-- dump date 20120504_133101 -- class Genbank::misc_feature -- table misc_feature_note -- id note 212042000001 DNA polymerase I; Provisional; Region: PRK05755 212042000002 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 212042000003 active site 212042000004 metal binding site 1 [ion binding]; metal-binding site 212042000005 putative 5' ssDNA interaction site; other site 212042000006 metal binding site 3; metal-binding site 212042000007 metal binding site 2 [ion binding]; metal-binding site 212042000008 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 212042000009 putative DNA binding site [nucleotide binding]; other site 212042000010 putative metal binding site [ion binding]; other site 212042000011 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 212042000012 active site 212042000013 catalytic site [active] 212042000014 substrate binding site [chemical binding]; other site 212042000015 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 212042000016 active site 212042000017 DNA binding site [nucleotide binding] 212042000018 catalytic site [active] 212042000019 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 212042000020 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 212042000021 substrate binding site [chemical binding]; other site 212042000022 hexamer interface [polypeptide binding]; other site 212042000023 metal binding site [ion binding]; metal-binding site 212042000024 Domain of unknown function DUF140; Region: DUF140; cl00510 212042000025 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 212042000026 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 212042000027 Walker A/P-loop; other site 212042000028 ATP binding site [chemical binding]; other site 212042000029 Q-loop/lid; other site 212042000030 ABC transporter signature motif; other site 212042000031 Walker B; other site 212042000032 D-loop; other site 212042000033 H-loop/switch region; other site 212042000034 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 212042000035 conserved cys residue [active] 212042000036 S-adenosylmethionine synthetase; Provisional; Region: PRK12459 212042000037 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 212042000038 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 212042000039 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 212042000040 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 212042000041 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 212042000042 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 attaches...; Region: class_II_aaRS-like_core; cl00268 212042000043 motif 1; other site 212042000044 dimer interface [polypeptide binding]; other site 212042000045 active site 212042000046 motif 2; other site 212042000047 motif 3; other site 212042000048 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 212042000049 chaperone protein DnaJ; Provisional; Region: PRK10767 212042000050 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 212042000051 HSP70 interaction site [polypeptide binding]; other site 212042000052 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 212042000053 substrate binding site [polypeptide binding]; other site 212042000054 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 212042000055 Zn binding sites [ion binding]; other site 212042000056 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 212042000057 dimer interface [polypeptide binding]; other site 212042000058 Nicotinate-nucleotide pyrophosphorylase [Coenzyme metabolism]; Region: NadC; COG0157 212042000059 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 212042000060 dimerization interface [polypeptide binding]; other site 212042000061 active site 212042000062 Domain of unknown function (DUF205); Region: DUF205; cl00410 212042000063 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 includes...; Region: RuvC_resolvase; cd00529 212042000064 active site 212042000065 putative DNA-binding cleft [nucleotide binding]; other site 212042000066 dimer interface [polypeptide binding]; other site 212042000067 Cytochrome c oxidase subunit III. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of...; Region: Cyt_c_Oxidase_III; cd01665 212042000068 Subunit III/VIIa interface [polypeptide binding]; other site 212042000069 Phospholipid binding site [chemical binding]; other site 212042000070 Subunit I/III interface [polypeptide binding]; other site 212042000071 Subunit III/VIb interface [polypeptide binding]; other site 212042000072 Subunit III/VIa interface; other site 212042000073 Subunit III/Vb interface [polypeptide binding]; other site 212042000074 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 212042000075 substrate binding site [chemical binding]; other site 212042000076 active site 212042000077 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 212042000078 Transporter associated domain; Region: CorC_HlyC; cl08393 212042000079 Caudovirus prohead protease; Region: Peptidase_U35; cl01521 212042000080 Phage-related protein [Function unknown]; Region: COG4695; cl01923 212042000081 Phage portal protein; Region: Phage_portal; pfam04860 212042000082 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 212042000083 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 212042000084 S-adenosylmethionine binding site [chemical binding]; other site 212042000085 Quinolinate synthetase A protein; Region: NadA; cl00420 212042000086 [FeFe] hydrogenase, group B1/B3; Region: FeFe_hydrog_B1; TIGR04105 212042000087 4Fe-4S binding domain; Region: Fer4; cl02805 212042000088 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 212042000089 alternate gene name: major outer membrane protein C-15 Infect. Immun. 70 (9), 5295-5298 (2002); identified by similarity to GB:AAL78181.1; similar to P44-63 outer membrane protein, silent 212042000090 similar to P44-64 outer membrane protein, silent 212042000091 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 212042000092 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 212042000093 active site 212042000094 HIGH motif; other site 212042000095 dimer interface [polypeptide binding]; other site 212042000096 KMSKS motif; other site 212042000097 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 212042000098 dimer interface [polypeptide binding]; other site 212042000099 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 212042000100 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 212042000101 catalytic motif [active] 212042000102 Zn binding site [ion binding]; other site 212042000103 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; cl00161 212042000104 CTP synthetase; Validated; Region: pyrG; PRK05380 212042000105 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 212042000106 Catalytic site [active] 212042000107 active site 212042000108 UTP binding site [chemical binding]; other site 212042000109 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 212042000110 active site 212042000111 putative oxyanion hole; other site 212042000112 catalytic triad [active] 212042000113 Preprotein translocase SecG subunit; Region: SecG; cl09123 212042000114 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 212042000115 tyrosine recombinase XerD; Region: recomb_XerD; TIGR02225 212042000116 DNA binding site [nucleotide binding] 212042000117 Int/Topo IB signature motif; other site 212042000118 active site 212042000119 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 212042000120 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 212042000121 Walker A/P-loop; other site 212042000122 ATP binding site [chemical binding]; other site 212042000123 Q-loop/lid; other site 212042000124 ABC transporter signature motif; other site 212042000125 Walker B; other site 212042000126 D-loop; other site 212042000127 H-loop/switch region; other site 212042000128 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 212042000129 Malic enzyme, N-terminal domain; Region: malic; pfam00390 212042000130 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 212042000131 putative NAD(P) binding site [chemical binding]; other site 212042000132 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 212042000133 putative assembly protein; Provisional; Region: PRK10833 212042000134 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK12662 212042000135 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 212042000136 mce related protein; Region: MCE; cl15431 212042000137 NADH ubiquinone oxidoreductase subunit NDUFA12; Region: NDUFA12; cl01534 212042000138 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 212042000139 ATP cone domain; Region: ATP-cone; pfam03477 212042000140 N-acetylmuramoyl-L-alanine amidase; Validated; Region: PRK08581 212042000141 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 212042000142 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 212042000143 Trm112p-like protein; Region: Trm112p; cl01066 212042000144 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 212042000145 metabolite-proton symporter; Region: 2A0106; TIGR00883 212042000146 putative substrate translocation pore; other site 212042000147 Ribosomal protein S16; Region: Ribosomal_S16; cl00368 212042000148 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 212042000149 NAD(P) binding site [chemical binding]; other site 212042000150 active site 212042000151 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 212042000152 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 212042000153 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 212042000154 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 212042000155 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 212042000156 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 212042000157 dimer interface [polypeptide binding]; other site 212042000158 motif 1; other site 212042000159 active site 212042000160 motif 2; other site 212042000161 motif 3; other site 212042000162 ribosomal protein L20; Region: rpl20; CHL00068 212042000163 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 212042000164 23S rRNA binding site [nucleotide binding]; other site 212042000165 L21 binding site [polypeptide binding]; other site 212042000166 L13 binding site [polypeptide binding]; other site 212042000167 Ribosomal protein L35; Region: Ribosomal_L35p; cl00392 212042000168 Protein of unknown function (DUF1013); Region: DUF1013; cl11533 212042000169 transcription termination factor Rho; Provisional; Region: rho; PRK09376 212042000170 Rho termination factor, N-terminal domain; Region: Rho_N; cl06505 212042000171 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 212042000172 RNA binding site [nucleotide binding]; other site 212042000173 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 212042000174 multimer interface [polypeptide binding]; other site 212042000175 Walker A motif; other site 212042000176 ATP binding site [chemical binding]; other site 212042000177 Walker B motif; other site 212042000178 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06416 212042000179 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 212042000180 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 212042000181 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 212042000182 Dna-J like membrane chaperone protein; Provisional; Region: djlA; PRK09430 212042000183 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 212042000184 HSP70 interaction site [polypeptide binding]; other site 212042000185 Scaffold protein Nfu/NifU N terminal; Region: Nfu_N; cl07364 212042000186 NifU-like domain; Region: NifU; cl00484 212042000187 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 212042000188 thiS-thiF/thiG interaction site; other site 212042000189 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 212042000190 ThiS interaction site; other site 212042000191 putative active site [active] 212042000192 tetramer interface [polypeptide binding]; other site 212042000193 Protein of unknown function (DUF2628); Region: DUF2628; pfam10947 212042000194 glutamyl-tRNA synthetase; Provisional; Region: PRK12558 212042000195 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 212042000196 active site 212042000197 HIGH motif; other site 212042000198 nucleotide binding site [chemical binding]; other site 212042000199 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 212042000200 active site 212042000201 KMSKS motif; other site 212042000202 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 212042000203 magnesium protoporphyrin IX methyltransferase; Region: PLN02585 212042000204 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 212042000205 S-adenosylmethionine binding site [chemical binding]; other site 212042000206 similar to P44-65 outer membrane protein, silent 212042000207 Membrane transport protein; Region: Mem_trans; cl09117 212042000208 ETC complex I subunit conserved region; Region: ETC_C1_NDUFA4; pfam04800 212042000209 Exonuclease VII small subunit; Region: Exonuc_VII_S; cl00750 212042000210 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 212042000211 catalytic residues [active] 212042000212 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 212042000213 VirB7 interaction site; other site 212042000214 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 212042000215 Thiamine pyrophosphate (TPP) family, E1 of PDC_ADC_BCADC subfamily, TPP-binding module; composed of proteins similar to the E1 components of the human pyruvate dehydrogenase complex (PDC), the acetoin dehydrogenase complex (ADC) and the branched chain...; Region: TPP_E1_PDC_ADC_BCADC; cd02000 212042000216 tetramer interface [polypeptide binding]; other site 212042000217 TPP-binding site [chemical binding]; other site 212042000218 heterodimer interface [polypeptide binding]; other site 212042000219 phosphorylation loop region [posttranslational modification] 212042000220 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 212042000221 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 212042000222 active site 212042000223 cosubstrate binding site; other site 212042000224 substrate binding site [chemical binding]; other site 212042000225 catalytic site [active] 212042000226 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 212042000227 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; cl09108 212042000228 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 key...; Region: CBS_pair_IMPDH; cd04601 212042000229 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 the guanine...; Region: IMPDH; cd00381 212042000230 active site 212042000231 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 212042000232 Ribosomal protein L31; Region: Ribosomal_L31; cl00377 212042000233 Phage-related protein [Function unknown]; Region: COG4695; cl01923 212042000234 Acyl transferase domain; Region: Acyl_transf_1; cl08282 212042000235 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 212042000236 thymidylate kinase; Validated; Region: tmk; PRK00698 212042000237 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 212042000238 TMP-binding site; other site 212042000239 ATP-binding site [chemical binding]; other site 212042000240 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 212042000241 putative substrate translocation pore; other site 212042000242 Major Facilitator Superfamily; Region: MFS_1; pfam07690 212042000243 Tim44-like domain; Region: Tim44; cl09208 212042000244 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 212042000245 SecA binding site; other site 212042000246 Preprotein binding site; other site 212042000247 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 212042000248 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 212042000249 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 212042000250 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 212042000251 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 212042000252 FMN binding site [chemical binding]; other site 212042000253 substrate binding site [chemical binding]; other site 212042000254 putative catalytic residue [active] 212042000255 Amino Acid Kinases (AAK) superfamily, catalytic domain; present in such enzymes like N-acetylglutamate kinase (NAGK), carbamate kinase (CK), aspartokinase (AK), glutamate-5-kinase (G5K) and UMP kinase (UMPK). The AAK superfamily includes kinases that...; Region: AAK; cl00452 212042000256 substrate binding site [chemical binding]; other site 212042000257 nucleotide binding site [chemical binding]; other site 212042000258 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 212042000259 Lumazine binding domain; Region: Lum_binding; pfam00677 212042000260 Lumazine binding domain; Region: Lum_binding; pfam00677 212042000261 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 212042000262 CarD-like/TRCF domain; Region: CarD_TRCF; cl00588 212042000263 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 212042000264 ATP binding site [chemical binding]; other site 212042000265 putative Mg++ binding site [ion binding]; other site 212042000266 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 212042000267 nucleotide binding region [chemical binding]; other site 212042000268 ATP-binding site [chemical binding]; other site 212042000269 TRCF domain; Region: TRCF; cl04088 212042000270 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 212042000271 RNA/DNA hybrid binding site [nucleotide binding]; other site 212042000272 active site 212042000273 Predicted membrane protein [Function unknown]; Region: COG3164 212042000274 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 212042000275 putative nucleotide binding site [chemical binding]; other site 212042000276 uridine monophosphate binding site [chemical binding]; other site 212042000277 homohexameric interface [polypeptide binding]; other site 212042000278 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 round of...; Region: RRF; cd00520 212042000279 ribosome recycling factor; Reviewed; Region: frr; PRK00083 212042000280 hinge region; other site 212042000281 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 212042000282 similar to P44-66 outer membrane protein, silent 212042000283 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 212042000284 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 212042000285 ATP binding site [chemical binding]; other site 212042000286 active site 212042000287 substrate binding site [chemical binding]; other site 212042000288 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 212042000289 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 ATP-dependent...; Region: HisRS-like_core; cd00773 212042000290 dimer interface [polypeptide binding]; other site 212042000291 motif 1; other site 212042000292 active site 212042000293 motif 2; other site 212042000294 motif 3; other site 212042000295 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 212042000296 anticodon binding site; other site 212042000297 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 212042000298 DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a CXXC...; Region: DsbA_Com1_like; cd03023 212042000299 catalytic residues [active] 212042000300 cytochrome c oxidase assembly protein; Provisional; Region: PTZ00127 212042000301 Cytochrome oxidase assembly protein; Region: COX15-CtaA; pfam02628 212042000302 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13539 212042000303 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 212042000304 Walker A/P-loop; other site 212042000305 ATP binding site [chemical binding]; other site 212042000306 Q-loop/lid; other site 212042000307 ABC transporter signature motif; other site 212042000308 Walker B; other site 212042000309 D-loop; other site 212042000310 H-loop/switch region; other site 212042000311 Tubulin/FtsZ: Family includes tubulin alpha-, beta-, gamma-, delta-, and epsilon-tubulins as well as FtsZ, all of which are involved in polymer formation. Tubulin is the major component of microtubules, but also exists as a heterodimer and as a curved...; Region: Tubulin_FtsZ; cl10017 212042000312 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 212042000313 trimer interface [polypeptide binding]; other site 212042000314 active site 212042000315 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 212042000316 similar to P44-21 outer membrane protein, silent 212042000317 similar to P44-80 outer membrane protein, truncation 212042000318 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein; Region: CSP_CDS; cd04458 212042000319 DNA-binding site [nucleotide binding]; DNA binding site 212042000320 RNA-binding motif; other site 212042000321 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 212042000322 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 212042000323 dimerization interface [polypeptide binding]; other site 212042000324 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cl00080 212042000325 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 212042000326 ATP binding site [chemical binding]; other site 212042000327 Mg2+ binding site [ion binding]; other site 212042000328 G-X-G motif; other site 212042000329 ribonuclease D; Region: rnd; TIGR01388 212042000330 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 212042000331 putative active site [active] 212042000332 catalytic site [active] 212042000333 putative substrate binding site [chemical binding]; other site 212042000334 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 212042000335 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 212042000336 nucleotide binding pocket [chemical binding]; other site 212042000337 K-X-D-G motif; other site 212042000338 catalytic site [active] 212042000339 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 212042000340 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 212042000341 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 212042000342 Dimer interface [polypeptide binding]; other site 212042000343 BRCT sequence motif; other site 212042000344 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 212042000345 putative GSH binding site [chemical binding]; other site 212042000346 catalytic residues [active] 212042000347 BolA-like protein; Region: BolA; cl00386 212042000348 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 212042000349 Surface antigen; Region: Surface_Ag_2; cl01155 212042000350 similar to P44-81 outer membrane protein, truncation 212042000351 Surface antigen; Region: Surface_Ag_2; cl01155 212042000352 Surface antigen; Region: Surface_Ag_2; cl01155 212042000353 Surface antigen; Region: Surface_Ag_2; cl01155 