binding]; other site 940296004895 homodimer interface [polypeptide binding]; other site 940296004896 active site 940296004897 UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]; Region: GalE; COG1087 940296004898 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 940296004899 NAD binding site [chemical binding]; other site 940296004900 homodimer interface [polypeptide binding]; other site 940296004901 active site 940296004902 substrate binding site [chemical binding]; other site 940296004903 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 940296004904 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 940296004905 Likely ribonuclease with RNase H fold; Region: YqgFc; smart00732 940296004906 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 940296004907 RNA binding site [nucleotide binding]; other site 940296004908 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 940296004909 DNA-methyltransferase (dcm); Region: dcm; TIGR00675 940296004910 cofactor binding site; other site 940296004911 DNA binding site [nucleotide binding] 940296004912 substrate interaction site [chemical binding]; other site 940296004913 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG3392 940296004914 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; pfam02086 940296004915 HNH endonuclease; Region: HNH_2; pfam13391 940296004916 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 940296004917 Na+/glutamate symporter [Amino acid transport and metabolism]; Region: GltS; COG0786 940296004918 Protein of unknown function (DUF1311); Region: DUF1311; cl01530 940296004919 Long-chain fatty acid transport protein [Lipid metabolism]; Region: FadL; COG2067 940296004920 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; cl17479 940296004921 pyruvate kinase; Provisional; Region: PRK05826 940296004922 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl17342 940296004923 domain interfaces; other site 940296004924 active site 940296004925 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 940296004926 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 940296004927 HlyD family secretion protein; Region: HlyD_3; pfam13437 940296004928 ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]; Region: SunT; COG2274 940296004929 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_C39C; cd02419 940296004930 putative active site [active] 940296004931 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 940296004932 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 940296004933 Walker A/P-loop; other site 940296004934 ATP binding site [chemical binding]; other site 940296004935 Q-loop/lid; other site 940296004936 ABC transporter signature motif; other site 940296004937 Walker B; other site 940296004938 D-loop; other site 940296004939 H-loop/switch region; other site 940296004940 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 940296004941 putative active site [active] 940296004942 Protein of unknown function (DUF3579); Region: DUF3579; pfam12112 940296004943 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 940296004944 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 940296004945 Coenzyme A binding pocket [chemical binding]; other site 940296004946 Aspartate carbamoyltransferase, catalytic chain [Nucleotide transport and metabolism]; Region: PyrB; COG0540 940296004947 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 940296004948 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 940296004949 aspartate carbamoyltransferase regulatory subunit; Reviewed; Region: PRK00893 940296004950 Aspartate carbamoyltransferase regulatory chain, allosteric domain; Region: PyrI; pfam01948 940296004951 Aspartate carbamoyltransferase regulatory chain, metal binding domain; Region: PyrI_C; pfam02748 940296004952 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 940296004953 Uncharacterized protein containing LysM domain [Function unknown]; Region: XkdP; COG1652 940296004954 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 940296004955 active site 940296004956 catalytic residues [active] 940296004957 metal binding site [ion binding]; metal-binding site 940296004958 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 940296004959 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 940296004960 putative active site [active] 940296004961 substrate binding site [chemical binding]; other site 940296004962 putative cosubstrate binding site; other site 940296004963 catalytic site [active] 940296004964 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 940296004965 substrate binding site [chemical binding]; other site 940296004966 16S rRNA methyltransferase B; Provisional; Region: PRK10901 940296004967 NusB family; Region: NusB; pfam01029 940296004968 putative RNA binding site [nucleotide binding]; other site 940296004969 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 940296004970 S-adenosylmethionine binding site [chemical binding]; other site 940296004971 Domain of unknown function (DUF4390); Region: DUF4390; pfam14334 940296004972 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 940296004973 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 940296004974 dimerization interface [polypeptide binding]; other site 940296004975 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 940296004976 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 940296004977 dimer interface [polypeptide binding]; other site 940296004978 phosphorylation site [posttranslational modification] 940296004979 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 940296004980 ATP binding site [chemical binding]; other site 940296004981 Mg2+ binding site [ion binding]; other site 940296004982 G-X-G motif; other site 940296004983 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 940296004984 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 940296004985 active site 940296004986 phosphorylation site [posttranslational modification] 940296004987 intermolecular recognition site; other site 940296004988 dimerization interface [polypeptide binding]; other site 940296004989 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 940296004990 Predicted transcriptional regulator [Transcription]; Region: COG3636; cl17681 940296004991 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 940296004992 DNA protecting protein DprA; Region: dprA; TIGR00732 940296004993 Protein of unknown function (DUF494); Region: DUF494; cl01103 940296004994 DNA topoisomerase I; Validated; Region: PRK06599 940296004995 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 940296004996 active site 940296004997 interdomain interaction site; other site 940296004998 putative metal-binding site [ion binding]; other site 940296004999 nucleotide binding site [chemical binding]; other site 940296005000 