-- dump date 20120504_154745 -- class Genbank::misc_feature -- table misc_feature_note -- id note 123214000001 AAA-like domain; Region: AAA_10; pfam12846 123214000002 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 123214000003 Walker A motif; other site 123214000004 ATP binding site [chemical binding]; other site 123214000005 Walker B motif; other site 123214000006 Flagellin N-methylase; Region: FliB; cl00497 123214000007 hypothetical protein; Validated; Region: PRK08116 123214000008 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 123214000009 Walker A motif; other site 123214000010 ATP binding site [chemical binding]; other site 123214000011 Walker B motif; other site 123214000012 arginine finger; other site 123214000013 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 123214000014 Phage integrase, N-terminal SAM-like domain; Region: Phage_integr_N; cl12235 123214000015 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 123214000016 active site 123214000017 Int/Topo IB signature motif; other site 123214000018 catalytic residues [active] 123214000019 DNA binding site [nucleotide binding] 123214000020 AAA domain; Region: AAA_33; pfam13671 123214000021 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 123214000022 active site 123214000023 conjugal transfer mating pair stabilization protein TraN; Reviewed; Region: PRK12355 123214000024 conjugal transfer mating pair stabilization protein TraN; Reviewed; Region: PRK12355 123214000025 Type-F conjugative transfer system pilin assembly protein; Region: TrbC_Ftype; cl09883 123214000026 TraU protein; Region: TraU; cl06067 123214000027 RelB antitoxin; Region: RelB; cl01171 123214000028 TraG-like protein, N-terminal region; Region: TraG_N; pfam07916 123214000029 Conjugative relaxosome accessory transposon protein; Region: TraH; cl05580 123214000030 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 123214000031 catalytic residues [active] 123214000032 Putative helicase; Region: TraI_2; pfam07514 123214000033 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 123214000034 type-IV secretion system protein TraC; Region: TraC-F-type; TIGR02746 123214000035 type IV conjugative transfer system lipoprotein TraV; Region: TraV; TIGR02747 123214000036 Type IV conjugative transfer system lipoprotein (TraV); Region: TraV; pfam09676 123214000037 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 123214000038 DsbA family, DsbC and DsbG subfamily; V-shaped homodimeric proteins containing a redox active CXXC motif imbedded in a TRX fold. They function as protein disulfide isomerases and chaperones in the bacterial periplasm to correct non-native disulfide bonds...; Region: DsbA_DsbC_DsbG; cd03020 123214000039 dimer interface [polypeptide binding]; other site 123214000040 catalytic residues [active] 123214000041 Bacterial conjugation TrbI-like protein; Region: TrbI; cl04242 123214000042 Bacterial SH3 domain; Region: SH3_3; cl02551 123214000043 TraE protein; Region: TraE; cl05060 123214000044 TraL protein; Region: TraL; cl06278 123214000045 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 123214000046 Antirestriction protein [DNA replication, recombination, and repair]; Region: COG4227 123214000047 Domain of unknown function (DUF1738); Region: DUF1738; pfam08401 123214000048 DNA topoisomerase III; Provisional; Region: PRK07726 123214000049 TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving...; Region: TOPRIM_TopoIA_TopoIII; cd03362 123214000050 active site 123214000051 putative interdomain interaction site [polypeptide binding]; other site 123214000052 putative metal-binding site [ion binding]; other site 123214000053 putative nucleotide binding site [chemical binding]; other site 123214000054 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 123214000055 domain I; other site 123214000056 DNA binding groove [nucleotide binding] 123214000057 phosphate binding site [ion binding]; other site 123214000058 domain II; other site 123214000059 domain III; other site 123214000060 nucleotide binding site [chemical binding]; other site 123214000061 catalytic site [active] 123214000062 domain IV; other site 123214000063 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 123214000064 DNA topoisomerase III; Validated; Region: PRK08173 123214000065 C-terminal repeat of topoisomerase; Region: Toprim_Crpt; pfam13342 123214000066 Initiator Replication protein; Region: Rep_3; cl03080 123214000067 PRTRC system protein D; Region: PRTRC_D; TIGR03739 123214000068 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 123214000069 oligomerisation interface [polypeptide binding]; other site 123214000070 mobile loop; other site 123214000071 roof hairpin; other site 123214000072 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 123214000073 [Protein-PII] uridylyltransferase; Region: UTase_glnD; TIGR01693 123214000074 metal binding triad; other site 123214000075 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 123214000076 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 123214000077 C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains; Region: ACT_ACR-UUR-like_2; cd04899 123214000078 DNA mismatch repair protein MutL; Region: mutl; TIGR00585 123214000079 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 123214000080 ATP binding site [chemical binding]; other site 123214000081 Mg2+ binding site [ion binding]; other site 123214000082 G-X-G motif; other site 123214000083 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 123214000084 ATP binding site [chemical binding]; other site 123214000085 MutL C terminal dimerisation domain; Region: MutL_C; cl07336 123214000086 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 123214000087 Chain length determinant protein; Region: Wzz; cl15801 123214000088 AAA domain; Region: AAA_32; pfam13654 123214000089 lon-related putative ATP-dependent protease; Region: lon_rel; TIGR00764 123214000090 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 123214000091 Protein of unknown function (DUF2914); Region: DUF2914; pfam11141 123214000092 phosphoribosylglycinamide formyltransferase; Reviewed; Region: purN; PRK05647 123214000093 Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART); Region: FMT_core_GART; cd08645 123214000094 active site 123214000095 substrate binding site [chemical binding]; other site 123214000096 cosubstrate binding site; other site 123214000097 catalytic site [active] 123214000098 alpha-glucosidase; Provisional; Region: PRK10137 123214000099 Bacterial alpha-L-rhamnosidase; Region: Bac_rhamnosid; cl01801 123214000100 Protein of unknown function, DUF547; Region: DUF547; pfam04784 123214000101 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 123214000102 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 123214000103 dimerization interface [polypeptide binding]; other site 123214000104 putative ATP binding site [chemical binding]; other site 123214000105 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 123214000106 N-carbamoylputrescine amidohydrolase (CPA) (class 11 nitrilases); Region: CPA; cd07573 123214000107 putative active site; other site 123214000108 catalytic triad [active] 123214000109 putative dimer interface [polypeptide binding]; other site 123214000110 Uncharacterized protein family UPF0047; Region: UPF0047; cl00439 123214000111 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 123214000112 active site 123214000113 D-Tyrosyl-tRNAtyr deacylases; a class of tRNA-dependent hydrolases which are capable of hydrolyzing the ester bond of D-Tyrosyl-tRNA reducing the level of cellular D-Tyrosine while recycling the peptidyl-tRNA; found in bacteria and in eukaryotes but not...; Region: Dtyr_deacylase; cd00563 123214000114 putative active site [active] 123214000115 dimerization interface [polypeptide binding]; other site 123214000116 putative tRNAtyr binding site [nucleotide binding]; other site 123214000117 Trehalose-6-Phosphate Synthase (TPS) is a glycosyltransferase that catalyses the synthesis of alpha,alpha-1,1-trehalose-6-phosphate from glucose-6-phosphate using a UDP-glucose donor. It is a key enzyme in the trehalose synthesis pathway. Trehalose is a...; Region: GT1_TPS; cd03788 123214000118 alpha,alpha-trehalose-phosphate synthase [UDP-forming]; Region: trehalose_OtsA; TIGR02400 123214000119 active site 123214000120 homotetramer interface [polypeptide binding]; other site 123214000121 GTP-binding protein Der; Reviewed; Region: PRK00093 123214000122 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 123214000123 G1 box; other site 123214000124 GTP/Mg2+ binding site [chemical binding]; other site 123214000125 Switch I region; other site 123214000126 G2 box; other site 123214000127 Switch II region; other site 123214000128 G3 box; other site 123214000129 G4 box; other site 123214000130 G5 box; other site 123214000131 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 123214000132 G1 box; other site 123214000133 GTP/Mg2+ binding site [chemical binding]; other site 123214000134 Switch I region; other site 123214000135 G2 box; other site 123214000136 G3 box; other site 123214000137 Switch II region; other site 123214000138 G4 box; other site 123214000139 G5 box; other site 123214000140 integral membrane protein MviN; Region: mviN; TIGR01695 123214000141 MatE; Region: MatE; cl10513 123214000142 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214000143 metal binding site [ion binding]; metal-binding site 123214000144 active site 123214000145 I-site; other site 123214000146 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 123214000147 pyruvate kinase; Provisional; Region: PRK05826 123214000148 domain interfaces; other site 123214000149 active site 123214000150 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 123214000151 metal binding site 2 [ion binding]; metal-binding site 123214000152 putative DNA binding helix; other site 123214000153 metal binding site 1 [ion binding]; metal-binding site 123214000154 dimer interface [polypeptide binding]; other site 123214000155 structural Zn2+ binding site [ion binding]; other site 123214000156 bacterial and archael members of the sulfite oxidase (SO) family of molybdopterin binding domains. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate reductase (NR) and...; Region: arch_bact_SO_family_Moco; cd02109 123214000157 Moco binding site; other site 123214000158 metal coordination site [ion binding]; other site 123214000159 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK08651 123214000160 Peptidase M20 acetylornithine deacetylase/succinyl-diaminopimelate desuccinylase (ArgE/DapE)-like; Region: M20_ArgE_DapE_like; cd08659 123214000161 metal binding site [ion binding]; metal-binding site 123214000162 dimer interface [polypeptide binding]; other site 123214000163 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 123214000164 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 123214000165 Coenzyme A binding pocket [chemical binding]; other site 123214000166 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; cl15377 123214000167 Radical SAM superfamily; Region: Radical_SAM; pfam04055 123214000168 GMP synthase; Reviewed; Region: guaA; PRK00074 123214000169 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 123214000170 AMP/PPi binding site [chemical binding]; other site 123214000171 candidate oxyanion hole; other site 123214000172 catalytic triad [active] 123214000173 potential glutamine specificity residues [chemical binding]; other site 123214000174 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 123214000175 ATP Binding subdomain [chemical binding]; other site 123214000176 Ligand Binding sites [chemical binding]; other site 123214000177 Dimerization subdomain; other site 123214000178 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: FabG; COG1028 123214000179 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214000180 NAD(P) binding site [chemical binding]; other site 123214000181 active site 123214000182 V-type ATP synthase subunit C; Provisional; Region: PRK01198; cl00660 123214000183 V-type ATP synthase subunit I; Validated; Region: PRK05771 123214000184 ATP synthase (F/14-kDa) subunit; Region: ATP-synt_F; cl00632 123214000185 V-type ATP synthase subunit A; Provisional; Region: PRK04192 123214000186 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 123214000187 V/A-type ATP synthase catalytic subunit A. These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi...; Region: V_A-ATPase_A; cd01134 123214000188 Walker A motif/ATP binding site; other site 123214000189 Walker B motif; other site 123214000190 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 123214000191 V-type ATP synthase subunit B; Provisional; Region: PRK04196 123214000192 V/A-type ATP synthase (non-catalytic) subunit B. These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi...; Region: V_A-ATPase_B; cd01135 123214000193 Walker A motif homologous position; other site 123214000194 Walker B motif; other site 123214000195 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 123214000196 ATP synthase subunit D; Region: ATP-synt_D; cl00613 123214000197 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 123214000198 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 123214000199 RNA binding site [nucleotide binding]; other site 123214000200 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 123214000201 RNA binding site [nucleotide binding]; other site 123214000202 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 123214000203 RNA binding site [nucleotide binding]; other site 123214000204 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 123214000205 RNA binding site [nucleotide binding]; other site 123214000206 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 123214000207 RNA binding site [nucleotide binding]; other site 123214000208 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 123214000209 RNA binding site [nucleotide binding]; other site 123214000210 Ca2+/Na+ antiporter [Inorganic ion transport and metabolism]; Region: ECM27; COG0530 