212042000354 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 212042000355 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 212042000356 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 212042000357 Domain of unknown function (DUF3394); Region: DUF3394; pfam11874 212042000358 Colicin V production protein; Region: Colicin_V; cl00567 212042000359 Ribosomal protein S6; Region: Ribosomal_S6; cl00414 212042000360 Ribosomal protein S18; Region: Ribosomal_S18; cl00373 212042000361 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 212042000362 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 212042000363 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 212042000364 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 212042000365 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 212042000366 dimer interface [polypeptide binding]; other site 212042000367 glycine-pyridoxal phosphate binding site [chemical binding]; other site 212042000368 active site 212042000369 folate binding site [chemical binding]; other site 212042000370 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 in...; Region: Frataxin; cl00238 212042000371 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 212042000372 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 212042000373 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 212042000374 Walker A/P-loop; other site 212042000375 ATP binding site [chemical binding]; other site 212042000376 Q-loop/lid; other site 212042000377 ABC transporter signature motif; other site 212042000378 Walker B; other site 212042000379 D-loop; other site 212042000380 H-loop/switch region; other site 212042000381 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK09078 212042000382 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 212042000383 domain; Region: Succ_DH_flav_C; pfam02910 212042000384 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 212042000385 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK09078 212042000386 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 212042000387 domain; Region: Succ_DH_flav_C; pfam02910 212042000388 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 212042000389 Thymidylate synthase complementing protein; Region: Thy1; cl03630 212042000390 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 212042000391 putative substrate translocation pore; other site 212042000392 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 212042000393 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 attaches...; Region: class_II_aaRS-like_core; cl00268 212042000394 motif 1; other site 212042000395 dimer interface [polypeptide binding]; other site 212042000396 active site 212042000397 motif 2; other site 212042000398 motif 3; other site 212042000399 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 212042000400 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 212042000401 Walker A motif; other site 212042000402 ATP binding site [chemical binding]; other site 212042000403 Walker B motif; other site 212042000404 arginine finger; other site 212042000405 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 212042000406 Holliday junction DNA helicase RuvA; Provisional; Region: ruvA; PRK14600 212042000407 RuvA N terminal domain; Region: RuvA_N; pfam01330 212042000408 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 212042000409 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 212042000410 catalytic site [active] 212042000411 G-X2-G-X-G-K; other site 212042000412 Surface antigen; Region: Surface_Ag_2; cl01155 212042000413 Surface antigen; Region: Surface_Ag_2; cl01155 212042000414 Surface antigen; Region: Surface_Ag_2; cl01155 212042000415 Surface antigen; Region: Surface_Ag_2; cl01155 212042000416 Surface antigen; Region: Surface_Ag_2; cl01155 212042000417 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14187 212042000418 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 212042000419 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 212042000420 homodimer interface [polypeptide binding]; other site 212042000421 NADP binding site [chemical binding]; other site 212042000422 substrate binding site [chemical binding]; other site 212042000423 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 212042000424 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 212042000425 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 212042000426 Cytochrome c; Region: Cytochrom_C; cl11414 212042000427 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK08375 212042000428 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 212042000429 pyruvate phosphate dikinase; Provisional; Region: PRK09279 212042000430 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 212042000431 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 212042000432 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; cl09155 212042000433 haloacid dehalogenase superfamily, subfamily IA, variant 1 with third motif having Dx(3-4)D or Dx(3-4)E; Region: HAD-SF-IA-v1; TIGR01549 212042000434 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 212042000435 motif II; other site 212042000436 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 212042000437 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 212042000438 dimer interface [polypeptide binding]; other site 212042000439 anticodon binding site; other site 212042000440 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 the...; Region: AspRS_core; cd00777 212042000441 homodimer interface [polypeptide binding]; other site 212042000442 motif 1; other site 212042000443 active site 212042000444 motif 2; other site 212042000445 GAD domain; Region: GAD; pfam02938 212042000446 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 attaches...; Region: class_II_aaRS-like_core; cl00268 212042000447 active site 212042000448 motif 3; other site 212042000449 BON domain; Region: BON; cl02771 212042000450 BON domain; Region: BON; cl02771 212042000451 glutathione synthetase; Provisional; Region: PRK05246 212042000452 Prokaryotic glutathione synthetase, N-terminal domain; Region: GSH-S_N; pfam02951 212042000453 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 212042000454 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 212042000455 Cell division protein FtsQ; Region: FtsQ; pfam03799 212042000456 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 212042000457 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 212042000458 active site 212042000459 phosphorylation site [posttranslational modification] 212042000460 intermolecular recognition site; other site 212042000461 dimerization interface [polypeptide binding]; other site 212042000462 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 212042000463 Walker A motif; other site 212042000464 ATP binding site [chemical binding]; other site 212042000465 Walker B motif; other site 212042000466 arginine finger; other site 212042000467 Helix-turn-helix domains; Region: HTH; cl00088 212042000468 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 212042000469 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 212042000470 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 212042000471 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 212042000472 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 212042000473 DNA binding site [nucleotide binding] 212042000474 Int/Topo IB signature motif; other site 212042000475 active site 212042000476 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 212042000477 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 212042000478 dimerization interface [polypeptide binding]; other site 212042000479 putative ATP binding site [chemical binding]; other site 212042000480 Uncharacterized protein conserved in bacteria (DUF2328); Region: DUF2328; pfam10090 212042000481 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 212042000482 I-site; other site 212042000483 active site 212042000484 metal binding site [ion binding]; metal-binding site 212042000485 Domain of unknown function DUF143; Region: DUF143; cl00519 212042000486 Peptidase family M48; Region: Peptidase_M48; cl12018 212042000487 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 212042000488 TPR motif; other site 212042000489 binding surface 212042000490 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 212042000491 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 212042000492 dimerization interface [polypeptide binding]; other site 212042000493 putative ATP binding site [chemical binding]; other site 212042000494 phosphoribosylformylglycinamidine synthase, clade II; Region: FGAM-synthase; TIGR01857 212042000495 AIR (aminoimidazole ribonucleotide) synthase related protein. This family includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM (formylglycinamidine ribonucleotide) synthase and Selenophosphate synthetase (SelD). The N-terminal domain...; Region: PurM-like; cl10019 212042000496 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 212042000497 catalytic center binding site [active] 212042000498 ATP binding site [chemical binding]; other site 212042000499 Phosphoribosylformylglycinamidine (FGAM) synthase, synthetase domain [Nucleotide transport and metabolism]; Region: PurL; COG0046 212042000500 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 212042000501 dimerization interface [polypeptide binding]; other site 212042000502 ATP binding site [chemical binding]; other site 212042000503 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 212042000504 dimerization interface [polypeptide binding]; other site 212042000505 ATP binding site [chemical binding]; other site 212042000506 identified by similarity to GB:AAP20811.1; similar to P44-88 outer membrane protein, silent 212042000507 Sec24-related protein; Provisional; Region: PTZ00395 212042000508 biotin synthase; Region: bioB; TIGR00433 212042000509 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 212042000510 FeS/SAM binding site; other site 212042000511 Biotin and Thiamin Synthesis associated domain; Region: BATS; cl06149 212042000512 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5388 212042000513 PAS domain; Region: PAS_5; pfam07310 212042000514 Peptidase family M23; Region: Peptidase_M23; pfam01551 212042000515 FIG, FBPase/IMPase/glpX-like domain. A superfamily of metal-dependent phosphatases with various substrates. Fructose-1,6-bisphospatase (both the major and the glpX-encoded variant) hydrolyze fructose-1,6,-bisphosphate to fructose-6-phosphate in...; Region: FIG; cl00289 212042000516 active site 212042000517 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 212042000518 tRNA (uracil-5-)-methyltransferase Gid; Reviewed; Region: PRK05335; cl15440 212042000519 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 212042000520 putative active site [active] 212042000521 catalytic triad [active] 212042000522 Surface antigen; Region: Surface_Ag_2; cl01155 212042000523 similar to P44-67 outer membrane protein, silent 212042000524 similar to P44-68 outer membrane protein, silent 212042000525 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 212042000526 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 212042000527 active site 212042000528 substrate binding site [chemical binding]; other site 212042000529 cosubstrate binding site; other site 212042000530 catalytic site [active] 212042000531 multifunctional aminopeptidase A; Provisional; Region: PRK00913 212042000532 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 212042000533 interface (dimer of trimers) [polypeptide binding]; other site 212042000534 Substrate-binding/catalytic site; other site 212042000535 Zn-binding sites [ion binding]; other site 212042000536 Intradiol dioxygenases catalyze the critical ring-cleavage step in the conversion of catecholate derivatives to citric acid cycle intermediates. This family contains catechol 1,2-dioxygenases and protocatechuate 3,4-dioxygenases which are mononuclear...; Region: intradiol_dioxygenase; cl01383 212042000537 active site 212042000538 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 212042000539 Clp amino terminal domain; Region: Clp_N; pfam02861 212042000540 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 212042000541 Walker A motif; other site 212042000542 ATP binding site [chemical binding]; other site 212042000543 Walker B motif; other site 212042000544 arginine finger; other site 212042000545 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 212042000546 Walker A motif; other site 212042000547 ATP binding site [chemical binding]; other site 212042000548 Walker B motif; other site 212042000549 arginine finger; other site 212042000550 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 212042000551 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 212042000552 classical (c) SDRs; Region: SDR_c; cd05233 212042000553 NAD(P) binding site [chemical binding]; other site 212042000554 active site 212042000555 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 212042000556 ring oligomerisation interface [polypeptide binding]; other site 212042000557 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 212042000558 ATP/Mg binding site [chemical binding]; other site 212042000559 stacking interactions; other site 212042000560 hinge regions; other site 212042000561 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 212042000562 oligomerisation interface [polypeptide binding]; other site 212042000563 mobile loop; other site 212042000564 roof hairpin; other site 212042000565 hypothetical protein; Reviewed; Region: PRK00024 212042000566 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 212042000567 MPN+ (JAMM) motif; other site 212042000568 Zinc-binding site [ion binding]; other site 212042000569 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 212042000570 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 212042000571 dihydroorotase; Validated; Region: pyrC; PRK09357 212042000572 Dihydroorotase (DHOase), subgroup IIa; DHOases catalyze the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in pyrimidine biosynthesis. This subgroup also contains proteins that lack the active site, like unc-33, a C; Region: DHOase_IIa; cd01317 212042000573 active site 212042000574 DNA / pantothenate metabolism flavoprotein; Region: DFP; cl04410 212042000575 fumarate hydratase; Reviewed; Region: fumC; PRK00485 212042000576 Class II fumarases; Region: Fumarase_classII; cd01362 212042000577 active site 212042000578 tetramer interface [polypeptide binding]; other site 212042000579 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 212042000580 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 212042000581 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 212042000582 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 212042000583 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 212042000584 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 212042000585 IMP binding site; other site 212042000586 dimer interface [polypeptide binding]; other site 212042000587 interdomain contacts; other site 212042000588 partial ornithine binding site; other site 212042000589 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 212042000590 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 212042000591 dihydropteroate synthase; Region: DHPS; TIGR01496 212042000592 substrate binding pocket [chemical binding]; other site 212042000593 dimer interface [polypeptide binding]; other site 212042000594 inhibitor binding site; inhibition site 212042000595 type I secretion system ABC transporter, PrtD family; Region: type_I_sec_PrtD; TIGR01842 212042000596 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 212042000597 Walker A/P-loop; other site 212042000598 ATP binding site [chemical binding]; other site 212042000599 Q-loop/lid; other site 212042000600 ABC transporter signature motif; other site 212042000601 Walker B; other site 212042000602 D-loop; other site 212042000603 H-loop/switch region; other site 212042000604 DNA polymerase III subunits gamma and tau; Validated; Region: PRK07003 212042000605 quinone oxidoreductase, NADPH-dependent; Provisional; Region: PRK10754 212042000606 Quinone oxidoreductase (QOR); Region: QOR2; cd05286 212042000607 NADP binding site [chemical binding]; other site 212042000608 dimer interface [polypeptide binding]; other site 212042000609 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 212042000610 exonuclease V subunit beta; Provisional; Region: recB; PRK10876 212042000611 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 212042000612 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 212042000613 A subgroup of the band 7 domain of flotillin (reggie) like proteins. This subgroup contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. Many of these band 7 domain-containing proteins are lipid raft-associated. Individual...; Region: Band_7_2; cd03402 212042000614 Predicted ATPase [General function prediction only]; Region: COG1485 212042000615 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 212042000616 Walker A motif; other site 212042000617 ATP binding site [chemical binding]; other site 212042000618 Walker B motif; other site 212042000619 ferrochelatase; Reviewed; Region: hemH; PRK00035 212042000620 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 212042000621 C-terminal domain interface [polypeptide binding]; other site 212042000622 active site 212042000623 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 212042000624 active site 212042000625 N-terminal domain interface [polypeptide binding]; other site 212042000626 Cell division protein ZapA; Region: ZapA; cl01146 212042000627 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK05683 212042000628 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cl00257 212042000629 IHF dimer interface [polypeptide binding]; other site 212042000630 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 212042000631 tandem repeat interface [polypeptide binding]; other site 212042000632 oligomer interface [polypeptide binding]; other site 212042000633 active site residues [active] 212042000634 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 212042000635 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 consists...; Region: S1_RPS1_repeat_ec1_hs1; cd05687 212042000636 RNA binding site [nucleotide binding]; other site 212042000637 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 consists...; Region: S1_RPS1_repeat_ec2_hs2; cd04465 212042000638 RNA binding site [nucleotide binding]; other site 212042000639 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 of...; Region: S1_RPS1_repeat_ec3; cd05688 212042000640 RNA binding site [nucleotide binding]; other site 212042000641 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cl09927 212042000642 RNA binding site [nucleotide binding]; other site 212042000643 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cl09927 212042000644 RNA binding site [nucleotide binding]; other site 212042000645 cytidylate kinase; Provisional; Region: cmk; PRK00023 212042000646 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 212042000647 CMP-binding site; other site 212042000648 The sites determining sugar specificity; other site 212042000649 rRNA methylase, putative, group 3; Region: rRNA_methyl_3; TIGR00186 212042000650 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; cl06870 212042000651 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 212042000652 elongation factor Tu; Reviewed; Region: PRK00049 212042000653 EF-Tu subfamily. This subfamily includes orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts. It is one of several GTP-binding translation factors found in the larger family of GTP-binding elongation factors; Region: EF_Tu; cd01884 212042000654 G1 box; other site 212042000655 GEF interaction site [polypeptide binding]; other site 212042000656 GTP/Mg2+ binding site [chemical binding]; other site 212042000657 Switch I region; other site 212042000658 G2 box; other site 212042000659 G3 box; other site 212042000660 Switch II region; other site 212042000661 G4 box; other site 212042000662 G5 box; other site 212042000663 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 212042000664 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 212042000665 Antibiotic Binding Site [chemical binding]; other site 212042000666 Ribosomal protein S10p/S20e; Region: Ribosomal_S10; cl00314 212042000667 Ribosomal protein L3; Region: Ribosomal_L3; cl00324 212042000668 Ribosomal protein L4/L1 family; Region: Ribosomal_L4; cl00325 212042000669 Ribosomal protein L23; Region: Ribosomal_L23; cl00326 212042000670 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 212042000671 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 212042000672 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 212042000673 Ribosomal protein S19; Region: Ribosomal_S19; cl00350 212042000674 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 212042000675 protein-rRNA interface [nucleotide binding]; other site 212042000676 putative translocon binding site; other site 212042000677 ribosomal protein S3, bacterial type; Region: rpsC_bact; TIGR01009 212042000678 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 212042000679 G-X-X-G motif; other site 212042000680 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 212042000681 Ribosomal_L16_L10e: L16 is an essential protein in the large ribosomal subunit of bacteria, mitochondria, and chloroplasts. Large subunits that lack L16 are defective in peptidyl transferase activity, peptidyl-tRNA hydrolysis activity, association with...; Region: Ribosomal_L16_L10e; cd01433 212042000682 23S rRNA interface [nucleotide binding]; other site 212042000683 5S rRNA interface [nucleotide binding]; other site 212042000684 putative antibiotic binding site [chemical binding]; other site 212042000685 L25 interface [polypeptide binding]; other site 212042000686 L27 interface [polypeptide binding]; other site 212042000687 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; cl09943 212042000688 Ribosomal protein S17; Region: Ribosomal_S17; cl00351 212042000689 Ribosomal protein L14p/L23e; Region: Ribosomal_L14; cl00328 212042000690 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 212042000691 KOW motif; Region: KOW; cl00354 212042000692 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 212042000693 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 212042000694 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 