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 940296005001 domain I; other site 940296005002 DNA binding groove [nucleotide binding] 940296005003 phosphate binding site [ion binding]; other site 940296005004 domain II; other site 940296005005 domain III; other site 940296005006 nucleotide binding site [chemical binding]; other site 940296005007 catalytic site [active] 940296005008 domain IV; other site 940296005009 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 940296005010 Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]; Region: TopA; COG0551 940296005011 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 940296005012 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 940296005013 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl17254 940296005014 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 940296005015 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 940296005016 S-adenosylmethionine binding site [chemical binding]; other site 940296005017 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 940296005018 elongation factor Tu; Reviewed; Region: PRK00049 940296005019 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 940296005020 G1 box; other site 940296005021 GEF interaction site [polypeptide binding]; other site 940296005022 GTP/Mg2+ binding site [chemical binding]; other site 940296005023 Switch I region; other site 940296005024 G2 box; other site 940296005025 G3 box; other site 940296005026 Switch II region; other site 940296005027 G4 box; other site 940296005028 G5 box; other site 940296005029 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 940296005030 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 940296005031 Antibiotic Binding Site [chemical binding]; other site 940296005032 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 940296005033 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 940296005034 L7/L12 interface [polypeptide binding]; other site 940296005035 23S rRNA interface [nucleotide binding]; other site 940296005036 L25 interface [polypeptide binding]; other site 940296005037 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 940296005038 50S ribosomal protein L10; Reviewed; Region: rplJ; PRK00099 940296005039 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 940296005040 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 940296005041 core dimer interface [polypeptide binding]; other site 940296005042 peripheral dimer interface [polypeptide binding]; other site 940296005043 L10 interface [polypeptide binding]; other site 940296005044 L11 interface [polypeptide binding]; other site 940296005045 putative EF-Tu interaction site [polypeptide binding]; other site 940296005046 putative EF-G interaction site [polypeptide binding]; other site 940296005047 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 940296005048 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 940296005049 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 940296005050 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 940296005051 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 940296005052 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 940296005053 RPB3 interaction site [polypeptide binding]; other site 940296005054 RPB1 interaction site [polypeptide binding]; other site 940296005055 RPB11 interaction site [polypeptide binding]; other site 940296005056 RPB10 interaction site [polypeptide binding]; other site 940296005057 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 940296005058 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 940296005059 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 940296005060 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 940296005061 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 940296005062 RNA polymerase Rpb1, domain 5; Region: RNA_pol_Rpb1_5; pfam04998 940296005063 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 940296005064 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 940296005065 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 940296005066 DNA binding site [nucleotide binding] 940296005067 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 940296005068 Protein of unknown function (DUF560); Region: DUF560; pfam04575 940296005069 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 940296005070 S17 interaction site [polypeptide binding]; other site 940296005071 16S rRNA interaction site [nucleotide binding]; other site 940296005072 streptomycin interaction site [chemical binding]; other site 940296005073 23S rRNA interaction site [nucleotide binding]; other site 940296005074 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 940296005075 30S ribosomal protein S7; Validated; Region: PRK05302 940296005076 elongation factor G; Reviewed; Region: PRK00007 940296005077 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 940296005078 G1 box; other site 940296005079 putative GEF interaction site [polypeptide binding]; other site 940296005080 GTP/Mg2+ binding site [chemical binding]; other site 940296005081 Switch I region; other site 940296005082 G2 box; other site 940296005083 G3 box; other site 940296005084 Switch II region; other site 940296005085 G4 box; other site 940296005086 G5 box; other site 940296005087 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 940296005088 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 940296005089 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 940296005090 elongation factor Tu; Reviewed; Region: PRK00049 940296005091 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 940296005092 G1 box; other site 940296005093 GEF interaction site [polypeptide binding]; other site 940296005094 GTP/Mg2+ binding site [chemical binding]; other site 940296005095 Switch I region; other site 940296005096 G2 box; other site 940296005097 G3 box; other site 940296005098 Switch II region; other site 940296005099 G4 box; other site 940296005100 G5 box; other site 940296005101 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 940296005102 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 940296005103 Antibiotic Binding Site [chemical binding]; other site 940296005104 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 940296005105 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 940296005106 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 940296005107 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 940296005108 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 940296005109 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 940296005110 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 940296005111 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 940296005112 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 