123214000211 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 123214000212 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 123214000213 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 123214000214 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 123214000215 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 123214000216 Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from...; Region: GT1_LPS_heptosyltransferase; cd03789 123214000217 putative active site [active] 123214000218 FOG: CBS domain [General function prediction only]; Region: COG0517 123214000219 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair_9; cd04622 123214000220 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 123214000221 M20 Peptidase Aminoacylase 1 family; Region: M20_Acy1; cd03886 123214000222 metal binding site [ion binding]; metal-binding site 123214000223 dimer interface [polypeptide binding]; other site 123214000224 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 123214000225 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 123214000226 copper-resistance protein, CopA family; Region: copper_res_A; TIGR01480 123214000227 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 123214000228 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 123214000229 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 123214000230 Copper resistance protein B precursor (CopB); Region: CopB; cl01476 123214000231 Ribosomal prokaryotic L21 protein; Region: Ribosomal_L21p; cl00382 123214000232 Ribosomal L27 protein; Region: Ribosomal_L27; cl00359 123214000233 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 123214000234 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 123214000235 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 123214000236 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 123214000237 alanyl-tRNA synthetase; Region: A-tRNA_syn_arch; TIGR03683 123214000238 rod shape-determining protein MreC; Region: MreC; pfam04085 123214000239 rod shape-determining protein MreB; Provisional; Region: PRK13927 123214000240 Actin; An ubiquitous protein involved in the formation of filaments that are a major component of the cytoskeleton. Interaction with myosin provides the basis of muscular contraction and many aspects of cell motility. Each actin protomer binds one...; Region: ACTIN; cl11528 123214000241 ATP binding site [chemical binding]; other site 123214000242 profilin binding site; other site 123214000243 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 123214000244 dihydrodipicolinate synthase; Region: dapA; TIGR00674 123214000245 dimer interface [polypeptide binding]; other site 123214000246 active site 123214000247 catalytic residue [active] 123214000248 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214000249 DegT/DnrJ/EryC1/StrS aminotransferase family; Region: DegT_DnrJ_EryC1; pfam01041 123214000250 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary...; Region: AHBA_syn; cd00616 123214000251 inhibitor-cofactor binding pocket; inhibition site 123214000252 pyridoxal 5'-phosphate binding site [chemical binding]; other site 123214000253 catalytic residue [active] 123214000254 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 123214000255 homopentamer interface [polypeptide binding]; other site 123214000256 active site 123214000257 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 123214000258 putative RNA binding site [nucleotide binding]; other site 123214000259 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 123214000260 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 123214000261 active site 123214000262 metal binding site [ion binding]; metal-binding site 123214000263 Preprotein translocase subunit; Region: YajC; cl00806 123214000264 poly-beta-1,6 N-acetyl-D-glucosamine export porin PgaA; Region: PGA_TPR_OMP; TIGR03939 123214000265 Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:...; Region: TRX_Fd_family; cd02980 123214000266 dimer interface [polypeptide binding]; other site 123214000267 [2Fe-2S] cluster binding site [ion binding]; other site 123214000268 Methylenetetrahydrofolate reductase; Region: MTHFR; pfam02219 123214000269 Methylenetetrahydrofolate reductase (MTHFR). 5,10-Methylenetetrahydrofolate is reduced to 5-methyltetrahydrofolate by methylenetetrahydrofolate reductase, a cytoplasmic, NAD(P)-dependent enzyme. 5-methyltetrahydrofolate is utilized by methionine synthase...; Region: MTHFR; cd00537 123214000270 FAD binding site [chemical binding]; other site 123214000271 phosphodiesterase; Provisional; Region: PRK12704 123214000272 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 123214000273 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; cl00360 123214000274 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 123214000275 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 123214000276 putative tRNA-binding site [nucleotide binding]; other site 123214000277 B3/4 domain; Region: B3_4; cl11458 123214000278 tRNA synthetase B5 domain; Region: B5; cl08394 123214000279 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 123214000280 dimer interface [polypeptide binding]; other site 123214000281 motif 1; other site 123214000282 motif 3; other site 123214000283 motif 2; other site 123214000284 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; cl08386 123214000285 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 123214000286 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 123214000287 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 123214000288 dimer interface [polypeptide binding]; other site 123214000289 motif 1; other site 123214000290 active site 123214000291 motif 2; other site 123214000292 motif 3; other site 123214000293 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 123214000294 23S rRNA binding site [nucleotide binding]; other site 123214000295 L21 binding site [polypeptide binding]; other site 123214000296 L13 binding site [polypeptide binding]; other site 123214000297 Ribosomal protein L35; Region: Ribosomal_L35p; cl00392 123214000298 Cytochrome C'; Region: Cytochrom_C_2; cl01610 123214000299 Cytochrome c554 and c-prime; Region: Cytochrome_C554; pfam13435 123214000300 Heme-binding domain of the class III cytochrome C family and related proteins; Region: Cytochrom_C3; cl03439 123214000301 heme-binding residues [chemical binding]; other site 123214000302 NTPase/HAM1. This family consists of the HAM1 protein and pyrophosphate-releasing xanthosine/ inosine triphosphatase. HAM1 protects the cell against mutagenesis by the base analog 6-N-hydroxylaminopurine (HAP) in E. Coli and S. cerevisiae. A...; Region: HAM1; cd00515 123214000303 active site 123214000304 dimerization interface [polypeptide binding]; other site 123214000305 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 123214000306 active site 123214000307 putative DNA-binding cleft [nucleotide binding]; other site 123214000308 dimer interface [polypeptide binding]; other site 123214000309 