212042000695 Ribosomal protein S14p/S29e; Region: Ribosomal_S14; cl00355 212042000696 Ribosomal protein S8; Region: Ribosomal_S8; cl00330 212042000697 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 212042000698 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 212042000699 Ribosomal L18/L5e: L18 (L5e) is a ribosomal protein found in the central protuberance (CP) of the large subunit. L18 binds 5S rRNA and induces a conformational change that stimulates the binding of L5 to 5S rRNA. Association of 5S rRNA with 23S rRNA...; Region: Ribosomal_L18_L5e; cd00432 212042000700 5S rRNA interface [nucleotide binding]; other site 212042000701 23S rRNA interface [nucleotide binding]; other site 212042000702 L5 interface [polypeptide binding]; other site 212042000703 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 212042000704 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 212042000705 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 212042000706 Ribosomal protein L18e/L15; Region: Ribosomal_L18e; cl12022 212042000707 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 212042000708 SecY translocase; Region: SecY; pfam00344 212042000709 adenylate kinase; Reviewed; Region: adk; PRK00279 212042000710 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 212042000711 AMP-binding site [chemical binding]; other site 212042000712 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 212042000713 Ribosomal protein S13/S18; Region: Ribosomal_S13; cl00331 212042000714 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 212042000715 Ribosomal protein S11; Region: Ribosomal_S11; cl00332 212042000716 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 212042000717 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 212042000718 alphaNTD - beta interaction site [polypeptide binding]; other site 212042000719 alphaNTD homodimer interface [polypeptide binding]; other site 212042000720 alphaNTD - beta' interaction site [polypeptide binding]; other site 212042000721 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; cl11613 212042000722 Ribosomal protein L17; Region: Ribosomal_L17; cl00356 212042000723 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 212042000724 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 212042000725 putative tRNA-binding site [nucleotide binding]; other site 212042000726 B3/4 domain; Region: B3_4; cl11458 212042000727 tRNA synthetase B5 domain; Region: B5; cl08394 212042000728 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 212042000729 dimer interface [polypeptide binding]; other site 212042000730 motif 1; other site 212042000731 motif 3; other site 212042000732 motif 2; other site 212042000733 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; cl08386 212042000734 Competence protein; Region: Competence; cl00471 212042000735 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 212042000736 Ribonuclease P; Region: Ribonuclease_P; cl00457 212042000737 Ribosomal protein L34; Region: Ribosomal_L34; cl00370 212042000738 UbiA prenyltransferase family; Region: UbiA; cl00337 212042000739 Flavin Reductases; Region: FlaRed; cl00801 212042000740 phosphate ABC transporter ATP-binding protein; Provisional; Region: PRK14244 212042000741 Phosphate uptake is of fundamental importance in the cell physiology of bacteria because phosphate is required as a nutrient. The Pst system of E. coli comprises four distinct subunits encoded by the pstS, pstA, pstB, and pstC genes. The PstS protein...; Region: ABC_PstB_phosphate_transporter; cd03260 212042000742 Walker A/P-loop; other site 212042000743 ATP binding site [chemical binding]; other site 212042000744 Q-loop/lid; other site 212042000745 ABC transporter signature motif; other site 212042000746 Walker B; other site 212042000747 D-loop; other site 212042000748 H-loop/switch region; other site 212042000749 Queuine tRNA-ribosyltransferase; Region: TGT; cl00409 212042000750 Ribosomal L32p protein family; Region: Ribosomal_L32p; cl09115 212042000751 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 212042000752 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 212042000753 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 212042000754 dimer interface [polypeptide binding]; other site 212042000755 active site 212042000756 CoA binding pocket [chemical binding]; other site 212042000757 similar to P44 outer membrane protein, N-terminal fragment 212042000758 similar to P44-69 outer membrane protein, silent 212042000759 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 212042000760 nucleoside/Zn binding site; other site 212042000761 dimer interface [polypeptide binding]; other site 212042000762 catalytic motif [active] 212042000763 replicative DNA helicase; Provisional; Region: PRK09165 212042000764 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 212042000765 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 212042000766 Walker A motif; other site 212042000767 ATP binding site [chemical binding]; other site 212042000768 Walker B motif; other site 212042000769 DNA binding loops [nucleotide binding] 212042000770 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 212042000771 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 212042000772 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 212042000773 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 212042000774 substrate binding pocket [chemical binding]; other site 212042000775 chain length determination region; other site 212042000776 substrate-Mg2+ binding site; other site 212042000777 catalytic residues [active] 212042000778 aspartate-rich region 1; other site 212042000779 active site lid residues [active] 212042000780 aspartate-rich region 2; other site 212042000781 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09102 212042000782 Class I ribonucleotide reductase; Region: RNR_I; cd01679 212042000783 active site 212042000784 dimer interface [polypeptide binding]; other site 212042000785 catalytic residues [active] 212042000786 effector binding site; other site 212042000787 R2 peptide binding site; other site 212042000788 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 includes...; Region: RuvC_resolvase; cl00243 212042000789 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 212042000790 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 212042000791 GDP-binding site [chemical binding]; other site 212042000792 ACT binding site; other site 212042000793 IMP binding site; other site 212042000794 primosome assembly protein PriA; Validated; Region: PRK05580 212042000795 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 212042000796 ligand binding site [chemical binding]; other site 212042000797 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 212042000798 Zn binding site [ion binding]; other site 212042000799 transketolase; Reviewed; Region: PRK05899 212042000800 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 212042000801 TPP-binding site [chemical binding]; other site 212042000802 dimer interface [polypeptide binding]; other site 212042000803 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 212042000804 PYR/PP interface [polypeptide binding]; other site 212042000805 dimer interface [polypeptide binding]; other site 212042000806 TPP binding site [chemical binding]; other site 212042000807 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 212042000808 Multiple resistance and pH regulation protein F (MrpF / PhaF); Region: MrpF_PhaF; cl09154 212042000809 Na+/H+ antiporter subunit; Region: PhaG_MnhG_YufB; cl00583 212042000810 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 212042000811 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cl09927 212042000812 RNA binding site [nucleotide binding]; other site 212042000813 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cl09927 212042000814 ribonuclease, Rne/Rng family; Region: RNaseEG; TIGR00757 212042000815 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 212042000816 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 212042000817 putative coenzyme Q binding site [chemical binding]; other site 212042000818 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK12664 212042000819 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 212042000820 signal recognition particle protein; Provisional; Region: PRK10867 212042000821 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 212042000822 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 212042000823 P loop; other site 212042000824 GTP binding site [chemical binding]; other site 212042000825 Signal peptide binding domain; Region: SRP_SPB; pfam02978 212042000826 GTPase Era; Reviewed; Region: era; PRK00089 212042000827 Era subfamily. Era (E. coli Ras-like protein) is a multifunctional GTPase found in all bacteria except some eubacteria. It binds to the 16S ribosomal RNA (rRNA) of the 30S subunit and appears to play a role in the assembly of the 30S subunit, possibly...; Region: Era; cd04163 212042000828 G1 box; other site 212042000829 GTP/Mg2+ binding site [chemical binding]; other site 212042000830 Switch I region; other site 212042000831 G2 box; other site 212042000832 Switch II region; other site 212042000833 G3 box; other site 212042000834 G4 box; other site 212042000835 G5 box; other site 212042000836 Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; Region: DNA_polB_like1_exo; cd05782 212042000837 active site 212042000838 catalytic site [active] 212042000839 substrate binding site [chemical binding]; other site 212042000840 Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; Region: DNA_pol_B_exo2; pfam10108 212042000841 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 212042000842 catalytic motif [active] 212042000843 Catalytic residue [active] 212042000844 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 212042000845 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 212042000846 active site 212042000847 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 212042000848 active site 212042000849 Uroporphyrinogen-III synthase HemD; Region: HEM4; pfam02602 212042000850 Predicted glutamine amidotransferases [General function prediction only]; Region: COG2071 212042000851 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 212042000852 primosome assembly protein PriA; Validated; Region: PRK05580 212042000853 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 212042000854 ATP binding site [chemical binding]; other site 212042000855 putative Mg++ binding site [ion binding]; other site 212042000856 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 212042000857 Ribosomal L28 family; Region: Ribosomal_L28; cl00367 212042000858 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 212042000859 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 212042000860 RNA binding surface [nucleotide binding]; other site 212042000861 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and...; Region: PseudoU_synth_RluCD_like; cd02869 212042000862 active site 212042000863 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 212042000864 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 212042000865 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 212042000866 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 212042000867 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 212042000868 carboxyltransferase (CT) interaction site; other site 212042000869 biotinylation site [posttranslational modification]; other site 212042000870 lipoyl synthase; Provisional; Region: PRK05481 212042000871 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 212042000872 FeS/SAM binding site; other site 212042000873 Domain of unknown function (DUF3333); Region: DUF3333; pfam11812 212042000874 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 212042000875 dimer interface [polypeptide binding]; other site 212042000876 conserved gate region; other site 212042000877 putative PBP binding loops; other site 212042000878 ABC-ATPase subunit interface; other site 212042000879 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 212042000880 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 212042000881 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 212042000882 Type IV secretory pathway, VirB3-like protein; Region: VirB3; cl01501 212042000883 type IV secretion system ATPase VirB4; Provisional; Region: PRK13898 212042000884 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 212042000885 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 212042000886 Walker A/P-loop; other site 212042000887 ATP binding site [chemical binding]; other site 212042000888 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 212042000889 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 212042000890 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 212042000891 Protein of unknown function (DUF3816); Region: DUF3816; pfam12822 212042000892 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 212042000893 K+-dependent Na+/Ca+ exchanger; Region: 2A1904; TIGR00927 212042000894 Conserved hypothetical protein 2217 (DUF2460); Region: DUF2460; cl02268 212042000895 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 212042000896 trimer interface [polypeptide binding]; other site 212042000897 active site 212042000898 LytB protein; Region: LYTB; cl00507 212042000899 (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate reductase (IPP and DMAPP forming); Region: ispH_lytB; TIGR00216 212042000900 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 212042000901 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; cl03056 212042000902 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 212042000903 catalytic site [active] 212042000904 subunit interface [polypeptide binding]; other site 212042000905 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 212042000906 Sulfatase; Region: Sulfatase; cl10460 212042000907 ribosome-associated GTPase EngA; Region: GTPase_EngA; TIGR03594 212042000908 EngA1 subfamily. This CD represents the first GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an...; Region: EngA1; cd01894 212042000909 G1 box; other site 212042000910 GTP/Mg2+ binding site [chemical binding]; other site 212042000911 Switch I region; other site 212042000912 G2 box; other site 212042000913 Switch II region; other site 212042000914 G3 box; other site 212042000915 G4 box; other site 212042000916 G5 box; other site 212042000917 EngA2 subfamily. This CD represents the second GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an...; Region: EngA2; cd01895 212042000918 G1 box; other site 212042000919 GTP/Mg2+ binding site [chemical binding]; other site 212042000920 Switch I region; other site 212042000921 G2 box; other site 212042000922 G3 box; other site 212042000923 Switch II region; other site 212042000924 G4 box; other site 212042000925 G5 box; other site 212042000926 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 212042000927 Trp docking motif [polypeptide binding]; other site 212042000928 active site 212042000929 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 212042000930 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 212042000931 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 212042000932 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 212042000933 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 212042000934 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 212042000935 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the...; Region: S1_IF1; cd04451 212042000936 rRNA binding site [nucleotide binding]; other site 212042000937 predicted 30S ribosome binding site; other site 212042000938 Maf-like protein; Region: Maf; pfam02545 212042000939 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 212042000940 active site 212042000941 dimer interface [polypeptide binding]; other site 212042000942 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 212042000943 rRNA interaction site [nucleotide binding]; other site 212042000944 S8 interaction site; other site 212042000945 putative laminin-1 binding site; other site 212042000946 elongation factor Ts; Provisional; Region: tsf; PRK09377 212042000947 Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been...; Region: UBA; cl00153 212042000948 Elongation factor TS; Region: EF_TS; pfam00889 212042000949 Elongation factor TS; Region: EF_TS; pfam00889 212042000950 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 212042000951 ABC-ATPase subunit interface; other site 212042000952 dimer interface [polypeptide binding]; other site 212042000953 putative PBP binding regions; other site 212042000954 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 212042000955 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 212042000956 [2Fe-2S] cluster binding site [ion binding]; other site 212042000957 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 212042000958 Qi binding site; other site 212042000959 intrachain domain interface; other site 212042000960 interchain domain interface [polypeptide binding]; other site 212042000961 cytochrome b; Provisional; Region: CYTB; MTH00156 212042000962 heme bH binding site [chemical binding]; other site 212042000963 heme bL binding site [chemical binding]; other site 212042000964 Qo binding site; other site 212042000965 Cytochrome b(C-terminus)/b6/petD: 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_C; cd00290 212042000966 interchain domain interface [polypeptide binding]; other site 212042000967 intrachain domain interface; other site 212042000968 Qi binding site; other site 212042000969 Qo binding site; other site 212042000970 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 212042000971 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 212042000972 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 212042000973 active site 212042000974 HIGH motif; other site 212042000975 KMSKS motif; other site 212042000976 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 212042000977 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 212042000978 DNA binding site [nucleotide binding] 212042000979 catalytic residue [active] 212042000980 H2TH interface [polypeptide binding]; other site 212042000981 putative catalytic residues [active] 212042000982 turnover-facilitating residue; other site 212042000983 intercalation triad [nucleotide binding]; other site 212042000984 8OG recognition residue [nucleotide binding]; other site 212042000985 putative reading head residues; other site 212042000986 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 212042000987 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 212042000988 methylmalonyl-CoA decarboxylase alpha subunit; Region: mmdA; TIGR01117 212042000989 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cl14780 212042000990 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cl14780 212042000991 type IV secretion system ATPase VirB4; Provisional; Region: PRK13898 212042000992 type IV secretion system ATPase VirB4; Provisional; Region: PRK13898 212042000993 peptide chain release factor 1; Validated; Region: prfA; PRK00591 212042000994 RF-1 domain; Region: RF-1; cl02875 212042000995 RF-1 domain; Region: RF-1; cl02875 212042000996 Predicted GTPase [General function prediction only]; Region: COG0218 212042000997 The YihA (EngB) subfamily. This subfamily of GTPases is typified by the E. coli YihA, an essential protein involved in cell division control. YihA and its orthologs are small proteins that typically contain less than 200 amino acid residues and...; Region: YihA_EngB; cd01876 212042000998 G1 box; other site 212042000999 GTP/Mg2+ binding site [chemical binding]; other site 212042001000 Switch I region; other site 212042001001 G2 box; other site 212042001002 G3 box; other site 212042001003 Switch II region; other site 212042001004 G4 box; other site 212042001005 G5 box; other site 212042001006 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 212042001007 feedback inhibition sensing region; other site 212042001008 homohexameric interface [polypeptide binding]; other site 212042001009 nucleotide binding site [chemical binding]; other site 212042001010 N-acetyl-L-glutamate binding site [chemical binding]; other site 212042001011 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; cl00433 212042001012 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 212042001013 seryl-tRNA synthetase; Provisional; Region: PRK05431 212042001014 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 212042001015 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 bound...; Region: SerRS_core; cd00770 212042001016 dimer interface [polypeptide binding]; other site 212042001017 active site 212042001018 motif 1; other site 212042001019 motif 2; other site 212042001020 motif 3; other site 212042001021 RmuC family; Region: RmuC; pfam02646 212042001022 VirB8 protein; Region: VirB8; cl01500 212042001023 IPP transferase; Region: IPPT; cl00403 212042001024 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 212042001025 NADH dehydrogenase I subunit F; Provisional; Region: PRK13596 212042001026 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 212042001027 SLBB domain; Region: SLBB; pfam10531 212042001028 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; cl11211 212042001029 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 212042001030 NADH dehydrogenase subunit J; Provisional; Region: PRK06433; cl14634 212042001031 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 212042001032 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 212042001033 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 212042001034 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 212042001035 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 212042001036 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 212042001037 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 212042001038 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 212042001039 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 212042001040 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 212042001041 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 212042001042 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 212042001043 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694; cl15446 212042001044 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 212042001045 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 212042001046 Protein export membrane protein; Region: SecD_SecF; cl14618 212042001047 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 212042001048 NusA N-terminal domain; Region: NusA_N; pfam08529 212042001049 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 212042001050 RNA binding site [nucleotide binding]; other site 212042001051 homodimer interface [polypeptide binding]; other site 212042001052 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 212042001053 G-X-X-G motif; other site 212042001054 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 212042001055 translation initiation factor IF-2; Region: IF-2; TIGR00487 212042001056 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 212042001057 IF2/eIF5B (initiation factors 2/ eukaryotic initiation factor 5B) subfamily. IF2/eIF5B contribute to ribosomal subunit joining and function as GTPases that are maximally activated by the presence of both ribosomal subunits. As seen in other GTPases; Region: IF2_eIF5B; cd01887 212042001058 G1 box; other site 212042001059 putative GEF interaction site [polypeptide binding]; other site 212042001060 GTP/Mg2+ binding site [chemical binding]; other site 212042001061 Switch I region; other site 212042001062 G2 box; other site 212042001063 G3 box; other site 212042001064 Switch II region; other site 212042001065 G4 box; other site 212042001066 G5 box; other site 212042001067 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 212042001068 Translation-initiation factor 2; Region: IF-2; pfam11987 212042001069 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 212042001070 Ribosome-binding factor A; Region: RBFA; cl00542 212042001071 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 212042001072 Integral membrane protein TerC family; Region: TerC; cl10468 212042001073 ATP-dependent Clp protease ATP-binding subunit clpA; Region: ClpA; TIGR02639 212042001074 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 212042001075 Walker A motif; other site 212042001076 ATP binding site [chemical binding]; other site 212042001077 Walker B motif; other site 212042001078 arginine finger; other site 212042001079 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 212042001080 Walker A motif; other site 212042001081 ATP binding site [chemical binding]; other site 212042001082 Walker B motif; other site 212042001083 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 212042001084 TypA (tyrosine phosphorylated protein A)/BipA subfamily. BipA is a protein belonging to the ribosome-binding family of GTPases and is widely distributed in bacteria and plants. BipA was originally described as a protein that is induced in Salmonella...; Region: TypA_BipA; cd01891 212042001085 GTP-binding protein TypA/BipA; Region: TypA_BipA; TIGR01394 212042001086 G1 box; other site 212042001087 putative GEF interaction site [polypeptide binding]; other site 212042001088 GTP/Mg2+ binding site [chemical binding]; other site 212042001089 Switch I region; other site 212042001090 G2 box; other site 212042001091 G3 box; other site 212042001092 Switch II region; other site 212042001093 G4 box; other site 212042001094 G5 box; other site 212042001095 BipA_TypA_II: domain II of BipA (also called TypA) having homology to domain II of the elongation factors (EFs) EF-G and EF-Tu. BipA is a highly conserved protein with global regulatory properties in Escherichia coli. BipA is phosphorylated on a...; Region: BipA_TypA_II; cd03691 212042001096 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 212042001097 peptide chain release factor 2; Validated; Region: prfB; PRK00578 212042001098 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 212042001099 dimer interface [polypeptide binding]; other site 212042001100 ssDNA binding site [nucleotide binding]; other site 212042001101 tetramer (dimer of dimers) interface [polypeptide binding]; other site 212042001102 RF-1 domain; Region: RF-1; cl02875 212042001103 RF-1 domain; Region: RF-1; cl02875 212042001104 Malonyl-CoA decarboxylase (MCD); Region: MCD; pfam05292 212042001105 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 212042001106 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 212042001107 GatB domain; Region: GatB_Yqey; cl11497 212042001108 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; Region: EEP; cl00490 212042001109 putative catalytic site [active] 212042001110 putative phosphate binding site [ion binding]; other site 212042001111 putative metal binding site [ion binding]; other site 212042001112 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK08159 212042001113 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 212042001114 NAD binding site [chemical binding]; other site 212042001115 homotetramer interface [polypeptide binding]; other site 212042001116 homodimer interface [polypeptide binding]; other site 212042001117 substrate binding site [chemical binding]; other site 212042001118 active site 212042001119 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 212042001120 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 212042001121 Walker A motif; other site 212042001122 ATP binding site [chemical binding]; other site 212042001123 Walker B motif; other site 212042001124 arginine finger; other site 212042001125 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 212042001126 DnaA box-binding interface [nucleotide binding]; other site 212042001127 peptide chain release factor 2; Validated; Region: prfB; PRK00578 212042001128 RF-1 domain; Region: RF-1; cl02875 212042001129 RF-1 domain; Region: RF-1; cl02875 212042001130 Domain of unknown function DUF28; Region: DUF28; cl00361 212042001131 Ribonuclease BN-like family; Region: Ribonuclease_BN; cl07918 212042001132 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 212042001133 adenosylmethionine-8-amino-7-oxononanoate transaminase; Region: bioA; TIGR00508 212042001134 inhibitor-cofactor binding pocket; inhibition site 212042001135 pyridoxal 5'-phosphate binding site [chemical binding]; other site 212042001136 catalytic residue [active] 212042001137 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 212042001138 G4 box; other site 212042001139 Transaldolase-like fructose-6-phosphate aldolases (FSA) found in bacteria and archaea; Region: Transaldolase_FSA; cd00956 212042001140 active site 212042001141 intersubunit interactions; other site 212042001142 catalytic residue [active] 212042001143 ATP synthase, Delta/Epsilon chain, beta-sandwich domain; Region: ATP-synt_DE_N; cl10033 212042001144 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 212042001145 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 212042001146 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 212042001147 alpha subunit interaction interface [polypeptide binding]; other site 212042001148 Walker A motif; other site 212042001149 ATP binding site [chemical binding]; other site 212042001150 Walker B motif; other site 212042001151 inhibitor binding site; inhibition site 212042001152 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 212042001153 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 212042001154 MgtE intracellular N domain; Region: MgtE_N; cl15244 212042001155 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 212042001156 Divalent cation transporter; Region: MgtE; cl00786 212042001157 identified by similarity to GB:AAS13832.1; match to protein family HMM PF01728; similar to putative ribosomal RNA large subunit methyltransferase J 212042001158 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 212042001159 PseudoU_synth_EcTruA: Pseudouridine synthase, Escherichia coli TruA like. This group consists of eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA, Pseudomonas aeruginosa truA and human pseudouridine synthase-like 1 (PUSL1); Region: PseudoU_synth_EcTruA; cd02570 212042001160 dimerization interface 3.5A [polypeptide binding]; other site 212042001161 active site 212042001162 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 212042001163 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 212042001164 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 212042001165 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 212042001166 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 212042001167 S-adenosylmethionine binding site [chemical binding]; other site 212042001168 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 212042001169 putative phosphate binding site [ion binding]; other site 212042001170 putative catalytic site [active] 212042001171 active site 212042001172 metal binding site A [ion binding]; metal-binding site 212042001173 DNA binding site [nucleotide binding] 212042001174 putative AP binding site [nucleotide binding]; other site 212042001175 putative metal binding site B [ion binding]; other site 212042001176 Ribosomal protein L36; Region: Ribosomal_L36; cl00380 212042001177 NADH:ubiquinone oxidoreductase 27 kD subunit [Energy production and conversion]; Region: NuoC; cl00365 212042001178 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2840 212042001179 Smr domain; Region: Smr; cl02619 212042001180 RNA polymerase Rpb6; Region: RNA_pol_Rpb6; cl14651 212042001181 Helix-turn-helix domains; Region: HTH; cl00088 212042001182 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3; Region: Oxidored_q4; cl00535 212042001183 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl00419 212042001184 NADH:ubiquinone oxidoreductase 27 kD subunit [Energy production and conversion]; Region: NuoC; cl00365 212042001185 Survival protein SurE; Region: SurE; cl00448 212042001186 CcmE; Region: CcmE; cl00994 212042001187 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 contains two...; Region: OMP_decarboxylase_like; cd04725 212042001188 active site 212042001189 dimer interface [polypeptide binding]; other site 212042001190 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 212042001191 active site 212042001192 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 212042001193 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 212042001194 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 212042001195 HIGH motif; other site 212042001196 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 212042001197 active site 212042001198 KMSKS motif; other site 212042001199 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 212042001200 tRNA binding surface [nucleotide binding]; other site 212042001201 similar to P44-82 outer membrane protein, truncation 212042001202 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 212042001203 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 212042001204 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 212042001205 The excision repair protein UvrA domain II; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_II; cd03271 212042001206 RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the...; Region: NusB_Sun; cl00223 212042001207 putative RNA binding site [nucleotide binding]; other site 212042001208 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 212042001209 homopentamer interface [polypeptide binding]; other site 212042001210 active site 212042001211 membrane protein insertase; Provisional; Region: PRK01318 212042001212 60Kd inner membrane protein; Region: 60KD_IMP; cl00489 212042001213 membrane protein insertase, YidC/Oxa1 family, N-terminal domain; Region: yidC_nterm; TIGR03593 212042001214 60Kd inner membrane protein; Region: 60KD_IMP; cl00489 212042001215 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 212042001216 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 212042001217 CDP-alcohol phosphatidyltransferase 2; Region: CDP-OH_P_tran_2; pfam08009 212042001218 Phosphatidylserine decarboxylase; Region: PS_Dcarbxylase; cl03656 212042001219 putative bifunctional glutamate synthase subunit beta/2-polyprenylphenol hydroxylase; Validated; Region: PRK06567 212042001220 FAD/NAD binding domain (electron transfer subunit) of dihydroorotate dehydrogenase-like proteins. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-dihydroorotate...; Region: DHOD_e_trans_like; cd06192 212042001221 FAD binding pocket [chemical binding]; other site 212042001222 FAD binding motif [chemical binding]; other site 212042001223 phosphate binding motif [ion binding]; other site 212042001224 beta-alpha-beta structure motif; other site 212042001225 NAD binding pocket [chemical binding]; other site 212042001226 Iron coordination center [ion binding]; other site 212042001227 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 212042001228 elongation factor P; Validated; Region: PRK00529 212042001229 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 212042001230 RNA binding site [nucleotide binding]; other site 212042001231 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 212042001232 RNA binding site [nucleotide binding]; other site 212042001233 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 212042001234 active site 212042001235 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 212042001236 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 212042001237 RNA binding surface [nucleotide binding]; other site 212042001238 PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and...; Region: PseudoU_synth_RluCD_like; cd02869 212042001239 active site 212042001240 response regulator PleD; Reviewed; Region: pleD; PRK09581 212042001241 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 212042001242 active site 212042001243 phosphorylation site [posttranslational modification] 212042001244 intermolecular recognition site; other site 212042001245 dimerization interface [polypeptide binding]; other site 212042001246 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 212042001247 active site 212042001248 phosphorylation site [posttranslational modification] 212042001249 intermolecular recognition site; other site 212042001250 dimerization interface [polypeptide binding]; other site 212042001251 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 212042001252 metal binding site [ion binding]; metal-binding site 212042001253 active site 212042001254 I-site; other site 212042001255 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 212042001256 Bacterial NAD-glutamate dehydrogenase; Region: Bac_GDH; pfam05088 212042001257 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 212042001258 Exopolysaccharide synthesis, ExoD; Region: ExoD; cl01617 212042001259 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 212042001260 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 212042001261 active site 212042001262 HIGH motif; other site 212042001263 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 212042001264 KMSKS motif; other site 212042001265 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 212042001266 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 212042001267 dimer interface [polypeptide binding]; other site 212042001268 putative radical transfer pathway; other site 212042001269 diiron center [ion binding]; other site 212042001270 tyrosyl radical; other site 212042001271 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 212042001272 catalytic residues [active] 212042001273 Protein of unknown function (DUF2610); Region: DUF2610; pfam11020 212042001274 Uncharacterized conserved protein [Function unknown]; Region: COG1565 212042001275 Uncharacterized ACR, COG1565; Region: DUF185; pfam02636 212042001276 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 212042001277 DNA primase; Validated; Region: dnaG; PRK05667 212042001278 CHC2 zinc finger; Region: zf-CHC2; cl15369 212042001279 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 212042001280 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 212042001281 active site 212042001282 metal binding site [ion binding]; metal-binding site 212042001283 interdomain interaction site; other site 212042001284 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 212042001285 Walker A/P-loop; other site 212042001286 ATP binding site [chemical binding]; other site 212042001287 Q-loop/lid; other site 212042001288 ABC transporter signature motif; other site 212042001289 Walker B; other site 212042001290 D-loop; other site 212042001291 H-loop/switch region; other site 212042001292 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: PRK14610 212042001293 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 212042001294 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 212042001295 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 212042001296 FMN binding site [chemical binding]; other site 212042001297 active site 212042001298 catalytic residues [active] 212042001299 substrate binding site [chemical binding]; other site 212042001300 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 212042001301 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 212042001302 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 212042001303 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 212042001304 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 212042001305 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 212042001306 DNA binding residues [nucleotide binding] 212042001307 CutA1 divalent ion tolerance protein; Region: CutA1; cl00584 212042001308 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 212042001309 dimer interface [polypeptide binding]; other site 212042001310 phosphorylation site [posttranslational modification] 212042001311 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 212042001312 ATP binding site [chemical binding]; other site 212042001313 Mg2+ binding site [ion binding]; other site 212042001314 G-X-G motif; other site 212042001315 Response regulator receiver domain; Region: Response_reg; pfam00072 212042001316 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 212042001317 active site 212042001318 phosphorylation site [posttranslational modification] 212042001319 intermolecular recognition site; other site 212042001320 dimerization interface [polypeptide binding]; other site 212042001321 Predicted O-methyltransferase [General function prediction only]; Region: COG4122 212042001322 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; cl12011 212042001323 ThiC family; Region: ThiC; cl08031 212042001324 YjeF-related protein N-terminus; Region: YjeF_N; cl00318 212042001325 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 212042001326 putative substrate binding site [chemical binding]; other site 212042001327 putative ATP binding site [chemical binding]; other site 212042001328 DNA topoisomerase I; Validated; Region: PRK06599 212042001329 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 212042001330 active site 212042001331 interdomain interaction site; other site 212042001332 putative metal-binding site [ion binding]; other site 212042001333 nucleotide binding site [chemical binding]; other site 212042001334 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 212042001335 domain I; other site 212042001336 DNA binding groove [nucleotide binding] 212042001337 phosphate binding site [ion binding]; other site 212042001338 domain II; other site 212042001339 domain III; other site 212042001340 nucleotide binding site [chemical binding]; other site 212042001341 catalytic site [active] 212042001342 domain IV; other site 212042001343 Uncharacterized C-terminal domain of topoisomerase IA [General function prediction only]; Region: COG1754 212042001344 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 212042001345 ThiC family; Region: ThiC; cl08031 212042001346 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 212042001347 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; cl12011 212042001348 lysyl-tRNA synthetase; Reviewed; Region: lysK; PRK00750 212042001349 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 212042001350 active site 212042001351 nucleotide binding site [chemical binding]; other site 212042001352 HIGH motif; other site 212042001353 KMSKS motif; other site 212042001354 periplasmic folding chaperone; Provisional; Region: PRK10788 212042001355 PPIC-type PPIASE domain; Region: Rotamase; cl08278 212042001356 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 212042001357 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 212042001358 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 212042001359 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 212042001360 rod shape-determining protein MreC; Region: MreC; pfam04085 212042001361 Protein of unknown function (DUF721); Region: DUF721; cl02324 212042001362 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; cl12011 212042001363 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 212042001364 substrate binding site [chemical binding]; other site 212042001365 dimer interface [polypeptide binding]; other site 212042001366 catalytic triad [active] 212042001367 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 212042001368 Tripartite tricarboxylate transporter family receptor; Region: TctC; cl15260 212042001369 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 212042001370 UGMP family protein; Validated; Region: PRK09604 212042001371 RDD family; Region: RDD; cl00746 212042001372 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 212042001373 active site 212042001374 malate dehydrogenase; Reviewed; Region: PRK06223 212042001375 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 212042001376 NAD(P) binding site [chemical binding]; other site 212042001377 dimer interface [polypeptide binding]; other site 212042001378 tetramer (dimer of dimers) interface [polypeptide binding]; other site 212042001379 substrate binding site [chemical binding]; other site 212042001380 Phage minor capsid protein 2; Region: Phage_min_cap2; pfam06152 212042001381 Head-Tail Connector Protein gp6 of Bacteriophage HK97 and similar proteins; Region: gp6; cd08054 212042001382 Ribose/Galactose Isomerase; Region: LacAB_rpiB; cl00485 212042001383 rod shape-determining protein MreB; Provisional; Region: PRK13930 212042001384 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 212042001385 prolyl-tRNA synthetase; Provisional; Region: PRK12325 212042001386 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 formation of...; Region: ProRS_core_prok; cd00779 212042001387 dimer interface [polypeptide binding]; other site 212042001388 motif 1; other site 212042001389 active site 212042001390 motif 2; other site 212042001391 motif 3; other site 212042001392 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 212042001393 anticodon binding site; other site 212042001394 