940296005113 protein-rRNA interface [nucleotide binding]; other site 940296005114 putative translocon binding site; other site 940296005115 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 940296005116 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 940296005117 G-X-X-G motif; other site 940296005118 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 940296005119 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 940296005120 23S rRNA interface [nucleotide binding]; other site 940296005121 putative translocon interaction site; other site 940296005122 signal recognition particle (SRP54) interaction site; other site 940296005123 L23 interface [polypeptide binding]; other site 940296005124 trigger factor interaction site; other site 940296005125 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 940296005126 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 940296005127 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 940296005128 KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); Region: KOW; cl00354 940296005129 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 940296005130 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 940296005131 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 940296005132 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 940296005133 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 940296005134 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 940296005135 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 940296005136 SecY translocase; Region: SecY; pfam00344 940296005137 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 940296005138 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 940296005139 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 940296005140 RNA binding surface [nucleotide binding]; other site 940296005141 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 940296005142 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 940296005143 alphaNTD homodimer interface [polypeptide binding]; other site 940296005144 alphaNTD - beta interaction site [polypeptide binding]; other site 940296005145 alphaNTD - beta' interaction site [polypeptide binding]; other site 940296005146 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 940296005147 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 940296005148 septum formation inhibitor; Reviewed; Region: minC; PRK04516 940296005149 Septum formation inhibitor MinC, N-terminal domain; Region: MinC_N; pfam05209 940296005150 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 940296005151 Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]; Region: MinD; COG2894 940296005152 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 940296005153 Switch I; other site 940296005154 Switch II; other site 940296005155 cell division topological specificity factor MinE; Provisional; Region: PRK13989 940296005156 Transcriptional regulator [Transcription]; Region: LysR; COG0583 940296005157 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 940296005158 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 940296005159 dimerization interface [polypeptide binding]; other site 940296005160 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 940296005161 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 940296005162 eyelet of channel; other site 940296005163 trimer interface [polypeptide binding]; other site 940296005164 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 940296005165 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 940296005166 dimerization interface 3.5A [polypeptide binding]; other site 940296005167 active site 940296005168 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 940296005169 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 940296005170 HIGH motif; other site 940296005171 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 940296005172 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 940296005173 active site 940296005174 KMSKS motif; other site 940296005175 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 940296005176 tRNA binding surface [nucleotide binding]; other site 940296005177 anticodon binding site; other site 940296005178 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 940296005179 D-amino acid dehydrogenase small subunit; Validated; Region: PRK00711 940296005180 hydroxyglutarate oxidase; Provisional; Region: PRK11728 940296005181 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 940296005182 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 940296005183 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 940296005184 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 940296005185 active site 940296005186 Abi-like protein; Region: Abi_2; cl01988 940296005187 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 940296005188 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 940296005189 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 940296005190 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 940296005191 trimer interface [polypeptide binding]; other site 940296005192 active site 940296005193 UDP-GlcNAc binding site [chemical binding]; other site 940296005194 lipid binding site [chemical binding]; lipid-binding site 940296005195 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: HlpA; COG2825 940296005196 periplasmic chaperone; Provisional; Region: PRK10780 940296005197 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 940296005198 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 940296005199 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 940296005200 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 940296005201 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 940296005202 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 940296005203 Surface antigen; Region: Bac_surface_Ag; pfam01103 940296005204 zinc metallopeptidase RseP; Provisional; Region: PRK10779 940296005205 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 940296005206 active site 940296005207 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 940296005208 protein binding site [polypeptide binding]; other site 940296005209 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 940296005210 protein binding site [polypeptide binding]; other site 940296005211 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 940296005212 putative substrate binding region [chemical binding]; other site 940296005213 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 940296005214 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 940296005215 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 940296005216 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 940296005217 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 