Transcriptional regulator; Region: Transcrip_reg; cl00361 123214000310 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]; Region: COG2231 123214000311 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 123214000312 minor groove reading motif; other site 123214000313 helix-hairpin-helix signature motif; other site 123214000314 substrate binding pocket [chemical binding]; other site 123214000315 active site 123214000316 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 123214000317 putative acyl-acceptor binding pocket; other site 123214000318 LytB protein; Region: LYTB; cl00507 123214000319 (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate reductase (IPP and DMAPP forming); Region: ispH_lytB; TIGR00216 123214000320 PilZ domain; Region: PilZ; cl01260 123214000321 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 123214000322 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 123214000323 Flagellar motor protein [Cell motility and secretion]; Region: MotB; COG1360 123214000324 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 123214000325 ligand binding site [chemical binding]; other site 123214000326 Flagellar motor protein [Cell motility and secretion]; Region: MotB; COG1360 123214000327 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 123214000328 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 123214000329 ligand binding site [chemical binding]; other site 123214000330 PUA domain; Region: PUA; cl00607 123214000331 Predicted SAM-dependent methyltransferases [General function prediction only]; Region: COG1092 123214000332 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 123214000333 S-adenosylmethionine binding site [chemical binding]; other site 123214000334 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 123214000335 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 123214000336 S-adenosylmethionine binding site [chemical binding]; other site 123214000337 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 123214000338 UDP-N-acetylglucosamine enolpyruvyl transferase catalyzes enolpyruvyl transfer as part of the first step in the biosynthesis of peptidoglycan, a component of the bacterial cell wall. The reaction is phosphoenolpyruvate + UDP-N-acetyl-D-glucosamine =...; Region: UdpNAET; cd01555 123214000339 hinge; other site 123214000340 active site 123214000341 RNA polymerase sigma factor RpoD, C-terminal domain; Region: RpoD_Cterm; TIGR02393 123214000342 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 123214000343 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 123214000344 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 123214000345 DNA binding residues [nucleotide binding] 123214000346 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 123214000347 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 123214000348 dimer interface [polypeptide binding]; other site 123214000349 anticodon binding site; other site 123214000350 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 123214000351 homodimer interface [polypeptide binding]; other site 123214000352 motif 1; other site 123214000353 active site 123214000354 motif 2; other site 123214000355 GAD domain; Region: GAD; pfam02938 123214000356 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 123214000357 motif 3; other site 123214000358 Tetratricopeptide repeat; Region: TPR_12; pfam13424 123214000359 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 123214000360 binding surface 123214000361 TPR motif; other site 123214000362 Tetratricopeptide repeat; Region: TPR_12; pfam13424 123214000363 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 123214000364 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 123214000365 argininosuccinate lyase; Provisional; Region: PRK00855 123214000366 Argininosuccinate lyase (argininosuccinase, ASAL); Region: Argininosuccinate_lyase; cd01359 123214000367 active sites [active] 123214000368 tetramer interface [polypeptide binding]; other site 123214000369 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214000370 metal binding site [ion binding]; metal-binding site 123214000371 active site 123214000372 I-site; other site 123214000373 competence damage-inducible protein A; Provisional; Region: PRK00549 123214000374 Competence-damaged protein. CinA is the first gene in the competence- inducible (cin) operon and is thought to be specifically required at some stage in the process of transformation. This domain is closely related to a domain, found in a variety of...; Region: cinA; cd00885 123214000375 putative MPT binding site; other site 123214000376 Competence-damaged protein; Region: CinA; cl00666 123214000377 SpoIVFB Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50B), regulates intramembrane proteolysis (RIP), and is involved in the pro-sigmaK pathway of bacterial spore formation. In this subgroup, SpoIVFB (sporulation protein, stage IV cell...; Region: S2P-M50_SpoIVFB_CBS; cd06164 123214000378 active site 123214000379 putative substrate binding region [chemical binding]; other site 123214000380 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cl15354 123214000381 Uncharacterized metal-binding protein (DUF2227); Region: DUF2227; cl01017 123214000382 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 123214000383 ligand binding site [chemical binding]; other site 123214000384 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 123214000385 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 123214000386 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 123214000387 P loop; other site 123214000388 GTP binding site [chemical binding]; other site 123214000389 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 123214000390 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 123214000391 Glutamate-cysteine ligase family 2(GCS2); Region: GCS2; cl00954 123214000392 carboxylate-amine ligase, YbdK family; Region: gshA_cyan_rel; TIGR02050 123214000393 Membrane-bound serine protease (ClpP class) [Posttranslational modification, protein turnover, chaperones]; Region: NfeD; COG1030 123214000394 Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Region: Clp_protease_NfeD_1; cd07020 123214000395 dimer interface [polypeptide binding]; other site 123214000396 active site residues [active] 123214000397 PRA1 family protein; Region: PRA1; cl02137 123214000398 NfeD-like C-terminal, partner-binding; Region: NfeD; cl00686 123214000399 carbon-monoxide dehydrogenase, catalytic subunit; Region: CO_DH_cata; TIGR01702 123214000400 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 123214000401 ACS interaction site; other site 123214000402 CODH interaction site; other site 123214000403 metal cluster binding site [ion binding]; other site 123214000404 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 123214000405 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 123214000406 catalytic residue [active] 123214000407 Glycine cleavage H-protein. Glycine cleavage H-proteins are part of the glycine cleavage system (GCS) found in bacteria, archea and the mitochondria of eukaryotes. GCS is a multienzyme complex consisting of 4 different components (P-, H-, T- and...; Region: GCS_H; cd06848 123214000408 lipoyl attachment site [posttranslational modification]; other site 123214000409 Glycine cleavage system regulatory protein [Amino acid transport and metabolism]; Region: GcvR; COG2716 123214000410 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 123214000411 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 123214000412 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 123214000413 active site 123214000414 catalytic residues [active] 123214000415 metal binding site [ion binding]; metal-binding site 123214000416 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257; cl15822 123214000417 Memo (mediator of ErbB2-driven cell motility) is co-precipitated with the C terminus of ErbB2, a protein involved in cell motility; Region: MEMO_like; cd07361 123214000418 putative ligand binding pocket/active site [active] 123214000419 putative metal binding site [ion binding]; other site 123214000420 AMMECR1; Region: AMMECR1; cl00911 123214000421 Ferritin-like domain; Region: Ferritin; pfam00210 123214000422 Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Region: Ferritin_like; cd00657 123214000423 dinuclear metal binding motif [ion binding]; other site 123214000424 Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an...; Region: beta_CA_cladeB; cd00884 123214000425 active site clefts [active] 123214000426 zinc binding site [ion binding]; other site 123214000427 dimer interface [polypeptide binding]; other site 123214000428 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 123214000429 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate (THDP) N-succinyltransferase (also called THP succinyltransferase): THDP N-succinyltransferase catalyzes the conversion of tetrahydrodipicolinate and succinyl-CoA to N-succinyltetrahydrodipicolinate and CoA; Region: LbH_THP_succinylT; cd03350 123214000430 trimer interface [polypeptide binding]; other site 123214000431 active site 123214000432 substrate binding site [chemical binding]; other site 123214000433 CoA binding site [chemical binding]; other site 123214000434 Protein of unknown function (DUF2628); Region: DUF2628; pfam10947 123214000435 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 123214000436 Deinococcus radiodurans DR1281 and related proteins, metallophosphatase domain; Region: MPP_DR1281; cd07382 123214000437 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 123214000438 putative active site [active] 123214000439 metal binding site [ion binding]; metal-binding site 123214000440 homodimer binding site [polypeptide binding]; other site 123214000441 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 123214000442 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cl00290 123214000443 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 123214000444 Pyridoxal phosphate biosynthetic protein PdxA; Region: PdxA; cl00873 123214000445 DsrE/DsrF-like family; Region: DrsE; cl00672 123214000446 DsrE/DsrF-like family; Region: DrsE; cl00672 123214000447 SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this...; Region: SirA_YedF_YeeD; cd00291 123214000448 CPxP motif; other site 123214000449 molybdopterin biosynthesis protein MoeB; Provisional; Region: PRK05690 123214000450 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 123214000451 ATP binding site [chemical binding]; other site 123214000452 substrate interface [chemical binding]; other site 123214000453 Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]; Region: COG2070 123214000454 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 123214000455 FMN binding site [chemical binding]; other site 123214000456 substrate binding site [chemical binding]; other site 123214000457 putative catalytic residue [active] 123214000458 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 123214000459 DHH family; Region: DHH; pfam01368 123214000460 DHHA1 domain; Region: DHHA1; pfam02272 123214000461 peroxiredoxin; Region: AhpC; TIGR03137 123214000462 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 123214000463 dimer interface [polypeptide binding]; other site 123214000464 decamer (pentamer of dimers) interface [polypeptide binding]; other site 123214000465 catalytic triad [active] 123214000466 peroxidatic and resolving cysteines [active] 123214000467 Ribosomal protein S21; Region: Ribosomal_S21; cl00529 123214000468 GatB domain; Region: GatB_Yqey; cl11497 123214000469 DsrE/DsrF-like family; Region: DrsE; cl00672 123214000470 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 123214000471 RIP metalloprotease RseP; Region: TIGR00054 123214000472 active site 123214000473 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 123214000474 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 123214000475 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 123214000476 putative substrate binding region [chemical binding]; other site 123214000477 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 123214000478 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 123214000479 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 123214000480 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 123214000481 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 123214000482 Glutaredoxin-like domain protein; Region: GlrX_arch; TIGR02187 123214000483 Thioredoxin (TRX)-Glutaredoxin (GRX)-like family; composed of archaeal and bacterial proteins that show similarity to both TRX and GRX, including the C-terminal TRX-fold subdomain of Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO). All...; Region: TRX_GRX_like; cd02973 123214000484 catalytic residues [active] 123214000485 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 123214000486 4Fe-4S binding domain; Region: Fer4; cl02805 123214000487 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; cl15771 123214000488 bifunctional NADH:ubiquinone oxidoreductase subunit C/D; Provisional; Region: PRK11742 123214000489 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; cl00417 123214000490 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 123214000491 tetramer interfaces [polypeptide binding]; other site 123214000492 binuclear metal-binding site [ion binding]; other site 123214000493 Porphyromonas-type peptidyl-arginine deiminase; Region: PAD_porph; cl01113 123214000494 agmatine deiminase; Region: agmatine_aguA; TIGR03380 123214000495 Bacterial SH3 domain; Region: SH3_3; cl02551 123214000496 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 123214000497 nucleoside/Zn binding site; other site 123214000498 dimer interface [polypeptide binding]; other site 123214000499 catalytic motif [active] 123214000500 cytidylate kinase; Provisional; Region: cmk; PRK00023 123214000501 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 123214000502 CMP-binding site; other site 123214000503 The sites determining sugar specificity; other site 