Predicted glutamine amidotransferases [General function prediction only]; Region: COG2071 212042001395 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 212042001396 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 212042001397 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 212042001398 active site 212042001399 (T/H)XGH motif; other site 212042001400 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 212042001401 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 212042001402 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 212042001403 Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic hydroperoxides; Region: PRX_Typ2cys; cd03015 212042001404 dimer interface [polypeptide binding]; other site 212042001405 decamer (pentamer of dimers) interface [polypeptide binding]; other site 212042001406 catalytic triad [active] 212042001407 peroxidatic and resolving cysteines [active] 212042001408 aspartate aminotransferase; Provisional; Region: PRK05764 212042001409 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 212042001410 pyridoxal 5'-phosphate binding site [chemical binding]; other site 212042001411 homodimer interface [polypeptide binding]; other site 212042001412 catalytic residue [active] 212042001413 Surface antigen; Region: Surface_Ag_2; cl01155 212042001414 Surface antigen; Region: Surface_Ag_2; cl01155 212042001415 Surface antigen; Region: Surface_Ag_2; cl01155 212042001416 Surface antigen; Region: Surface_Ag_2; cl01155 212042001417 Surface antigen; Region: Surface_Ag_2; cl01155 212042001418 Surface antigen; Region: Surface_Ag_2; cl01155 212042001419 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 212042001420 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 212042001421 NAD(P) binding site [chemical binding]; other site 212042001422 homotetramer interface [polypeptide binding]; other site 212042001423 homodimer interface [polypeptide binding]; other site 212042001424 active site 212042001425 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed; Region: PRK11904 212042001426 Proline dehydrogenase; Region: Pro_dh; cl03282 212042001427 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 212042001428 Glutamate binding site [chemical binding]; other site 212042001429 NAD binding site [chemical binding]; other site 212042001430 catalytic residues [active] 212042001431 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 212042001432 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 212042001433 Helix-turn-helix domains; Region: HTH; cl00088 212042001434 cysteine desulfurase DndA; Region: DNA_S_dndA; TIGR03235 212042001435 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 212042001436 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 212042001437 catalytic residue [active] 212042001438 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 212042001439 cysteine desulfurase DndA; Region: DNA_S_dndA; TIGR03235 212042001440 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 212042001441 catalytic residue [active] 212042001442 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 212042001443 trimerization site [polypeptide binding]; other site 212042001444 active site 212042001445 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 212042001446 co-chaperone HscB; Provisional; Region: hscB; PRK01356 212042001447 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 212042001448 HSP70 interaction site [polypeptide binding]; other site 212042001449 Fe-S protein assembly chaperone HscA; Region: HscA; TIGR01991 212042001450 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; cl00159 212042001451 GTA TIM-barrel-like domain; Region: GTA_TIM; pfam13547 212042001452 Putative phage tail protein; Region: Phage-tail_3; pfam13550 212042001453 Cytochrome C biogenesis protein; Region: CcmH; cl01179 212042001454 Uncharacterized conserved protein (DUF2163); Region: DUF2163; pfam09931 212042001455 phage conserved hypothetical protein BR0599; Region: phg_TIGR02218 212042001456 Phage conserved hypothetical protein BR0599; Region: Phage_BR0599; pfam09356 212042001457 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG0275 212042001458 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; cl12011 212042001459 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; cl00360 212042001460 GTPase CgtA; Reviewed; Region: obgE; PRK12299 212042001461 GTP1/OBG; Region: GTP1_OBG; pfam01018 212042001462 Obg subfamily. The Obg nucleotide binding protein subfamily has been implicated in stress response, chromosome partitioning, replication initiation, mycelium development, and sporulation. Obg proteins are among a large group of GTP binding proteins...; Region: Obg; cd01898 212042001463 G1 box; other site 212042001464 GTP/Mg2+ binding site [chemical binding]; other site 212042001465 Switch I region; other site 212042001466 G2 box; other site 212042001467 G3 box; other site 212042001468 Switch II region; other site 212042001469 G4 box; other site 212042001470 enolase; Provisional; Region: eno; PRK00077 212042001471 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 212042001472 dimer interface [polypeptide binding]; other site 212042001473 metal binding site [ion binding]; metal-binding site 212042001474 substrate binding pocket [chemical binding]; other site 212042001475 GTA TIM-barrel-like domain; Region: GTA_TIM; pfam13547 212042001476 Ribosomal prokaryotic L21 protein; Region: Ribosomal_L21p; cl00382 212042001477 Ribosomal L27 protein; Region: Ribosomal_L27; cl00359 212042001478 arginyl-tRNA synthetase; Reviewed; Region: argS; PRK01611 212042001479 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; cl04104 212042001480 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 212042001481 active site 212042001482 HIGH motif; other site 212042001483 KMSK motif region; other site 212042001484 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 212042001485 tRNA binding surface [nucleotide binding]; other site 212042001486 anticodon binding site; other site 212042001487 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 212042001488 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 212042001489 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 212042001490 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 212042001491 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 212042001492 active site 212042001493 F0F1 ATP synthase subunit gamma; Provisional; Region: PRK13422 212042001494 ATP synthase; Region: ATP-synt; pfam00231 212042001495 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 212042001496 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 212042001497 ankyrin-like protein; Provisional; Region: PHA03095 212042001498 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 212042001499 NADH dehydrogenase; Region: NADHdh; cl00469 212042001500 NADH dehydrogenase subunit G; Validated; Region: PRK09130 212042001501 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 212042001502 catalytic loop [active] 212042001503 iron binding site [ion binding]; other site 212042001504 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; cl11210 212042001505 MopB_Res_Cmplx1_Nad11: The second domain of the Nad11/75-kDa subunit of the NADH-quinone oxidoreductase/respiratory complex I/NADH dehydrogenase-1(NDH-1) of eukaryotes and the Nqo3/G subunit of alphaproteobacteria NDH-1. The NADH-quinone oxidoreductase...; Region: MopB_Res-Cmplx1_Nad11; cd02773 212042001506 Domain of unknown function (DUF1982); Region: DUF1982; pfam09326 212042001507 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 212042001508 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 212042001509 Mg2+ binding site [ion binding]; other site 212042001510 G-X-G motif; other site 212042001511 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 212042001512 anchoring element; other site 212042001513 dimer interface [polypeptide binding]; other site 212042001514 ATP binding site [chemical binding]; other site 212042001515 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 212042001516 active site 212042001517 putative metal-binding site [ion binding]; other site 212042001518 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 212042001519 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 212042001520 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 212042001521 active site 212042001522 substrate binding site [chemical binding]; other site 212042001523 catalytic site [active] 212042001524 Respiratory-chain NADH dehydrogenase 24 Kd subunit; Region: Complex1_24kDa; pfam01257 212042001525 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 212042001526 putative dimer interface [polypeptide binding]; other site 212042001527 [2Fe-2S] cluster binding site [ion binding]; other site 212042001528 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; cl00417 212042001529 Respiratory-chain NADH dehydrogenase, 49 Kd subunit; Region: Complex1_49kDa; pfam00346 212042001530 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 212042001531 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 212042001532 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 212042001533 thiamine monophosphate kinase; Provisional; Region: PRK05731 212042001534 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 212042001535 ATP binding site [chemical binding]; other site 212042001536 dimerization interface [polypeptide binding]; other site 212042001537 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 212042001538 Recombination protein O N terminal; Region: RecO_N; pfam11967 212042001539 Recombination protein O C terminal; Region: RecO_C; pfam02565 212042001540 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 212042001541 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 212042001542 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 212042001543 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 212042001544 FOG: Ankyrin repeat [General function prediction only]; Region: Arp; COG0666 212042001545 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 212042001546 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 212042001547 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 212042001548 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 212042001549 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 212042001550 FAD binding domain; Region: FAD_binding_4; pfam01565 212042001551 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 212042001552 porphobilinogen deaminase; Region: hemC; TIGR00212 212042001553 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; cl03189 212042001554 domain interfaces; other site 212042001555 active site 212042001556 folylpolyglutamate synthase/dihydrofolate synthase; Region: folC; TIGR01499 212042001557 Mur ligase middle domain; Region: Mur_ligase_M; cl15713 212042001558 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 212042001559 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cl11426 212042001560 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Provisional; Region: PRK06029 212042001561 Flavoprotein; Region: Flavoprotein; cl08021 212042001562 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 212042001563 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 212042001564 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 212042001565 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 212042001566 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 212042001567 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 212042001568 DNA binding residues [nucleotide binding] 212042001569 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5410 212042001570 Phage-related terminase [General function prediction only]; Region: COG5362; cl02216 212042001571 GTP-binding protein LepA; Provisional; Region: PRK05433 212042001572 LepA subfamily. LepA belongs to the GTPase family of and exhibits significant homology to the translation factors EF-G and EF-Tu, indicating its possible involvement in translation and association with the ribosome. LepA is ubiquitous in bacteria and...; Region: LepA; cd01890 212042001573 G1 box; other site 212042001574 putative GEF interaction site [polypeptide binding]; other site 212042001575 GTP/Mg2+ binding site [chemical binding]; other site 212042001576 Switch I region; other site 212042001577 G2 box; other site 212042001578 G3 box; other site 212042001579 Switch II region; other site 212042001580 G4 box; other site 212042001581 G5 box; other site 212042001582 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 212042001583 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 212042001584 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 212042001585 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 212042001586 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; cl12011 212042001587 polyribonucleotide nucleotidyltransferase; Region: polynuc_phos; TIGR03591 212042001588 3' exoribonuclease family, domain 1; Region: RNase_PH; pfam01138 212042001589 3' exoribonuclease family, domain 2; Region: RNase_PH_C; pfam03725 212042001590 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 212042001591 3' exoribonuclease family, domain 1; Region: RNase_PH; pfam01138 212042001592 3' exoribonuclease family, domain 2; Region: RNase_PH_C; pfam03725 212042001593 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 212042001594 putative nucleic acid binding region [nucleotide binding]; other site 212042001595 G-X-X-G motif; other site 212042001596 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 212042001597 RNA binding site [nucleotide binding]; other site 212042001598 domain interface; other site 212042001599 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 212042001600 16S/18S rRNA binding site [nucleotide binding]; other site 212042001601 S13e-L30e interaction site [polypeptide binding]; other site 212042001602 25S rRNA binding site [nucleotide binding]; other site 212042001603 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK05389 212042001604 PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like. This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of specific...; Region: PseudoU_synth_EcTruB; cd02573 212042001605 RNA binding site [nucleotide binding]; other site 212042001606 active site 212042001607 rod shape-determining protein MreB; Provisional; Region: PRK13927 212042001608 Cell division protein FtsA; Region: FtsA; cl11496 212042001609 Stringent starvation protein B; Region: SspB; cl01120 212042001610 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 212042001611 CoA-binding site [chemical binding]; other site 212042001612 ATP-binding [chemical binding]; other site 212042001613 yrdC domain; Region: Sua5_yciO_yrdC; cl00305 212042001614 DNA polymerase III, delta' subunit; Region: holB; TIGR00678 212042001615 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 212042001616 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 212042001617 IHF - DNA interface [nucleotide binding]; other site 212042001618 IHF dimer interface [polypeptide binding]; other site 212042001619 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 the...; Region: PNPsynthase; cd00003 212042001620 active site 212042001621 hydrophilic channel; other site 212042001622 dimerization interface [polypeptide binding]; other site 212042001623 catalytic residues [active] 212042001624 active site lid [active] 212042001625 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 212042001626 Cytidylyltransferase; Region: CTP_transf_2; pfam01467 212042001627 active site 212042001628 (T/H)XGH motif; other site 212042001629 RNA methyltransferase; Region: Methyltrans_RNA; cl00611 212042001630 RNA methyltransferase, RsmE family; Region: TIGR00046 212042001631 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 212042001632 catalytic triad [active] 212042001633 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK06039 212042001634 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 212042001635 HIGH motif; other site 212042001636 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 212042001637 active site 212042001638 KMSKS motif; other site 212042001639 Anticodon-binding domain of archaeal, bacterial, and eukaryotic cytoplasmic isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_ABEc; cd07961 212042001640 tRNA binding surface [nucleotide binding]; other site 212042001641 anticodon binding site; other site 212042001642 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 212042001643 4Fe-4S binding domain; Region: Fer4; cl02805 212042001644 4Fe-4S binding domain; Region: Fer4; cl02805 212042001645 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 212042001646 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 212042001647 Catalytic site [active] 212042001648 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 212042001649 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 212042001650 ATP synthase; Region: ATP-synt; pfam00231 212042001651 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 212042001652 active site 212042001653 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; cl12011 212042001654 metabolite-proton symporter; Region: 2A0106; TIGR00883 212042001655 double-strand break repair protein AddB, alphaproteobacterial type; Region: addB_alphas; TIGR02786 212042001656 double-strand break repair protein AddB, alphaproteobacterial type; Region: addB_alphas; TIGR02786 212042001657 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 212042001658 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 212042001659 dimer interface [polypeptide binding]; other site 212042001660 allosteric magnesium binding site [ion binding]; other site 212042001661 active site 212042001662 aspartate-rich active site metal binding site; other site 212042001663 Schiff base residues; other site 212042001664 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cl11424 212042001665 NAD synthase; Region: NAD_synthase; pfam02540 212042001666 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 212042001667 homodimer interface [polypeptide binding]; other site 212042001668 NAD binding pocket [chemical binding]; other site 212042001669 ATP binding pocket [chemical binding]; other site 212042001670 Mg binding site [ion binding]; other site 212042001671 active-site loop [active] 212042001672 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 212042001673 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 212042001674 MutS domain I; Region: MutS_I; pfam01624 212042001675 MutS domain II; Region: MutS_II; pfam05188 212042001676 MutS family domain IV; Region: MutS_IV; pfam05190 212042001677 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 212042001678 Walker A/P-loop; other site 212042001679 ATP binding site [chemical binding]; other site 212042001680 Q-loop/lid; other site 212042001681 ABC transporter signature motif; other site 212042001682 Walker B; other site 212042001683 D-loop; other site 212042001684 H-loop/switch region; other site 212042001685 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 212042001686 nucleotide binding site/active site [active] 212042001687 HIT family signature motif; other site 212042001688 catalytic residue [active] 212042001689 phage major capsid protein, HK97 family; Region: major_cap_HK97; TIGR01554 212042001690 Phage capsid family; Region: Phage_capsid; pfam05065 212042001691 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 212042001692 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 212042001693 TPP-binding site [chemical binding]; other site 212042001694 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 212042001695 PYR/PP interface [polypeptide binding]; other site 212042001696 dimer interface [polypeptide binding]; other site 212042001697 TPP binding site [chemical binding]; other site 212042001698 adenylosuccinate lyase; Provisional; Region: PRK07492 212042001699 Adenylsuccinate lyase (ASL)_subgroup 1; Region: Adenylsuccinate_lyase_1; cd01360 212042001700 tetramer interface [polypeptide binding]; other site 212042001701 active site 212042001702 Lyase class I_like superfamily: contains the lyase class I family, histidine ammonia-lyase and phenylalanine ammonia-lyase, which catalyze similar beta-elimination reactions; Region: Lyase_I_like; cl00013 212042001703 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 212042001704 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 212042001705 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 212042001706 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 212042001707 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 212042001708 FeS/SAM binding site; other site 212042001709 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 212042001710 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 212042001711 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 212042001712 GIY-YIG motif/motif A; other site 212042001713 active site 212042001714 catalytic site [active] 212042001715 putative DNA binding site [nucleotide binding]; other site 212042001716 metal binding site [ion binding]; metal-binding site 212042001717 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 212042001718 heat shock protein 90; Provisional; Region: PRK05218 212042001719 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cl00075 212042001720 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4649 212042001721 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; cl11420 212042001722 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 212042001723 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 212042001724 minor groove reading motif; other site 212042001725 helix-hairpin-helix signature motif; other site 212042001726 substrate binding pocket [chemical binding]; other site 212042001727 active site 212042001728 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 212042001729 DNA gyrase subunit A; Validated; Region: PRK05560 212042001730 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 in DNA...; Region: TOP4c; cd00187 212042001731 CAP-like domain; other site 212042001732 active site 212042001733 primary dimer interface [polypeptide binding]; other site 212042001734 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 212042001735 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 212042001736 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 212042001737 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 212042001738 similar to P44-57 outer membrane