940296005218 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 940296005219 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 940296005220 Undecaprenyl pyrophosphate synthase [Lipid metabolism]; Region: UppS; COG0020 940296005221 catalytic residue [active] 940296005222 putative FPP diphosphate binding site; other site 940296005223 putative FPP binding hydrophobic cleft; other site 940296005224 dimer interface [polypeptide binding]; other site 940296005225 putative IPP diphosphate binding site; other site 940296005226 ribosome recycling factor; Reviewed; Region: frr; PRK00083 940296005227 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 940296005228 hinge region; other site 940296005229 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 940296005230 C-5 cytosine-specific DNA methylase; Region: DNA_methylase; pfam00145 940296005231 cofactor binding site; other site 940296005232 DNA binding site [nucleotide binding] 940296005233 substrate interaction site [chemical binding]; other site 940296005234 Predicted membrane protein [Function unknown]; Region: COG1289 940296005235 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 940296005236 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 940296005237 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 940296005238 S-adenosylmethionine binding site [chemical binding]; other site 940296005239 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 940296005240 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 940296005241 P-loop; other site 940296005242 Magnesium ion binding site [ion binding]; other site 940296005243 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 940296005244 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 940296005245 Magnesium ion binding site [ion binding]; other site 940296005246 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 940296005247 RNA/DNA hybrid binding site [nucleotide binding]; other site 940296005248 active site 940296005249 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 940296005250 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 940296005251 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 940296005252 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 940296005253 Sodium:alanine symporter family; Region: Na_Ala_symp; pfam01235 940296005254 4-hydroxythreonine-4-phosphate dehydrogenase; Reviewed; Region: pdxA; PRK00232 940296005255 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 940296005256 Ribonucleases G and E [Translation, ribosomal structure and biogenesis]; Region: CafA; COG1530 940296005257 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 940296005258 homodimer interface [polypeptide binding]; other site 940296005259 oligonucleotide binding site [chemical binding]; other site 940296005260 23S rRNA pseudouridylate synthase C; Provisional; Region: PRK11025 940296005261 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 940296005262 RNA binding surface [nucleotide binding]; other site 940296005263 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 940296005264 active site 940296005265 Lipid A disaccharide synthetase [Cell envelope biogenesis, outer membrane]; Region: LpxB; COG0763 940296005266 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 940296005267 dihydrodipicolinate reductase; Provisional; Region: PRK00048 940296005268 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 940296005269 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 940296005270 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 940296005271 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 940296005272 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 940296005273 metal binding site 2 [ion binding]; metal-binding site 940296005274 putative DNA binding helix; other site 940296005275 metal binding site 1 [ion binding]; metal-binding site 940296005276 dimer interface [polypeptide binding]; other site 940296005277 structural Zn2+ binding site [ion binding]; other site 940296005278 Leu/Phe-tRNA-protein transferase [Posttranslational modification, protein turnover, chaperones]; Region: Aat; COG2360 940296005279 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 940296005280 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 940296005281 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 940296005282 ferredoxin; Provisional; Region: PRK08764 940296005283 Putative Fe-S cluster; Region: FeS; cl17515 940296005284 4Fe-4S binding domain; Region: Fer4; pfam00037 940296005285 4Fe-4S binding domain; Region: Fer4; pfam00037 940296005286 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 940296005287 putative cation:proton antiport protein; Provisional; Region: PRK10669 940296005288 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 940296005289 TrkA-N domain; Region: TrkA_N; pfam02254 940296005290 TrkA-C domain; Region: TrkA_C; pfam02080 940296005291 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG3392 940296005292 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 940296005293 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 940296005294 Serine dehydratase alpha chain; Region: SDH_alpha; pfam03313 940296005295 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 940296005296 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 940296005297 Mg2+ binding site [ion binding]; other site 940296005298 G-X-G motif; other site 940296005299 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 940296005300 anchoring element; other site 940296005301 dimer interface [polypeptide binding]; other site 940296005302 ATP binding site [chemical binding]; other site 940296005303 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 940296005304 active site 940296005305 putative metal-binding site [ion binding]; other site 940296005306 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 940296005307 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 940296005308 Mechanosensitive ion channel; Region: MS_channel; pfam00924 940296005309 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 940296005310 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 940296005311 active site 940296005312 Zn binding site [ion binding]; other site 940296005313 Di-haem cytochrome c peroxidase; Region: CCP_MauG; pfam03150 940296005314 Predicted membrane protein [Function unknown]; Region: COG1971 940296005315 Domain of unknown function DUF; Region: DUF204; pfam02659 940296005316 Domain of unknown function DUF; Region: DUF204; pfam02659 940296005317 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 940296005318 Clade 3 of the heme-binding enzyme catalase; Region: catalase_clade_3; cd08156 940296005319 tetramer interface [polypeptide binding]; other site 940296005320 heme binding pocket [chemical binding]; other site 940296005321 