123214000504 oligosaccharide amylase; Region: oligosac_amyl; TIGR01577 123214000505 Glycosyl hydrolases family 15; Region: Glyco_hydro_15; pfam00723 123214000506 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 123214000507 MoaE interaction surface [polypeptide binding]; other site 123214000508 MoeB interaction surface [polypeptide binding]; other site 123214000509 thiocarboxylated glycine; other site 123214000510 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 123214000511 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 123214000512 ketol-acid reductoisomerase; Provisional; Region: PRK05479 123214000513 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214000514 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 123214000515 acetolactate synthase 3 regulatory subunit; Reviewed; Region: ilvH; PRK11895 123214000516 N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS); Region: ACT_AHAS; cd04878 123214000517 putative valine binding site [chemical binding]; other site 123214000518 dimer interface [polypeptide binding]; other site 123214000519 Small subunit of acetolactate synthase; Region: ALS_ss_C; pfam10369 123214000520 acetolactate synthase, large subunit, biosynthetic type; Region: acolac_lg; TIGR00118 123214000521 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 123214000522 PYR/PP interface [polypeptide binding]; other site 123214000523 dimer interface [polypeptide binding]; other site 123214000524 TPP binding site [chemical binding]; other site 123214000525 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; cl00815 123214000526 Thiamine pyrophosphate (TPP) family, Acetohydroxyacid synthase (AHAS) subfamily, TPP-binding module; composed of proteins similar to the large catalytic subunit of AHAS. AHAS catalyzes the condensation of two molecules of pyruvate to give the...; Region: TPP_AHAS; cd02015 123214000527 TPP-binding site [chemical binding]; other site 123214000528 dimer interface [polypeptide binding]; other site 123214000529 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214000530 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 123214000531 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 123214000532 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 123214000533 MoaE family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor for a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoaE; cd00756 123214000534 MoaE homodimer interface [polypeptide binding]; other site 123214000535 MoaD interaction [polypeptide binding]; other site 123214000536 active site residues [active] 123214000537 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 123214000538 aspartate aminotransferase; Provisional; Region: PRK05764 123214000539 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 123214000540 pyridoxal 5'-phosphate binding site [chemical binding]; other site 123214000541 homodimer interface [polypeptide binding]; other site 123214000542 catalytic residue [active] 123214000543 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 123214000544 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 123214000545 RNA binding surface [nucleotide binding]; other site 123214000546 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; cl15754 123214000547 Transcriptional regulator [Transcription]; Region: LysR; COG0583 123214000548 Helix-turn-helix domains; Region: HTH; cl00088 123214000549 C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold; Region: PBP2_CysL_like; cd08420 123214000550 putative dimerization interface [polypeptide binding]; other site 123214000551 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 123214000552 KpsF-like protein. KpsF is an arabinose-5-phosphate isomerase which contains SIS (Sugar ISomerase) domains. SIS domains are found in many phosphosugar isomerases and phosphosugar binding proteins. KpsF catalyzes the reversible reaction of ribulose...; Region: SIS_Kpsf; cd05014 123214000553 putative active site [active] 123214000554 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with KpsF/GutQ domains in the API [A5P (D-arabinose 5-phosphate) isomerase] protein. These APIs catalyze the conversion of the pentose pathway...; Region: CBS_pair_KpsF_GutQ_assoc; cd04604 123214000555 PSP1 C-terminal conserved region; Region: PSP1; cl00770 123214000556 DNA polymerase III, delta' subunit; Region: holB; TIGR00678 123214000557 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 123214000558 thymidylate kinase; Validated; Region: tmk; PRK00698 123214000559 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 123214000560 TMP-binding site; other site 123214000561 ATP-binding site [chemical binding]; other site 123214000562 NifU-like domain; Region: NifU; cl00484 123214000563 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 123214000564 metal binding triad; other site 123214000565 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 123214000566 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 123214000567 metal binding triad; other site 123214000568 GlnD PII-uridylyltransferase; Region: GlnD_UR_UTase; pfam08335 123214000569 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 123214000570 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 123214000571 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 123214000572 protein binding site [polypeptide binding]; other site 123214000573 RNA polymerase sigma factor RpoD, C-terminal domain; Region: RpoD_Cterm; TIGR02393 123214000574 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 123214000575 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 123214000576 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 123214000577 DNA binding residues [nucleotide binding] 123214000578 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 123214000579 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 123214000580 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 123214000581 active site 123214000582 HIGH motif; other site 123214000583 dimer interface [polypeptide binding]; other site 123214000584 KMSKS motif; other site 123214000585 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 123214000586 RNA binding surface [nucleotide binding]; other site 123214000587 acetylornithine aminotransferase; Provisional; Region: PRK02627 123214000588 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 123214000589 inhibitor-cofactor binding pocket; inhibition site 123214000590 pyridoxal 5'-phosphate binding site [chemical binding]; other site 123214000591 catalytic residue [active] 123214000592 ribonuclease R; Region: RNase_R; TIGR02063 123214000593 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 123214000594 RNB domain; Region: RNB; pfam00773 123214000595 S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important...; Region: S1_RNase_R; cd04471 123214000596 RNA binding site [nucleotide binding]; other site 123214000597 Plant ATP synthase F0; Region: YMF19; cl07975 123214000598 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 123214000599 Plant