protein, silent 212042001739 similar to P44-73 outer membrane protein, silent 212042001740 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 212042001741 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 212042001742 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 212042001743 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 212042001744 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 212042001745 Ligand Binding Site [chemical binding]; other site 212042001746 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 212042001747 diiron binding motif [ion binding]; other site 212042001748 Disulfide bond formation protein DsbB; Region: DsbB; cl00649 212042001749 Ribosomal protein L33; Region: Ribosomal_L33; cl00383 212042001750 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 212042001751 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 212042001752 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 212042001753 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 212042001754 Phosphopantetheine attachment site; Region: PP-binding; cl09936 212042001755 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 212042001756 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 212042001757 dimer interface [polypeptide binding]; other site 212042001758 active site 212042001759 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 212042001760 DNA recombination-mediator protein A; Region: DNA_processg_A; pfam02481 212042001761 similar to P44-34 outer membrane protein, silent 212042001762 similar to P44-85 outer membrane protein, truncation 212042001763 similar to P44-86 outer membrane protein, truncation 212042001764 Surface antigen; Region: Surface_Ag_2; cl01155 212042001765 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 212042001766 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 212042001767 ATP binding site [chemical binding]; other site 212042001768 Mg2+ binding site [ion binding]; other site 212042001769 G-X-G motif; other site 212042001770 MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is...; Region: MutL_Trans; cd00782 212042001771 ATP binding site [chemical binding]; other site 212042001772 MutL C terminal dimerisation domain; Region: MutL_C; cl07336 212042001773 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 212042001774 TolA protein; Region: tolA_full; TIGR02794 212042001775 sensor protein ZraS; Provisional; Region: PRK10364 212042001776 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 212042001777 dimer interface [polypeptide binding]; other site 212042001778 phosphorylation site [posttranslational modification] 212042001779 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 212042001780 ATP binding site [chemical binding]; other site 212042001781 Mg2+ binding site [ion binding]; other site 212042001782 G-X-G motif; other site 212042001783 acetylornithine transaminase protein; Provisional; Region: argD; PRK01278 212042001784 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 212042001785 inhibitor-cofactor binding pocket; inhibition site 212042001786 pyridoxal 5'-phosphate binding site [chemical binding]; other site 212042001787 catalytic residue [active] 212042001788 similar to P44 outer membrane protein, C-terminal fragment 212042001789 similar to P44 outer membrane protein, C-terminal fragment 212042001790 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 212042001791 Ftsk gamma domain; Region: Ftsk_gamma; cl09645 212042001792 YGGT family; Region: YGGT; cl00508 212042001793 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 212042001794 Domain of unknown function DUF21; Region: DUF21; pfam01595 212042001795 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 212042001796 Transporter associated domain; Region: CorC_HlyC; cl08393 212042001797 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 212042001798 thiamine phosphate binding site [chemical binding]; other site 212042001799 active site 212042001800 pyrophosphate binding site [ion binding]; other site 212042001801 Domain of unknown function (DUF299); Region: DUF299; cl00780 212042001802 Predicted sulfurtransferase [General function prediction only]; Region: COG1054 212042001803 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 212042001804 active site residue [active] 212042001805 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 212042001806 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 212042001807 putative active site [active] 212042001808 substrate binding site [chemical binding]; other site 212042001809 putative cosubstrate binding site; other site 212042001810 catalytic site [active] 212042001811 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 212042001812 substrate binding site [chemical binding]; other site 212042001813 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 212042001814 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 212042001815 Walker A motif; other site 212042001816 ATP binding site [chemical binding]; other site 212042001817 Walker B motif; other site 212042001818 arginine finger; other site 212042001819 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 212042001820 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 212042001821 ClpX C4-type zinc finger; Region: zf-C4_ClpX; cl05964 212042001822 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 212042001823 Walker A motif; other site 212042001824 ATP binding site [chemical binding]; other site 212042001825 Walker B motif; other site 212042001826 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 212042001827 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 212042001828 oligomer interface [polypeptide binding]; other site 212042001829 active site residues [active] 212042001830 trigger factor; Region: tig; TIGR00115 212042001831 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 212042001832 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 212042001833 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 212042001834 tetramer interfaces [polypeptide binding]; other site 212042001835 binuclear metal-binding site [ion binding]; other site 212042001836 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 212042001837 Coenzyme A binding pocket [chemical binding]; other site 212042001838 Protein of unknown function (DUF528); Region: DUF528; cl01123 212042001839 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 212042001840 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 212042001841 catalytic residue [active] 212042001842 similar to P44 outer membrane protein, C-terminal fragment 212042001843 similar to P44-44 outer membrane protein, silent 212042001844 Zinc binding protein ZnuA. These proteins have been shown to function as initial receptors in the ABC uptake of Zn2+. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism; Region: ZnuA; cd01019 212042001845 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 212042001846 metal binding site [ion binding]; metal-binding site 212042001847 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 212042001848 ABC component of the metal-type transporters. This family includes transporters involved in the uptake of various metallic cations such as iron, manganese, and zinc. The ATPases of this group of transporters are very similar to members of...; Region: ABC_Metallic_Cations; cd03235 212042001849 Predicted unusual protein kinase [General function prediction only]; Region: AarF; COG0661 212042001850 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs); Region: APH_ChoK_like; cl15691 212042001851 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs); Region: APH_ChoK_like; cl15691 212042001852 ATP binding site [chemical binding]; other site 212042001853 Uncharacterized protein predicted to be involved in C-type cytochrome biogenesis [Posttranslational modification, protein turnover, chaperones / Energy production and conversion]; Region: COG4233 212042001854 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 212042001855 ABC Carbohydrate and Solute Transporters-like subgroup. This family is comprised of proteins involved in the transport of apparently unrelated solutes and proteins specific for di- and oligosaccharides and polyols. ABC transporters are a large family...; Region: ABC_Carb_Solutes_like; cd03259 212042001856 Walker A/P-loop; other site 212042001857 ATP binding site [chemical binding]; other site 212042001858 Q-loop/lid; other site 212042001859 ABC transporter signature motif; other site 212042001860 Walker B; other site 212042001861 D-loop; other site 212042001862 H-loop/switch region; other site 212042001863 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 212042001864 recombination protein RecR; Reviewed; Region: recR; PRK00076 212042001865 RecR protein; Region: RecR; pfam02132 212042001866 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 212042001867 putative active site [active] 212042001868 putative metal-binding site [ion binding]; other site 212042001869 tetramer interface [polypeptide binding]; other site 212042001870 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 212042001871 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 212042001872 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 212042001873 RNA binding surface [nucleotide binding]; other site 212042001874 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 212042001875 dimer interface [polypeptide binding]; other site 212042001876 substrate binding site [chemical binding]; other site 212042001877 ATP binding site [chemical binding]; other site 212042001878 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 212042001879 Domain of unknown function DUF20; Region: UPF0118; cl00465 212042001880 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase D (SdhD) subunit-like; composed of predominantly uncharacterized bacterial proteins with similarity to the E. coli SdhD subunit. One characterized protein is the respiratory...; Region: SQR_TypeC_SdhD_like; cd03495 212042001881 putative SdhC subunit interface [polypeptide binding]; other site 212042001882 putative proximal heme binding site [chemical binding]; other site 212042001883 putative Iron-sulfur protein interface [polypeptide binding]; other site 212042001884 putative proximal quinone binding site; other site 212042001885 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 212042001886 Iron-sulfur protein interface; other site 212042001887 proximal quinone binding site [chemical binding]; other site 212042001888 SdhD (CybS) interface [polypeptide binding]; other site 212042001889 proximal heme binding site [chemical binding]; other site 212042001890 This domain family includes the Enolpyruvate transferase (EPT) family and the RNA 3' phosphate cyclase family (RTPC). These 2 families differ in that EPT is formed by 3 repeats of an alpha-beta structural domain while RTPC has 3 similar repeats with a...; Region: EPT_RTPC-like; cl00288 212042001891 3-phosphoshikimate 1-carboxyvinyltransferase; Region: aroA; TIGR01356 212042001892 putative active site [active] 212042001893 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 212042001894 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 212042001895 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 212042001896 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 212042001897 generic binding surface I; other site 212042001898 generic binding surface II; other site 212042001899 BolA-like protein; Region: BolA; cl00386 212042001900 pyridoxamine-phosphate oxidase; Region: pdxH; TIGR00558 212042001901 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 212042001902 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 212042001903 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 212042001904 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 212042001905 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 212042001906 active site 212042001907 catalytic residues [active] 212042001908 metal binding site [ion binding]; metal-binding site 212042001909 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 212042001910 quinone interaction residues [chemical binding]; other site 212042001911 Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]; Region: PyrD; COG0167 212042001912 active site 212042001913 catalytic residues [active] 212042001914 FMN binding site [chemical binding]; other site 212042001915 substrate binding site [chemical binding]; other site 212042001916 Bordetella pertussis Bvg accessory factor family; Region: Bvg_acc_factor; cl09130 212042001917 Na+/H+ ion antiporter subunit; Region: MNHE; cl00807 212042001918 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 212042001919 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 212042001920 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 212042001921 catalytic residue [active] 212042001922 Surface antigen; Region: Surface_Ag_2; cl01155 212042001923 Surface antigen; Region: Surface_Ag_2; cl01155 212042001924 similar to P44-62 outer membrane protein, silent 212042001925 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 212042001926 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 212042001927 RNA/DNA hybrid binding site [nucleotide binding]; other site 212042001928 active site 212042001929 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 212042001930 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 212042001931 RNA polymerase Rpb1, domain 2; Region: RNA_pol_Rpb1_2; cl11591 212042001932 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 212042001933 DNA-directed RNA polymerase subunit beta'; Provisional; Region: rpoC2; PRK02597 212042001934 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 212042001935 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 212042001936 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 212042001937 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed; Region: PRK09603 212042001938 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 212042001939 DNA binding site [nucleotide binding] 212042001940 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 212042001941 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; cl04593 212042001942 RNA polymerase beta subunit; Region: RNA_pol_Rpb2_1; cl04591 212042001943 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 212042001944 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; cl04593 212042001945 RPB11 interaction site [polypeptide binding]; other site 212042001946 RPB12 interaction site [polypeptide binding]; other site 212042001947 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 212042001948 RPB3 interaction site [polypeptide binding]; other site 212042001949 RPB1 interaction site [polypeptide binding]; other site 212042001950 RPB11 interaction site [polypeptide binding]; other site 212042001951 RPB10 interaction site [polypeptide binding]; other site 212042001952 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 212042001953 peripheral dimer interface [polypeptide binding]; other site 212042001954 core dimer interface [polypeptide binding]; other site 212042001955 L10 interface [polypeptide binding]; other site 212042001956 L11 interface [polypeptide binding]; other site 212042001957 putative EF-Tu interaction site [polypeptide binding]; other site 212042001958 putative EF-G interaction site [polypeptide binding]; other site 212042001959 Ribosomal protein L10 family, L10 subfamily; composed of bacterial 50S ribosomal protein and eukaryotic mitochondrial 39S ribosomal protein, L10. L10 occupies the L7/L12 stalk of the ribosome. The N-terminal domain (NTD) of L10 interacts with L11 protein...; Region: Ribosomal_L10; cd05797 212042001960 23S rRNA interface [nucleotide binding]; other site 212042001961 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 212042001962 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 212042001963 mRNA/rRNA interface [nucleotide binding]; other site 212042001964 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 212042001965 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 212042001966 23S rRNA interface [nucleotide binding]; other site 212042001967 L7/L12 interface [polypeptide binding]; other site 212042001968 putative thiostrepton binding site; other site 212042001969 L25 interface [polypeptide binding]; other site 212042001970 transcription termination/antitermination factor NusG; Region: nusG; TIGR00922 212042001971 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 212042001972 putative homodimer interface [polypeptide binding]; other site 212042001973 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 212042001974 elongation factor Tu; Reviewed; Region: PRK00049 212042001975 EF-Tu subfamily. This subfamily includes orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts. It is one of several GTP-binding translation factors found in the larger family of GTP-binding elongation factors; Region: EF_Tu; cd01884 212042001976 G1 box; other site 212042001977 GEF interaction site [polypeptide binding]; other site 212042001978 GTP/Mg2+ binding site [chemical binding]; other site 212042001979 Switch I region; other site 212042001980 G2 box; other site 212042001981 G3 box; other site 212042001982 Switch II region; other site 212042001983 G4 box; other site 212042001984 G5 box; other site 212042001985 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 212042001986 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 212042001987 Antibiotic Binding Site [chemical binding]; other site 212042001988 elongation factor G; Reviewed; Region: PRK00007 212042001989 Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved so...; Region: EF-G; cd01886 212042001990 G1 box; other site 212042001991 putative GEF interaction site [polypeptide binding]; other site 212042001992 GTP/Mg2+ binding site [chemical binding]; other site 212042001993 Switch I region; other site 212042001994 G2 box; other site 212042001995 G3 box; other site 212042001996 Switch II region; other site 212042001997 G4 box; other site 212042001998 G5 box; other site 212042001999 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 212042002000 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 212042002001 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 212042002002 Ribosomal protein S7p/S5e; Region: Ribosomal_S7; cl00313 212042002003 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 212042002004 S17 interaction site [polypeptide binding]; other site 212042002005 S8 interaction site; other site 212042002006 16S rRNA interaction site [nucleotide binding]; other site 212042002007 streptomycin interaction site [chemical binding]; other site 212042002008 23S rRNA interaction site [nucleotide binding]; other site 212042002009 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 212042002010 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 212042002011 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 212042002012 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 212042002013 translocation protein TolB; Provisional; Region: tolB; PRK05137 212042002014 TolB amino-terminal domain; Region: TolB_N; cl00639 212042002015 WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from...; Region: WD40; cl02567 212042002016 structural tetrad; other site 212042002017 Helix-turn-helix domains; Region: HTH; cl00088 212042002018 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 212042002019 ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]; Region: ThiP; COG1178 212042002020 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 212042002021 dimer interface [polypeptide binding]; other site 212042002022 conserved gate region; other site 212042002023 putative PBP binding loops; other site 212042002024 ABC-ATPase subunit interface; other site 212042002025 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 212042002026 dimer interface [polypeptide binding]; other site 212042002027 conserved gate region; other site 212042002028 putative PBP binding loops; other site 212042002029 ABC-ATPase subunit interface; other site 212042002030 putative enoyl-[acyl-carrier-protein] reductase II; Region: enACPred_II; TIGR03151 212042002031 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 212042002032 FMN binding site [chemical binding]; other site 212042002033 substrate binding site [chemical binding]; other site 212042002034 putative catalytic residue [active] 212042002035 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 212042002036 Cu(I) binding site [ion binding]; other site 212042002037 The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_LTTR_substrate; cl11398 212042002038 Ribosomal protein S21; Region: Ribosomal_S21; cl00529 212042002039 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 212042002040 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 212042002041 CoA-ligase; Region: Ligase_CoA; pfam00549 212042002042 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 212042002043 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 212042002044 CoA-ligase; Region: Ligase_CoA; pfam00549 212042002045 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 212042002046 NADH dehydrogenase subunit J; Provisional; Region: PRK06433; cl14634 212042002047 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 212042002048 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 formation of...; Region: AlaRS_core; cd00673 212042002049 motif 1; other site 212042002050 active site 212042002051 motif 2; other site 212042002052 motif 3; other site 212042002053 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 212042002054 phosphate ABC transporter, permease protein PstC; Region: phosphate_pstC; TIGR02138 212042002055 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 212042002056 dimer interface [polypeptide binding]; other site 212042002057 conserved gate region; other site 212042002058 putative PBP binding loops; other site 212042002059 ABC-ATPase subunit interface; other site 212042002060 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 212042002061 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 212042002062 similar to P44-38 outer membrane protein, silent 212042002063 similar to P44-42 outer membrane protein, silent 212042002064 similar to P44-74 outer membrane protein, silent 212042002065 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06416 212042002066 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 212042002067 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 212042002068 