NADPH binding site [chemical binding]; other site 940296005322 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 940296005323 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 940296005324 This family is most closely related to the GT1 family of glycosyltransferases. cap1E in Streptococcus pneumoniae is required for the synthesis of type 1 capsular polysaccharides; Region: GT1_cap1E_like; cd03808 940296005325 putative ADP-binding pocket [chemical binding]; other site 940296005326 Major Facilitator Superfamily; Region: MFS_1; pfam07690 940296005327 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 940296005328 putative substrate translocation pore; other site 940296005329 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 940296005330 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 940296005331 dimer interface [polypeptide binding]; other site 940296005332 active site 940296005333 acyl carrier protein; Provisional; Region: acpP; PRK00982 940296005334 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK05286 940296005335 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 940296005336 quinone interaction residues [chemical binding]; other site 940296005337 active site 940296005338 catalytic residues [active] 940296005339 FMN binding site [chemical binding]; other site 940296005340 substrate binding site [chemical binding]; other site 940296005341 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4304 940296005342 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed; Region: PRK11072 940296005343 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 940296005344 metal binding triad; other site 940296005345 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 940296005346 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 940296005347 metal binding triad; other site 940296005348 DNA helicase II; Region: uvrD; TIGR01075 940296005349 Part of AAA domain; Region: AAA_19; pfam13245 940296005350 Family description; Region: UvrD_C_2; pfam13538 940296005351 Bacterial mobilisation protein (MobC); Region: MobC; pfam05713 940296005352 Replicase family; Region: Replicase; pfam03090 940296005353 Primase C terminal 1 (PriCT-1); Region: PriCT_1; pfam08708 940296005354 HTH domain; Region: HTH_11; cl17392 940296005355 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG1451 940296005356 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 940296005357 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 940296005358 putative acyl-acceptor binding pocket; other site 940296005359 D,D-heptose 1,7-bisphosphate phosphatase; Validated; Region: PRK08942 940296005360 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 940296005361 active site 940296005362 motif I; other site 940296005363 motif II; other site 940296005364 Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]; Region: MdoB; COG1368 940296005365 Sulfatase; Region: Sulfatase; cl17466 940296005366 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 940296005367 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 940296005368 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 940296005369 aromatic amino acid transport protein; Region: araaP; TIGR00837 940296005370 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 940296005371 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 940296005372 S-adenosylmethionine binding site [chemical binding]; other site 940296005373 Putative homoserine kinase type II (protein kinase fold) [General function prediction only]; Region: COG2334 940296005374 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 940296005375 putative active site [active] 940296005376 putative substrate binding site [chemical binding]; other site 940296005377 ATP binding site [chemical binding]; other site 940296005378 Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate. The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits; Region: GntK; cd02021 940296005379 ATP-binding site [chemical binding]; other site 940296005380 Gluconate-6-phosphate binding site [chemical binding]; other site 940296005381 H+/gluconate symporter and related permeases [Carbohydrate transport and metabolism / Amino acid transport and metabolism]; Region: GntT; COG2610 940296005382 fructuronate transporter; Provisional; Region: PRK10034; cl15264 940296005383 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 940296005384 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 940296005385 dimer interface [polypeptide binding]; other site 940296005386 conserved gate region; other site 940296005387 ABC-ATPase subunit interface; other site 940296005388 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 940296005389 dimer interface [polypeptide binding]; other site 940296005390 ABC-ATPase subunit interface; other site 940296005391 putative PBP binding loops; other site 940296005392 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_cladeD; cd03379 940296005393 active site clefts [active] 940296005394 zinc binding site [ion binding]; other site 940296005395 dimer interface [polypeptide binding]; other site 940296005396 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 940296005397 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 940296005398 active site 940296005399 (T/H)XGH motif; other site 940296005400 iojap-like ribosome-associated protein; Region: iojap_ybeB; TIGR00090 940296005401 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 940296005402 oxidative damage protection protein; Provisional; Region: PRK05408 940296005403 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 940296005404 YccA-like proteins; Region: YccA_like; cd10433 940296005405 pantetheine-phosphate adenylyltransferase, bacterial; Region: coaD_prev_kdtB; TIGR01510 940296005406 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 940296005407 active site 940296005408 (T/H)XGH motif; other site 940296005409 YadA-like, left-handed beta-roll; Region: LbR_YadA-like; cd12820 940296005410 trimer interface [polypeptide binding]; other site 940296005411 YadA-like, left-handed beta-roll; Region: LbR_YadA-like; cd12820 940296005412 trimer interface [polypeptide binding]; other site 940296005413 Haemagglutinin; Region: HIM; pfam05662 940296005414 YadA-like C-terminal region; Region: YadA; pfam03895 940296005415 ABC-type enterochelin transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CeuD; COG4604 940296005416 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 940296005417 Walker A/P-loop; other site 940296005418 ATP binding site [chemical binding]; other site 940296005419 Q-loop/lid; other site 940296005420 ABC transporter signature motif; other site 940296005421 Walker B; other site 940296005422 D-loop; other site 940296005423 H-loop/switch region; other site 940296005424 