ATP synthase F0; Region: YMF19; cl07975 123214000600 Plant ATP synthase F0; Region: YMF19; cl07975 123214000601 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 123214000602 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 123214000603 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 123214000604 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 123214000605 beta subunit interaction interface [polypeptide binding]; other site 123214000606 Walker A motif; other site 123214000607 ATP binding site [chemical binding]; other site 123214000608 Walker B motif; other site 123214000609 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 123214000610 ATP synthase; Region: ATP-synt; cl00365 123214000611 F0F1 ATP synthase subunit gamma; Provisional; Region: PRK13422 123214000612 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 123214000613 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 123214000614 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 123214000615 alpha subunit interaction interface [polypeptide binding]; other site 123214000616 Walker A motif; other site 123214000617 ATP binding site [chemical binding]; other site 123214000618 Walker B motif; other site 123214000619 inhibitor binding site; inhibition site 123214000620 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 123214000621 UGMP family protein; Validated; Region: PRK09604 123214000622 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 123214000623 Carbamoyltransferase; Region: CmcH_NodU; pfam02543 123214000624 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 123214000625 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 123214000626 PDZ domain of C-terminal processing-, tail-specific-, and tricorn proteases, which function in posttranslational protein processing, maturation, and disassembly or degradation, in Bacteria, Archaea, and plant chloroplasts. May be responsible for...; Region: PDZ_CTP_protease; cd00988 123214000627 protein binding site [polypeptide binding]; other site 123214000628 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 123214000629 Catalytic dyad [active] 123214000630 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214000631 metal binding site [ion binding]; metal-binding site 123214000632 active site 123214000633 I-site; other site 123214000634 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 123214000635 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 123214000636 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 123214000637 Tetramer interface [polypeptide binding]; other site 123214000638 active site 123214000639 FMN-binding site [chemical binding]; other site 123214000640 ATP synthase A chain; Region: ATP-synt_A; cl00413 123214000641 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 123214000642 ATP synthase subunit C; Region: ATP-synt_C; cl00466 123214000643 Haemolytic domain; Region: Haemolytic; cl00506 123214000644 membrane protein insertase; Provisional; Region: PRK01318 123214000645 60Kd inner membrane protein; Region: 60KD_IMP; cl00489 123214000646 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 123214000647 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 123214000648 trmE is a tRNA modification GTPase; Region: trmE; cd04164 123214000649 G1 box; other site 123214000650 GTP/Mg2+ binding site [chemical binding]; other site 123214000651 Switch I region; other site 123214000652 G2 box; other site 123214000653 Switch II region; other site 123214000654 G3 box; other site 123214000655 G4 box; other site 123214000656 G5 box; other site 123214000657 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 123214000658 transcription termination factor Rho; Provisional; Region: rho; PRK09376 123214000659 Rho termination factor, N-terminal domain; Region: Rho_N; cl06505 123214000660 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 123214000661 RNA binding site [nucleotide binding]; other site 123214000662 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 123214000663 multimer interface [polypeptide binding]; other site 123214000664 Walker A motif; other site 123214000665 ATP binding site [chemical binding]; other site 123214000666 Walker B motif; other site 123214000667 Ribosomal protein L31; Region: Ribosomal_L31; cl00377 123214000668 peptide chain release factor 1; Validated; Region: prfA; PRK00591 123214000669 RF-1 domain; Region: RF-1; cl02875 123214000670 RF-1 domain; Region: RF-1; cl02875 123214000671 prolyl-tRNA synthetase; Provisional; Region: PRK09194 123214000672 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 123214000673 dimer interface [polypeptide binding]; other site 123214000674 motif 1; other site 123214000675 active site 123214000676 motif 2; other site 123214000677 INS is an amino acid-editing domain inserted (INS) into the bacterial class II prolyl-tRNA synthetase (ProRS) however, this CD is not exclusively bacterial. It is also found at the N-terminus of the eukaryotic/archaea-like ProRS's of yeasts and...; Region: ProRS-INS; cd04334 123214000678 putative deacylase active site [active] 123214000679 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 123214000680 active site 123214000681 motif 3; other site 123214000682 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 123214000683 anticodon binding site; other site 123214000684 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 123214000685 GAF domain; Region: GAF; cl15785 123214000686 PAS fold; Region: PAS; pfam00989 123214000687 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 123214000688 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 123214000689 Type II/IV secretion system protein; Region: T2SE; pfam00437 123214000690 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 123214000691 Walker A motif; other site 123214000692 ATP binding site [chemical binding]; other site 123214000693 Walker B motif; other site 123214000694 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 123214000695 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214000696 GTP-binding protein YchF; Reviewed; Region: PRK09601 123214000697 YchF GTPase; Region: YchF; cd01900 123214000698 G1 box; other site 123214000699 GTP/Mg2+ binding site [chemical binding]; other site 123214000700 Switch I region; other site 123214000701 G2 box; other site 123214000702 Switch II region; other site 123214000703 G3 box; other site 123214000704 G4 box; other site 123214000705 G5 box; other site 123214000706 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 123214000707 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 123214000708 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 123214000709 Membrane transport protein; Region: Mem_trans; cl09117 123214000710 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 123214000711 cysteine desulfurase DndA; Region: DNA_S_dndA; TIGR03235 123214000712 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 123214000713 catalytic residue [active] 123214000714 Anti-sigma-28 factor, FlgM; Region: FlgM; cl01052 