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 212042002069 transcription termination factor Rho; Provisional; Region: rho; PRK09376 212042002070 Rho termination factor, N-terminal domain; Region: Rho_N; cl06505 212042002071 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 212042002072 RNA binding site [nucleotide binding]; other site 212042002073 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 212042002074 multimer interface [polypeptide binding]; other site 212042002075 Walker A motif; other site 212042002076 ATP binding site [chemical binding]; other site 212042002077 Walker B motif; other site 212042002078 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a...; Region: Ntn_hydrolase; cl00467 212042002079 active site 212042002080 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 212042002081 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 212042002082 Walker A motif; other site 212042002083 ATP binding site [chemical binding]; other site 212042002084 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 212042002085 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 212042002086 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 212042002087 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 212042002088 S-adenosylmethionine binding site [chemical binding]; other site 212042002089 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; cl12011 212042002090 Surface antigen; Region: Surface_Ag_2; cl01155 212042002091 similar to P44-41 outer membrane protein, silent 212042002092 similar to P44-56 outer membrane protein, silent 212042002093 methionyl-tRNA synthetase; Reviewed; Region: PRK11893 212042002094 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 212042002095 active site 212042002096 HIGH motif; other site 212042002097 KMSKS motif; other site 212042002098 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 212042002099 tRNA binding surface [nucleotide binding]; other site 212042002100 anticodon binding site; other site 212042002101 similar to P44-50 outer membrane protein, silent 212042002102 identified by match to protein family HMM PF01617; similar to P44-28 outer membrane protein, silent 212042002103 similar to P44-52 outer membrane protein, silent 212042002104 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 212042002105 cytochrome c oxidase subunit II; Provisional; Region: COX2; MTH00140 212042002106 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 212042002107 cytochrome c oxidase subunit I; Validated; Region: COX1; MTH00007 212042002108 Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of...; Region: Cyt_c_Oxidase_I; cd01663 212042002109 Subunit I/III interface [polypeptide binding]; other site 212042002110 D-pathway; other site 212042002111 Subunit I/VIIc interface [polypeptide binding]; other site 212042002112 Subunit I/IV interface [polypeptide binding]; other site 212042002113 Subunit I/II interface [polypeptide binding]; other site 212042002114 Low-spin heme (heme a) binding site [chemical binding]; other site 212042002115 Subunit I/VIIa interface [polypeptide binding]; other site 212042002116 Subunit I/VIa interface [polypeptide binding]; other site 212042002117 Dimer interface; other site 212042002118 Putative water exit pathway; other site 212042002119 Binuclear center (heme a3/CuB) [ion binding]; other site 212042002120 K-pathway; other site 212042002121 Subunit I/Vb interface [polypeptide binding]; other site 212042002122 Putative proton exit pathway; other site 212042002123 Subunit I/VIb interface; other site 212042002124 Subunit I/VIc interface [polypeptide binding]; other site 212042002125 Electron transfer pathway; other site 212042002126 Subunit I/VIIIb interface [polypeptide binding]; other site 212042002127 Subunit I/VIIb interface [polypeptide binding]; other site 212042002128 UbiA prenyltransferase family; Region: UbiA; cl00337 212042002129 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 212042002130 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 212042002131 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 212042002132 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 212042002133 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 212042002134 Preprotein translocase subunit; Region: YajC; cl00806 212042002135 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 212042002136 NADH dehydrogenase subunit J; Provisional; Region: PRK06433; cl14634 212042002137 putative glycoprotease GCP; Region: bact_gcp; TIGR03723 212042002138 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 212042002139 DNA polymerase III subunit beta; Validated; Region: PRK05643 212042002140 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 212042002141 putative DNA binding surface [nucleotide binding]; other site 212042002142 dimer interface [polypeptide binding]; other site 212042002143 beta-clamp/clamp loader binding surface; other site 212042002144 beta-clamp/translesion DNA polymerase binding surface; other site 212042002145 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 212042002146 putative active site [active] 212042002147 catalytic site [active] 212042002148 putative substrate binding site [chemical binding]; other site 212042002149 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 212042002150 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 212042002151 active site 212042002152 phosphorylation site [posttranslational modification] 212042002153 intermolecular recognition site; other site 212042002154 dimerization interface [polypeptide binding]; other site 212042002155 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 212042002156 DNA binding site [nucleotide binding] 212042002157 Predicted transcriptional regulator [Transcription]; Region: COG2932 212042002158 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 212042002159 non-specific DNA binding site [nucleotide binding]; other site 212042002160 salt bridge; other site 212042002161 sequence-specific DNA binding site [nucleotide binding]; other site 212042002162 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 212042002163 Catalytic site [active] 212042002164 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 212042002165 dimer interface [polypeptide binding]; other site 212042002166 substrate binding site [chemical binding]; other site 212042002167 metal binding sites [ion binding]; metal-binding site 212042002168 Ribosomal protein S9/S16; Region: Ribosomal_S9; cl00334 212042002169 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 212042002170 23S rRNA interface [nucleotide binding]; other site 212042002171 L3 interface [polypeptide binding]; other site 212042002172 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 212042002173 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 212042002174 Phosphoribosylpyrophosphate synthetase [Nucleotide transport and metabolism / Amino acid transport and metabolism]; Region: PrsA; COG0462 212042002175 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 212042002176 Glu-tRNAGln amidotransferase C subunit; Region: Glu-tRNAGln; cl00495 212042002177 Surface antigen; Region: Surface_Ag_2; cl01155 212042002178 Surface antigen; Region: Surface_Ag_2; cl01155 212042002179 similar to P44 outer membrane protein, C-terminal fragment 212042002180 aconitate hydratase; Validated; Region: PRK09277 212042002181 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 212042002182 substrate binding site [chemical binding]; other site 212042002183 ligand binding site [chemical binding]; other site 212042002184 Aconitase A swivel domain. This is the major form of the TCA cycle enzyme aconitate hydratase, also known as aconitase and citrate hydro-lyase. It includes bacterial and archaeal aconitase A, and the eukaryotic cytosolic form of aconitase. This group...; Region: AcnA_IRP_Swivel; cd01580 212042002185 substrate binding site [chemical binding]; other site 212042002186 identified by match to protein family HMM PF01617; similar to P44-7b outer membrane protein, silent 212042002187 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed; Region: PRK06019 212042002188 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; cl03087 212042002189 Protein of unknown function (DUF525); Region: DUF525; cl01119 212042002190 similar to P44-6 outer membrane protein, silent 212042002191 similar to P44-75 outer membrane protein, silent 212042002192 similar to P44-3 outer membrane protein, silent 212042002193 Surface antigen; Region: Surface_Ag_2; cl01155 212042002194 Surface antigen; Region: Surface_Ag_2; cl01155 212042002195 similar to P44-76 outer membrane protein, silent 212042002196 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 212042002197 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 212042002198 TrbC/VIRB2 family; Region: TrbC; cl01583 212042002199 TrbC/VIRB2 family; Region: TrbC; cl01583 212042002200 TrbC/VIRB2 family; Region: TrbC; cl01583 212042002201 TrbC/VIRB2 family; Region: TrbC; cl01583 212042002202 TrbC/VIRB2 family; Region: TrbC; cl01583 212042002203 TrbC/VIRB2 family; Region: TrbC; cl01583 212042002204 TrbC/VIRB2 family; Region: TrbC; cl01583 212042002205 Band_7_HflK: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfK (High frequency of lysogenization K). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflK; cd03404 212042002206 HflK protein; Region: hflK; TIGR01933 212042002207 HflC protein; Region: hflC; TIGR01932 212042002208 Band_7_HflC: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfC (High frequency of lysogenization C). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflC; cd03405 212042002209 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 212042002210 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad...; Region: Tryp_SPc; cl00149 212042002211 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 212042002212 protein binding site [polypeptide binding]; other site 212042002213 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 212042002214 protein binding site [polypeptide binding]; other site 212042002215 ribonuclease III; Reviewed; Region: rnc; PRK00102 212042002216 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 212042002217 dimerization interface [polypeptide binding]; other site 212042002218 active site 212042002219 metal binding site [ion binding]; metal-binding site 212042002220 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 212042002221 dsRNA binding site [nucleotide binding]; other site 212042002222 Cytochrome c oxidase assembly protein CtaG/Cox11; Region: CtaG_Cox11; cl01240 212042002223 similar to P44-47 outer membrane protein, silent 212042002224 identified by similarity to GB:AAL86382.1; similar to P44-4 outer membrane protein, silent 212042002225 Surface antigen; Region: Surface_Ag_2; cl01155 212042002226 Surface antigen; Region: Surface_Ag_2; cl01155 212042002227 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 212042002228 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 212042002229 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 212042002230 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 212042002231 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 212042002232 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 212042002233 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 212042002234 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 212042002235 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 212042002236 active site 212042002237 Riboflavin kinase; Region: Flavokinase; cl03312 212042002238 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 212042002239 GSH binding site [chemical binding]; other site 212042002240 catalytic residues [active] 212042002241 identified by match to protein family HMM PF01617; similar to P44-53b outer membrane protein, silent 212042002242 cell division protein FtsA; Region: ftsA; TIGR01174 212042002243 Cell division protein FtsA; Region: FtsA; cl11496 212042002244 Cell division protein FtsA; Region: FtsA; cl11496 212042002245 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 212042002246 DHH family; Region: DHH; pfam01368 212042002247 DHHA1 domain; Region: DHHA1; pfam02272 212042002248 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 212042002249 isocitrate dehydrogenase; Region: ICDH_alpha; TIGR02924 212042002250 Surface antigen; Region: Surface_Ag_2; cl01155 212042002251 Surface antigen; Region: Surface_Ag_2; cl01155 212042002252 Surface antigen; Region: Surface_Ag_2; cl01155 212042002253 Surface antigen; Region: Surface_Ag_2; cl01155 212042002254 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 212042002255 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 212042002256 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 212042002257 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 212042002258 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 212042002259 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 212042002260 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 212042002261 SURF1 superfamily. Surf1/Shy1 has been implicated in the posttranslational steps of the biogenesis of the mitochondrially-encoded Cox1 subunit of cytochrome c oxidase (complex IV). Cytochrome c oxidase (complex IV), the terminal electron-transferring...; Region: SURF1; cd06662 212042002262 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 212042002263 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 2 [Coenzyme metabolism]; Region: ThiF; COG0476 212042002264 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 212042002265 ATP binding site [chemical binding]; other site 212042002266 substrate interface [chemical binding]; other site 212042002267 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 212042002268 Surface antigen; Region: Surface_Ag_2; cl01155 212042002269 similar to P44-54 outer membrane protein, silent 212042002270 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 212042002271 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 212042002272 SecA preprotein cross-linking domain; Region: SecA_PP_bind; cl03078 212042002273 SEC-C motif; Region: SEC-C; pfam02810 212042002274 FtsH Extracellular; Region: FtsH_ext; pfam06480 212042002275 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 212042002276 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 212042002277 Walker A motif; other site 212042002278 ATP binding site [chemical binding]; other site 212042002279 Walker B motif; other site 212042002280 arginine finger; other site 212042002281 Peptidase family M41; Region: Peptidase_M41; pfam01434 212042002282 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 212042002283 Ligand Binding Site [chemical binding]; other site 212042002284 NADH dehydrogenase subunit J; Provisional; Region: PRK06433; cl14634 212042002285 Cation transport protein; Region: TrkH; cl10514 212042002286 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 212042002287 cell division protein FtsA; Region: ftsA; TIGR01174 212042002288 Cell division protein FtsA; Region: FtsA; cl11496 212042002289 Cell division protein FtsA; Region: FtsA; cl11496 212042002290 similar to P44-43 outer membrane protein 212042002291 similar to P44 outer membrane protein, C-terminal fragment 212042002292 similar to P44-40 outer membrane protein, silent 212042002293 Mitochondrial ATP synthase B chain precursor (ATP-synt_B); Region: Mt_ATP-synt_B; cl07975 212042002294 ATP synthase subunit C; Region: ATP-synt_C; cl00466 212042002295 ATP synthase A chain; Region: ATP-synt_A; cl00413 212042002296 Glycerol-1-phosphate dehydrogenase (G1PDH) catalyzes the reversible reduction of dihydroxyacetone phosphate (DHAP) to glycerol-1-phosphate (G1P) in an NADH-dependent manner; Region: G1PDH; cd08175 212042002297 active site 212042002298 metal binding site [ion binding]; metal-binding site 212042002299 similar to P44-18 outer membrane protein, silent 212042002300 Surface antigen; Region: Surface_Ag_2; cl01155 212042002301 Surface antigen; Region: Surface_Ag_2; cl01155 212042002302 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 212042002303 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 212042002304 trimer interface [polypeptide binding]; other site 212042002305 putative metal binding site [ion binding]; other site 212042002306 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 212042002307 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 212042002308 E3 interaction surface; other site 212042002309 lipoyl attachment site [posttranslational modification]; other site 212042002310 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 212042002311 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 212042002312 active site 212042002313 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 212042002314 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 212042002315 S-adenosylmethionine binding site [chemical binding]; other site 212042002316 similar to P44-77 outer membrane protein, silent 212042002317 similar to P44-34b outer membrane protein, silent 212042002318 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 212042002319 Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is...; Region: Heme_Cu_Oxidase_I; cl00275 212042002320 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 212042002321 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 212042002322 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 212042002323 purine monophosphate binding site [chemical binding]; other site 212042002324 dimer interface [polypeptide binding]; other site 212042002325 putative catalytic residues [active] 212042002326 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 212042002327 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 212042002328 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 212042002329 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 212042002330 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 212042002331 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 212042002332 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 212042002333 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 212042002334 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 212042002335 Surface antigen; Region: Bac_surface_Ag; cl03097 212042002336 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]; Region: COG0750 212042002337 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 212042002338 active site 212042002339 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 212042002340 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 212042002341 putative substrate binding region [chemical binding]; other site 212042002342 Flavinator of succinate dehydrogenase; Region: Sdh5; cl01110 212042002343 Thiol:disulfide interchange protein [Posttranslational modification, protein turnover, chaperones / Energy production and conversion]; Region: COG4232 212042002344 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 212042002345 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 212042002346 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; cl06814 212042002347 Surface antigen; Region: Surface_Ag_2; cl01155 212042002348 Surface antigen; Region: Surface_Ag_2; cl01155 212042002349 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 212042002350 active site 212042002351 NTP binding site [chemical binding]; other site 212042002352 metal binding triad [ion binding]; metal-binding site 212042002353 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 212042002354 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 212042002355 active site 212042002356 multimer interface [polypeptide binding]; other site 212042002357 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 212042002358 non-specific DNA binding site [nucleotide binding]; other site 212042002359 salt bridge; other site 212042002360 sequence-specific DNA binding site [nucleotide binding]; other site 212042002361 Surface antigen; Region: Surface_Ag_2; cl01155 212042002362 Surface antigen; Region: Surface_Ag_2; cl01155 212042002363 Surface antigen; Region: Surface_Ag_2; cl01155 212042002364 Surface antigen; Region: Surface_Ag_2; cl01155 212042002365 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 212042002366 Walker A motif; other site 212042002367 valyl-tRNA synthetase; Reviewed; Region: valS; PRK13208 212042002368 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 212042002369 active site 212042002370 HIGH motif; other site 212042002371 nucleotide binding site [chemical binding]; other site 212042002372 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 212042002373 active site 212042002374 KMSKS motif; other site 212042002375 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 212042002376 tRNA binding surface [nucleotide binding]; other site 212042002377 anticodon binding site; other site 212042002378 C4-dicarboxylate anaerobic carrier; Region: DcuC; cl15356 212042002379 similar to P44-15 outer membrane protein, silent 212042002380 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 212042002381 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 212042002382 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 212042002383 P loop; other site 212042002384 GTP binding site [chemical binding]; other site 212042002385 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 212042002386 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 212042002387 Surface antigen; Region: Surface_Ag_2; cl01155 212042002388 Surface antigen; Region: Surface_Ag_2; cl01155 212042002389 similar to P44 outer membrane protein, C-terminal fragment 212042002390 Glutamate-cysteine ligase; Region: GshA; pfam08886 212042002391 glutamate--cysteine ligase, T. ferrooxidans family; Region: gshA_ferroox; TIGR02049 212042002392 Citrate synthase (CS), citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CS catalyzes the condensation of acetyl coenzyme A; Region: CS_ACL-C_CCL; cl00416 212042002393 Citrate synthase; Region: Citrate_synt; pfam00285 212042002394 oxalacetate binding site [chemical binding]; other site 212042002395 citrylCoA binding site [chemical binding]; other site 212042002396 coenzyme A binding site [chemical binding]; other site 212042002397 catalytic triad [active] 212042002398 GMP synthase; Reviewed; Region: guaA; PRK00074 212042002399 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 212042002400 AMP/PPi binding site [chemical binding]; other site 212042002401 candidate oxyanion hole; other site 212042002402 catalytic triad [active] 212042002403 potential glutamine specificity residues [chemical binding]; other site 212042002404 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 212042002405 ATP Binding subdomain [chemical binding]; other site 212042002406 Ligand Binding sites [chemical binding]; other site 212042002407 Dimerization subdomain; other site 212042002408 similar to P44-13 outer membrane protein, silent 212042002409 Surface antigen; Region: Surface_Ag_2; cl01155 212042002410 Surface antigen; Region: Surface_Ag_2; cl01155 212042002411 Surface antigen; Region: Surface_Ag_2; cl01155 212042002412 alternate gene name:major outer membrane protein C-17.Infect Immun. 