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]; Region: COG2191 940296005425 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 940296005426 ABC-ATPase subunit interface; other site 940296005427 dimer interface [polypeptide binding]; other site 940296005428 putative PBP binding regions; other site 940296005429 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 940296005430 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 940296005431 ABC-ATPase subunit interface; other site 940296005432 dimer interface [polypeptide binding]; other site 940296005433 putative PBP binding regions; other site 940296005434 ABC-type enterochelin transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: CeuA; COG4607 940296005435 Siderophore binding protein FatB. These proteins have been shown to function as ABC-type initial receptors in the siderophore-mediated iron uptake in some eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins...; Region: FatB; cd01140 940296005436 putative ligand binding residues [chemical binding]; other site 940296005437 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 940296005438 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 940296005439 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 940296005440 oligomerisation interface [polypeptide binding]; other site 940296005441 mobile loop; other site 940296005442 roof hairpin; other site 940296005443 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 940296005444 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 940296005445 ring oligomerisation interface [polypeptide binding]; other site 940296005446 ATP/Mg binding site [chemical binding]; other site 940296005447 stacking interactions; other site 940296005448 hinge regions; other site 940296005449 uncharacterized bacterial and archaeal solute carrier 6 subfamily; solute-binding domain; Region: SLC6sbd_u1; cd10334 940296005450 Na2 binding site [ion binding]; other site 940296005451 putative substrate binding site 1 [chemical binding]; other site 940296005452 Na binding site 1 [ion binding]; other site 940296005453 putative substrate binding site 2 [chemical binding]; other site 940296005454 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2849 940296005455 diaminopimelate decarboxylase; Region: lysA; TIGR01048 940296005456 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 940296005457 active site 940296005458 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 940296005459 substrate binding site [chemical binding]; other site 940296005460 catalytic residues [active] 940296005461 dimer interface [polypeptide binding]; other site 940296005462 Frataxin is a nuclear-encoded mitochondrial protein implicated in Friedreich's ataxia (FRDA), an human autosomal recessive neurodegenerative disease; Frataxin is found in eukaryotes and in purple bacteria; lack of frataxin causes iron to accumulate...; Region: Frataxin; cd00503 940296005463 putative iron binding site [ion binding]; other site 940296005464 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4316 940296005465 S-ribosylhomocysteinase; Provisional; Region: PRK02260 940296005466 DNA polymerase I; Provisional; Region: PRK05755 940296005467 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 940296005468 active site 940296005469 putative 5' ssDNA interaction site; other site 940296005470 metal binding site 3; metal-binding site 940296005471 metal binding site 1 [ion binding]; metal-binding site 940296005472 metal binding site 2 [ion binding]; metal-binding site 940296005473 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 940296005474 putative DNA binding site [nucleotide binding]; other site 940296005475 putative metal binding site [ion binding]; other site 940296005476 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 940296005477 active site 940296005478 catalytic site [active] 940296005479 substrate binding site [chemical binding]; other site 940296005480 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 940296005481 active site 940296005482 DNA binding site [nucleotide binding] 940296005483 catalytic site [active] 940296005484 Fic/DOC family; Region: Fic; pfam02661 940296005485 Immunoglobulin A1 protease; Region: Peptidase_S6; pfam02395 940296005486 Pertactin-like passenger domains (virulence factors), C-terminal, subgroup 1, of autotransporter proteins of the type V secretion system of Gram-negative bacteria. This subgroup includes the passenger domains of Neisseria and Haemophilus IgA1 proteases; Region: PL1_Passenger_AT; cd01343 940296005487 Autotransporter beta-domain; Region: Autotransporter; pfam03797 940296005488 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 940296005489 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 940296005490 trmE is a tRNA modification GTPase; Region: trmE; cd04164 940296005491 G1 box; other site 940296005492 GTP/Mg2+ binding site [chemical binding]; other site 940296005493 Switch I region; other site 940296005494 G2 box; other site 940296005495 Switch II region; other site 940296005496 G3 box; other site 940296005497 G4 box; other site 940296005498 G5 box; other site 940296005499 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 940296005500 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 940296005501 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 940296005502 N-terminal plug; other site 940296005503 ligand-binding site [chemical binding]; other site 940296005504 Protein of unknown function (DUF560); Region: DUF560; pfam04575 940296005505 aminodeoxychorismate synthase; Provisional; Region: PRK07508 940296005506 chorismate binding enzyme; Region: Chorismate_bind; cl10555 940296005507 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 940296005508 homodimer interface [polypeptide binding]; other site 940296005509 substrate-cofactor binding pocket; other site 940296005510 Aminotransferase class IV; Region: Aminotran_4; pfam01063 940296005511 pyridoxal 5'-phosphate binding site [chemical binding]; other site 940296005512 catalytic residue [active] 940296005513 polyphosphate kinase 2, PA0141 family; Region: PPK2_P_aer; TIGR03707 940296005514 Escherichia coli lactaldehyde dehydrogenase AldA-like; Region: ALDH_LactADH-AldA; cd07088 940296005515 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 940296005516 NAD binding site [chemical binding]; other site 940296005517 catalytic residues [active] 940296005518 substrate binding site [chemical binding]; other site 940296005519 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 940296005520 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 940296005521 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 940296005522 Walker A/P-loop; other site 940296005523 ATP binding site [chemical binding]; other site 940296005524 Q-loop/lid; other site 940296005525 