1998 Aug;66(8):3711-8.; similar to P44-33 outer membrane protein, silent 212042002413 identified by match to protein family HMM PF01617; similar to P44-49 outer membrane protein, silent 212042002414 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 212042002415 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 212042002416 substrate-cofactor binding pocket; other site 212042002417 pyridoxal 5'-phosphate binding site [chemical binding]; other site 212042002418 catalytic residue [active] 212042002419 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 212042002420 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 212042002421 active site 212042002422 HIGH motif; other site 212042002423 dimer interface [polypeptide binding]; other site 212042002424 KMSKS motif; other site 212042002425 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 212042002426 RNA binding surface [nucleotide binding]; other site 212042002427 glutamine synthetase, type I; Region: GlnA; TIGR00653 212042002428 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 212042002429 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 212042002430 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 212042002431 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 212042002432 substrate binding pocket [chemical binding]; other site 212042002433 chain length determination region; other site 212042002434 substrate-Mg2+ binding site; other site 212042002435 catalytic residues [active] 212042002436 aspartate-rich region 1; other site 212042002437 active site lid residues [active] 212042002438 aspartate-rich region 2; other site 212042002439 similar to P44-27 outer membrane protein, silent 212042002440 Surface antigen; Region: Surface_Ag_2; cl01155 212042002441 Surface antigen; Region: Surface_Ag_2; cl01155 212042002442 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK06585 212042002443 similar to P44-39 outer membrane protein, silent 212042002444 identified by match to protein family HMM PF01617; similar to P44-10 outer membrane protein, silent 212042002445 Surface antigen; Region: Surface_Ag_2; cl01155 212042002446 Surface antigen; Region: Surface_Ag_2; cl01155 212042002447 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed; Region: PRK11856 212042002448 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 212042002449 E3 interaction surface; other site 212042002450 lipoyl attachment site [posttranslational modification]; other site 212042002451 e3 binding domain; Region: E3_binding; pfam02817 212042002452 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 212042002453 DhnA-type fructose-1,6-bisphosphate aldolase and related enzymes [Carbohydrate transport and metabolism]; Region: FbaB; COG1830 212042002454 Class I fructose-1,6-bisphosphate (FBP) aldolases of the archaeal type (DhnA homologs); Region: DhnA; cd00958 212042002455 putative active site; other site 212042002456 catalytic residue [active] 212042002457 similar to P44-46 outer membrane protein, silent 212042002458 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 212042002459 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 212042002460 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 212042002461 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 212042002462 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 212042002463 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 212042002464 active site 212042002465 dimer interface [polypeptide binding]; other site 212042002466 motif 1; other site 212042002467 motif 2; other site 212042002468 motif 3; other site 212042002469 HGTP anticodon binding domain, as found at the C-terminus of histidyl, glycyl, threonyl and prolyl tRNA synthetases, which are classified as a group of class II aminoacyl-tRNA synthetases (aaRS). In aaRSs, the anticodon binding domain is responsible for...; Region: HGTP_anticodon; cl00266 212042002470 anticodon binding site; other site 212042002471 Competence-damaged protein; Region: CinA; cl00666 212042002472 Ribosomal protein L19; Region: Ribosomal_L19; cl00406 212042002473 tRNA (Guanine-1)-methyltransferase; Region: tRNA_m1G_MT; cl00407 212042002474 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK14592 212042002475 RimM N-terminal domain; Region: RimM; pfam01782 212042002476 Surface antigen; Region: Surface_Ag_2; cl01155 212042002477 Surface antigen; Region: Surface_Ag_2; cl01155 212042002478 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 212042002479 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 212042002480 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 212042002481 Surface antigen; Region: Surface_Ag_2; cl01155 212042002482 identified by match to protein family HMM PF01617; similar to P44-25 outer membrane protein, silent 212042002483 Surface antigen; Region: Surface_Ag_2; cl01155 212042002484 Surface antigen; Region: Surface_Ag_2; cl01155 212042002485 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 212042002486 homotrimer interaction site [polypeptide binding]; other site 212042002487 zinc binding site [ion binding]; other site 212042002488 CDP-binding sites; other site 212042002489 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 212042002490 substrate binding site; other site 212042002491 dimer interface; other site 212042002492 AIR carboxylase; Region: AIRC; cl00310 212042002493 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 212042002494 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 212042002495 IHF - DNA interface [nucleotide binding]; other site 212042002496 IHF dimer interface [polypeptide binding]; other site 212042002497 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Region: HTH_MlrA-like_sg2; cd04765 212042002498 DNA binding residues [nucleotide binding] 212042002499 similar to P44 outer membrane protein, C-terminal fragment 212042002500 GTP-binding protein YchF; Reviewed; Region: PRK09601 212042002501 YchF subfamily. YchF is a member of the Obg family, which includes four other subfamilies of GTPases: Obg, DRG, Ygr210, and NOG1. Obg is an essential gene that is involved in DNA replication in C. crescentus and Streptomyces griseus and is associated...; Region: YchF; cd01900 212042002502 G1 box; other site 212042002503 GTP/Mg2+ binding site [chemical binding]; other site 212042002504 Switch I region; other site 212042002505 G2 box; other site 212042002506 Switch II region; other site 212042002507 G3 box; other site 212042002508 G4 box; other site 212042002509 G5 box; other site 212042002510 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 212042002511 Surface antigen; Region: Surface_Ag_2; cl01155 212042002512 Surface antigen; Region: Surface_Ag_2; cl01155 212042002513 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 212042002514 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 212042002515 TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in bacteria and eukaryotes. It controls modification of the uridine at the wobble position (U34) of tRNAs that read codons ending with A or G in the mixed codon family boxes. TrmE contains a GTPase...; Region: trmE; cd04164 212042002516 G1 box; other site 212042002517 GTP/Mg2+ binding site [chemical binding]; other site 212042002518 Switch I region; other site 212042002519 G2 box; other site 212042002520 Switch II region; other site 212042002521 G3 box; other site 212042002522 G4 box; other site 212042002523 G5 box; other site 212042002524 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 212042002525 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 212042002526 EVE domain; Region: EVE; cl00728 212042002527 cell division protein FtsZ; Validated; Region: PRK09330 212042002528 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 212042002529 nucleotide binding site [chemical binding]; other site 212042002530 SulA interaction site; other site 212042002531 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 includes...; Region: RuvC_resolvase; cl00243 212042002532 Heme-copper oxidase subunit III. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which couple the reduction of molecular oxygen to water to, proton pumping across the membrane. The...; Region: Heme_Cu_Oxidase_III_like; cl00211 212042002533 Flavoprotein; Region: Flavoprotein; cl08021 212042002534 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 212042002535 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 212042002536 ssDNA binding site; other site 212042002537 generic binding surface II; other site 212042002538 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 212042002539 ATP binding site [chemical binding]; other site 212042002540 putative Mg++ binding site [ion binding]; other site 212042002541 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 212042002542 nucleotide binding region [chemical binding]; other site 212042002543 ATP-binding site [chemical binding]; other site 212042002544 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs; Region: NDUFA9_like_SDR_a; cd05271 212042002545 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 212042002546 putative NAD(P) binding site [chemical binding]; other site 212042002547 active site 212042002548 amidophosphoribosyltransferase; Provisional; Region: PRK09123 212042002549 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 212042002550 active site 212042002551 tetramer interface [polypeptide binding]; other site 212042002552 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 212042002553 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 212042002554 putative active site [active] 212042002555 catalytic residue [active] 212042002556 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 212042002557 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 212042002558 5S rRNA interface [nucleotide binding]; other site 212042002559 CTC domain interface [polypeptide binding]; other site 212042002560 L16 interface [polypeptide binding]; other site 212042002561 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 212042002562 Phosphoribosyl transferase domain; Region: Pribosyltran; cl00309 212042002563 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 212042002564 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 212042002565 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 212042002566 Peroxiredoxin (PRX)-like 1 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a conserved cysteine that aligns to the first cysteine in the CXXC motif of TRX. This does not correspond to the peroxidatic...; Region: PRX_like1; cd02969 212042002567 putative catalytic residue [active] 212042002568 Uncharacterised protein family (UPF0093); Region: UPF0093; cl00863 212042002569 pyruvate dehydrogenase subunit beta; Validated; Region: PRK09212 212042002570 Pyrimidine (PYR) binding domain of the beta subunits of the E1 components of human pyruvate dehydrogenase complex (E1- PDHc) and related proteins; Region: TPP_PYR_E1-PDHc-beta_like; cd07036 212042002571 alpha subunit interface [polypeptide binding]; other site 212042002572 TPP binding site [chemical binding]; other site 212042002573 heterodimer interface [polypeptide binding]; other site 212042002574 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 212042002575 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; cl00398 212042002576 Putative modulator of DNA gyrase; Region: PmbA_TldD; pfam01523 212042002577 Surface antigen; Region: Surface_Ag_2; cl01155 212042002578 Surface antigen; Region: Surface_Ag_2; cl01155 212042002579 identified by match to protein family HMM PF01617; similar to P44-5 outer membrane protein, silent 212042002580 similar to P44-26 outer membrane protein, silent 212042002581 GTP cyclohydrolase; Provisional; Region: PRK08815 212042002582 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 212042002583 dimerization interface [polypeptide binding]; other site 212042002584 active site 212042002585 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 212042002586 binding surface 212042002587 TPR motif; other site 212042002588 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 212042002589 S-adenosylmethionine binding site [chemical binding]; other site 212042002590 Phosphoglycerate kinase; Region: PGK; pfam00162 212042002591 Phosphoglycerate kinase (PGK) is a monomeric enzyme which catalyzes the transfer of the high-energy phosphate group of 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate. This reaction represents the first of the two substrate-level...; Region: Phosphoglycerate_kinase; cl00198 212042002592 substrate binding site [chemical binding]; other site 212042002593 hinge regions; other site 212042002594 ADP binding site [chemical binding]; other site 212042002595 catalytic site [active] 212042002596 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 212042002597 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 212042002598 generic binding surface II; other site 212042002599 generic binding surface I; other site 212042002600 MJ0042 family finger-like domain; Region: MJ0042_CXXC; TIGR02098 212042002601 Protein of unknown function (DUF3426); Region: DUF3426; pfam11906 212042002602 similar to P44 outer membrane protein, N-terminal fragment 212042002603 Surface antigen; Region: Surface_Ag_2; cl01155 212042002604 Surface antigen; Region: Surface_Ag_2; cl01155 212042002605 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 212042002606 Protein export membrane protein; Region: SecD_SecF; cl14618 212042002607 similar to P44-17 outermembrane protein, silent 212042002608 identified by match to protein family HMM PF01617; similar to P44-60 outer membrane protein, silent 212042002609 similar to P44-29 outer membrane protein, silent 212042002610 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 212042002611 SmpB-tmRNA interface; other site 212042002612 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; cl00336 212042002613 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 212042002614 domain; Region: GreA_GreB_N; pfam03449 212042002615 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 212042002616 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 212042002617 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 212042002618 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 212042002619 beta subunit interaction interface [polypeptide binding]; other site 212042002620 Walker A motif; other site 212042002621 ATP binding site [chemical binding]; other site 212042002622 Walker B motif; other site 212042002623 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 212042002624 F0F1-type ATP synthase, delta subunit (mitochondrial oligomycin sensitivity protein) [Energy production and conversion]; Region: AtpH; cl15360 212042002625 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 212042002626 Protein of unknown function (DUF1467); Region: DUF1467; cl11569 212042002627 Uncharacterized membrane-bound protein [Function unknown]; Region: COG3898 212042002628 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 212042002629 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 212042002630 FtsX-like permease family; Region: FtsX; pfam02687 212042002631 similar to P44-31 outer membrane protein, silent 212042002632 similar to P44-58 outer membrane protein, silent 212042002633 Uncharacterised P-loop hydrolase UPF0079; Region: UPF0079; cl00520 212042002634 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 212042002635 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 212042002636 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 212042002637 Semialdehyde dehydrogenase, dimerisation domain; Region: Semialdhyde_dhC; pfam02774 212042002638 Uncharacterised BCR, YbaB family COG0718; Region: DUF149; cl00494 212042002639 DNA polymerase III subunits gamma and tau; Provisional; Region: PRK14964 212042002640 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 212042002641 Walker A motif; other site 212042002642 ATP binding site [chemical binding]; other site 212042002643 Walker B motif; other site 212042002644 arginine finger; other site 212042002645 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 212042002646 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; cl15267 212042002647 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 212042002648 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 212042002649 similar to P44-51 outer membrane protein, silent 212042002650 identified by similarity to GB:AAO30097.1; match to protein family HMM PF01617; similar to P44-35 outer membrane protein, silent 212042002651 identified by match to protein family HMM PF01617; similar to P44-30 outer membrane protein, silent 212042002652 recombinase A; Provisional; Region: recA; PRK09354 212042002653 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 212042002654 hexamer interface [polypeptide binding]; other site 212042002655 Walker A motif; other site 212042002656 ATP binding site [chemical binding]; other site 212042002657 Walker B motif; other site 212042002658 Surface antigen; Region: Surface_Ag_2; cl01155 212042002659 Surface antigen; Region: Surface_Ag_2; cl01155 212042002660 identified by Glimmer2; putative; similar to hypothetical protein 212042002661 Surface antigen; Region: Surface_Ag_2; cl01155 212042002662 Surface antigen; Region: Surface_Ag_2; cl01155 212042002663 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 212042002664 Surface antigen; Region: Surface_Ag_2; cl01155 212042002665 Zinc-finger domain; Region: zf-CHCC; cl01821 212042002666 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 212042002667 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 212042002668 Protein export membrane protein; Region: SecD_SecF; cl14618 212042002669 excinuclease ABC subunit B; Provisional; Region: PRK05298 212042002670 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 212042002671 ATP binding site [chemical binding]; other site 212042002672 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 212042002673 nucleotide binding region [chemical binding]; other site 212042002674 ATP-binding site [chemical binding]; other site 212042002675 Ultra-violet resistance protein B; Region: UvrB; pfam12344 212042002676 UvrB/uvrC motif; Region: UVR; pfam02151 212042002677 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 212042002678 Fe-S cluster binding site [ion binding]; other site 212042002679 active site 212042002680 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 212042002681 active site 212042002682 catalytic residues [active] 212042002683 metal binding site [ion binding]; metal-binding site 212042002684 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 212042002685 putative acyl-acceptor binding pocket; other site 212042002686 Ribosomal protein S20; Region: Ribosomal_S20p; cl00384 212042002687 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; cl00234 212042002688 active site 212042002689 metal binding site [ion binding]; metal-binding site 212042002690 catalytic residues [active] 212042002691 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 212042002692 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 212042002693 MatE; Region: MatE; cl10513 212042002694 similar to P44 outer membrane protein, C-terminal fragment 212042002695 similar to P44-20 outer membrane protein, silent 212042002696 identified by match to protein family HMM PF01617; similar to P44-9 outer membrane protein, silent 212042002697 Surface antigen; Region: Surface_Ag_2; cl01155 212042002698 Surface antigen; Region: Surface_Ag_2; cl01155 212042002699 ABC-type transport system involved in resistance to organic solvents, auxiliary component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2D; cl01074 212042002700 Cation efflux family; Region: Cation_efflux; cl00316 212042002701 CcmB protein; Region: CcmB; cl01016 212042002702 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 212042002703 similar to P44 outer membrane protein, C-terminal fragment 212042002704 similar to P44-37 outer membrane protein, silent 212042002705 similar to P44-22 outer membrane protein, silent 212042002706 type IV secretion system component VirD4; Provisional; Region: PRK13897 212042002707 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion. These proteins aid the transfer of DNA from the plasmid into the host bacterial chromosome. They contain an ATP binding domain. VirD4 is involved in DNA transfer...; Region: TraG_VirD4; cd01126 212042002708 Walker A motif; other site 212042002709 ATP binding site [chemical binding]; other site 212042002710 Walker B motif; other site 212042002711 P-type DNA transfer ATPase VirB11; Region: VirB11; TIGR02788 212042002712 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 212042002713 Walker A motif; other site 212042002714 hexamer interface [polypeptide binding]; other site 212042002715 ATP binding site [chemical binding]; other site 212042002716 Walker B motif; other site 212042002717 Bacterial conjugation TrbI-like protein; Region: TrbI; cl04242 212042002718 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cl11423 212042002719 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 212042002720 VirB7 interaction site; other site 212042002721 VirB8 protein; Region: VirB8; cl01500 212042002722 similar to P44-59 outer membrane protein, silent 212042002723 Recombinational DNA repair ATPase (RecF pathway) [DNA replication, recombination, and repair]; Region: RecF; COG1195 212042002724 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 212042002725 Walker A/P-loop; other site 212042002726 ATP binding site [chemical binding]; other site 212042002727 Q-loop/lid; other site 212042002728 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 212042002729 ABC transporter signature motif; other site 212042002730 Walker B; other site 212042002731 D-loop; other site 212042002732 H-loop/switch region; other site