ABC transporter signature motif; other site 940296005526 Walker B; other site 940296005527 D-loop; other site 940296005528 H-loop/switch region; other site 940296005529 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 940296005530 Permease; Region: Permease; pfam02405 940296005531 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 940296005532 mce related protein; Region: MCE; pfam02470 940296005533 ABC-type transport system involved in resistance to organic solvents, auxiliary component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2D; COG2854 940296005534 Surface lipoprotein [Cell envelope biogenesis, outer membrane]; Region: VacJ; COG2853 940296005535 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 940296005536 active site 940296005537 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 940296005538 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 940296005539 catalytic residues [active] 940296005540 50S ribosomal protein L31; Reviewed; Region: rpmE; PRK00019 940296005541 Cadmium resistance transporter; Region: Cad; pfam03596 940296005542 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 940296005543 stringent starvation protein A; Provisional; Region: sspA; PRK09481 940296005544 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 940296005545 C-terminal domain interface [polypeptide binding]; other site 940296005546 putative GSH binding site (G-site) [chemical binding]; other site 940296005547 dimer interface [polypeptide binding]; other site 940296005548 C-terminal, alpha helical domain of Stringent starvation protein A; Region: GST_C_SspA; cd03186 940296005549 dimer interface [polypeptide binding]; other site 940296005550 N-terminal domain interface [polypeptide binding]; other site 940296005551 ClpXP protease specificity-enhancing factor; Provisional; Region: PRK11798 940296005552 Uncharacterized conserved protein [Function unknown]; Region: COG1610 940296005553 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 940296005554 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 940296005555 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 940296005556 N-acetyl-D-glucosamine binding site [chemical binding]; other site 940296005557 catalytic residue [active] 940296005558 ATP-binding cassette domain of methionine transporter; Region: ABC_MetN_methionine_transporter; cd03258 940296005559 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 940296005560 Walker A/P-loop; other site 940296005561 ATP binding site [chemical binding]; other site 940296005562 Q-loop/lid; other site 940296005563 ABC transporter signature motif; other site 940296005564 Walker B; other site 940296005565 D-loop; other site 940296005566 H-loop/switch region; other site 940296005567 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 940296005568 dimer interface [polypeptide binding]; other site 940296005569 conserved gate region; other site 940296005570 ABC-ATPase subunit interface; other site 940296005571 ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]; Region: NlpA; COG1464 940296005572 NLPA lipoprotein; Region: Lipoprotein_9; pfam03180 940296005573 3-polyprenyl-4-hydroxybenzoate decarboxylase [Coenzyme metabolism]; Region: UbiX; COG0163 940296005574 Flavoprotein; Region: Flavoprotein; pfam02441 940296005575 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 940296005576 ParB-like nuclease domain; Region: ParBc; pfam02195 940296005577 KorB domain; Region: KorB; pfam08535 940296005578 F0F1-type ATP synthase, subunit I [Energy production and conversion]; Region: AtpI; COG3312 940296005579 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 940296005580 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 940296005581 F0F1 ATP synthase subunit C; Validated; Region: PRK06876 940296005582 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 940296005583 F0F1 ATP synthase subunit B; Validated; Region: PRK05759 940296005584 F0F1 ATP synthase subunit delta; Provisional; Region: PRK13429 940296005585 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 940296005586 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 940296005587 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 940296005588 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 940296005589 beta subunit interaction interface [polypeptide binding]; other site 940296005590 Walker A motif; other site 940296005591 ATP binding site [chemical binding]; other site 940296005592 Walker B motif; other site 940296005593 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 940296005594 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 940296005595 delta subunit interface [polypeptide binding]; other site 940296005596 core domain interface [polypeptide binding]; other site 940296005597 epsilon subunit interface [polypeptide binding]; other site 940296005598 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 940296005599 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 940296005600 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 940296005601 alpha subunit interaction interface [polypeptide binding]; other site 940296005602 Walker A motif; other site 940296005603 ATP binding site [chemical binding]; other site 940296005604 Walker B motif; other site 940296005605 inhibitor binding site; inhibition site 940296005606 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 940296005607 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 940296005608 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 940296005609 gamma subunit interface [polypeptide binding]; other site 940296005610 epsilon subunit interface [polypeptide binding]; other site 940296005611 LBP interface [polypeptide binding]; other site 940296005612 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 940296005613 dimer interface [polypeptide binding]; other site 940296005614 motif 1; other site 940296005615 active site 940296005616 motif 2; other site 940296005617 motif 3; other site 940296005618 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 940296005619 DALR anticodon binding domain; Region: DALR_1; pfam05746 940296005620 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 940296005621 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 940296005622 active site 940296005623 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of...; Region: Glyco_transf_25; cd06532 940296005624 A4GalT_like proteins catalyze the addition of galactose or glucose residues to the lipooligosaccharide (LOS) or lipopolysaccharide (LPS) of the bacterial cell surface; Region: GT8_A4GalT_like; cd04194 940296005625 Glycosyl transferase family 8; Region: Glyco_transf_8; pfam01501 940296005626 Ligand binding site; other site 940296005627 metal-binding site 940296005628 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 940296005629 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 940296005630 active site 940296005631 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of...; Region: Glyco_transf_25; cd06532 940296005632 RNA methyltransferase, RsmE family; Region: TIGR00046 940296005633 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385 940296005634 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 940296005635 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 940296005636 active site 940296005637 hypothetical protein; Provisional; Region: PRK01752 940296005638 SEC-C motif; Region: SEC-C; pfam02810 940296005639 SEC-C motif; Region: SEC-C; pfam02810 940296005640 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 940296005641 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 940296005642 NAD(P) binding site [chemical binding]; other site 940296005643 homotetramer interface [polypeptide binding]; other site 940296005644 homodimer interface [polypeptide binding]; other site 940296005645 active site 940296005646 GMP synthase; Reviewed; Region: guaA; PRK00074 940296005647 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 940296005648 AMP/PPi binding site [chemical binding]; other site 940296005649 candidate oxyanion hole; other site 940296005650 catalytic triad [active] 940296005651 potential glutamine specificity residues [chemical binding]; other site 940296005652 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 940296005653 ATP Binding subdomain [chemical binding]; other site 940296005654 Ligand Binding sites [chemical binding]; other site 940296005655 Dimerization subdomain; other site 940296005656 lipid A export permease/ATP-binding protein MsbA; Region: MsbA_lipidA; TIGR02203 940296005657 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 940296005658 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 940296005659 Walker A/P-loop; other site 940296005660 ATP binding site [chemical binding]; other site 940296005661 Q-loop/lid; other site 940296005662 ABC transporter signature motif; other site 940296005663 Walker B; other site 940296005664 D-loop; other site 940296005665 H-loop/switch region; other site 940296005666 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 940296005667 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 940296005668 Predicted membrane protein [Function unknown]; Region: COG3326 940296005669 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 940296005670 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 940296005671 dimer interface [polypeptide binding]; other site 940296005672 active site 940296005673 CoA binding pocket [chemical binding]; other site 940296005674 putative phosphate acyltransferase; Provisional; Region: PRK05331 940296005675 Predicted phosphoribosyltransferases [General function prediction only]; Region: COG2236 940296005676 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 940296005677 active site 940296005678 50S ribosomal protein L32; Validated; Region: rpmF; PRK01110 940296005679 Predicted metal-binding, possibly nucleic acid-binding protein [General function prediction only]; Region: COG1399 940296005680 Maf-like protein; Region: Maf; pfam02545 940296005681 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 940296005682 active site 940296005683 dimer interface [polypeptide binding]; other site 940296005684 Predicted methyltransferases [General function prediction only]; Region: COG0313 940296005685 Uncharacterized subfamily of the tetrapyrrole methylase family similar to ribosomal RNA small subunit methyltransferase I (RsmI); Region: RsmI_like; cd11649 940296005686 putative SAM binding site [chemical binding]; other site 940296005687 homodimer interface [polypeptide binding]; other site 940296005688 membrane protein insertase; Provisional; Region: PRK01318 940296005689 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 940296005690 hypothetical protein; Provisional; Region: PRK14373 940296005691 ribonuclease P; Reviewed; Region: rnpA; PRK04390 940296005692 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 940296005693 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 940296005694 Walker A motif; other site 940296005695 ATP binding site [chemical binding]; other site 940296005696 Walker B motif; other site 940296005697 arginine finger; other site 940296005698 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 940296005699 DnaA box-binding interface [nucleotide binding]; other site 940296005700 DNA polymerase III subunit beta; Validated; Region: PRK05643 940296005701 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 940296005702 putative DNA binding surface [nucleotide binding]; other site 940296005703 dimer interface [polypeptide binding]; other site 940296005704 beta-clamp/clamp loader binding surface; other site 940296005705 beta-clamp/translesion DNA polymerase binding surface; other site 940296005706 polyphosphate kinase; Provisional; Region: PRK05443 940296005707 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 940296005708 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 940296005709 Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C1_like; cd09165 940296005710 putative domain interface [polypeptide binding]; other site 940296005711 putative active site [active] 940296005712 catalytic site [active] 940296005713 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 940296005714 putative domain interface [polypeptide binding]; other site 940296005715 putative active site [active] 940296005716 catalytic site [active] 940296005717 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 940296005718 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 940296005719 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 940296005720 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 940296005721 HIGH motif; other site 940296005722 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 940296005723 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 940296005724 active site 940296005725 KMSKS motif; other site 940296005726 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 940296005727 tRNA binding surface [nucleotide binding]; other site 940296005728 Dam-replacing family; Region: DRP; pfam06044 940296005729 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 940296005730 DNA methylase; Region: N6_N4_Mtase; pfam01555 940296005731 Predicted transcriptional regulator [Transcription]; Region: COG2944 940296005732 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 940296005733 non-specific DNA binding site [nucleotide binding]; other site 940296005734 salt bridge; other site 940296005735 sequence-specific DNA binding site [nucleotide binding]; other site 940296005736 Protein of unknown function (DUF1044); Region: DUF1044; cl01955