123214000715 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 123214000716 Ppx/GppA phosphatase family; Region: Ppx-GppA; cl15449 123214000717 NIL domain; Region: NIL; cl09633 123214000718 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 123214000719 MoaE interaction surface [polypeptide binding]; other site 123214000720 MoeB interaction surface [polypeptide binding]; other site 123214000721 thiocarboxylated glycine; other site 123214000722 threonine synthase; Validated; Region: PRK07591 123214000723 Threonine synthase is a pyridoxal phosphate (PLP) dependent enzyme that catalyses the last reaction in the synthesis of threonine from aspartate. It proceeds by converting O-phospho-L-homoserine (OPH) into threonine and inorganic phosphate. In plants; Region: Thr-synth_1; cd01563 123214000724 homodimer interface [polypeptide binding]; other site 123214000725 pyridoxal 5'-phosphate binding site [chemical binding]; other site 123214000726 catalytic residue [active] 123214000727 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 123214000728 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 123214000729 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 123214000730 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 123214000731 active site 123214000732 Phosphoglycerate kinase; Region: PGK; pfam00162 123214000733 Phosphoglycerate kinase (PGK) is a monomeric enzyme which catalyzes the transfer of the high-energy phosphate group of 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate. This reaction represents the first of the two substrate-level...; Region: Phosphoglycerate_kinase; cd00318 123214000734 substrate binding site [chemical binding]; other site 123214000735 hinge regions; other site 123214000736 ADP binding site [chemical binding]; other site 123214000737 catalytic site [active] 123214000738 IMPase, inositol monophosphatase and related domains. A family of Mg++ dependent phosphatases, inhibited by lithium, many of which may act on inositol monophosphate substrate. They dephosphorylate inositol phosphate to generate inositol, which may be...; Region: IMPase; cd01639 123214000739 active site 123214000740 dimerization interface [polypeptide binding]; other site 123214000741 Chorismate mutase type II; Region: CM_2; cl00693 123214000742 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 123214000743 Prephenate dehydratase; Region: PDT; pfam00800 123214000744 C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme; Region: ACT_CM-PDT; cd04905 123214000745 putative L-Phe binding site [chemical binding]; other site 123214000746 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 123214000747 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 123214000748 rRNA interaction site [nucleotide binding]; other site 123214000749 S8 interaction site; other site 123214000750 putative laminin-1 binding site; other site 123214000751 elongation factor Ts; Reviewed; Region: tsf; PRK12332 123214000752 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 123214000753 Elongation factor TS; Region: EF_TS; pfam00889 123214000754 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 123214000755 putative nucleotide binding site [chemical binding]; other site 123214000756 uridine monophosphate binding site [chemical binding]; other site 123214000757 homohexameric interface [polypeptide binding]; other site 123214000758 ribosome recycling factor; Reviewed; Region: frr; PRK00083 123214000759 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 123214000760 hinge region; other site 123214000761 ribosome maturation protein RimP; Reviewed; Region: PRK00092 123214000762 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of...; Region: Sm_like; cl00259 123214000763 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of...; Region: Sm_like; cl00259 123214000764 Sm1 motif; other site 123214000765 D1 - D2 interaction site; other site 123214000766 D3 - B interaction site; other site 123214000767 Hfq - Hfq interaction site; other site 123214000768 RNA binding pocket [nucleotide binding]; other site 123214000769 Sm2 motif; other site 123214000770 NusA N-terminal domain; Region: NusA_N; pfam08529 123214000771 transcription termination factor NusA; Region: NusA; TIGR01953 123214000772 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 123214000773 RNA binding site [nucleotide binding]; other site 123214000774 homodimer interface [polypeptide binding]; other site 123214000775 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that...; Region: KH-I; cl00098 123214000776 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 123214000777 G-X-X-G motif; other site 123214000778 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; Region: Ribosomal_L7Ae; cl00600 123214000779 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 123214000780 translation initiation factor IF-2; Region: IF-2; TIGR00487 123214000781 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 123214000782 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 123214000783 G1 box; other site 123214000784 putative GEF interaction site [polypeptide binding]; other site 123214000785 GTP/Mg2+ binding site [chemical binding]; other site 123214000786 Switch I region; other site 123214000787 G2 box; other site 123214000788 G3 box; other site 123214000789 Switch II region; other site 123214000790 G4 box; other site 123214000791 G5 box; other site 123214000792 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 123214000793 Translation-initiation factor 2; Region: IF-2; pfam11987 123214000794 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 123214000795 PilZ domain; Region: PilZ; cl01260 123214000796 DNA recombination-mediator protein A; Region: DNA_processg_A; pfam02481 123214000797 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 123214000798 Spore germination protein; Region: Spore_permease; cl15802 123214000799 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 123214000800 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 123214000801 RNase E interface [polypeptide binding]; other site 123214000802 trimer interface [polypeptide binding]; other site 123214000803 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 123214000804 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 123214000805 RNase E interface [polypeptide binding]; other site 123214000806 trimer interface [polypeptide binding]; other site 123214000807 active site 123214000808 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 123214000809 putative nucleic acid binding region [nucleotide binding]; other site 123214000810 G-X-X-G motif; other site 123214000811 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 123214000812 RNA binding site [nucleotide binding]; other site 123214000813 domain interface; other site 123214000814 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 123214000815 16S/18S rRNA binding site [nucleotide binding]; other site 123214000816 S13e-L30e interaction site [polypeptide binding]; other site 123214000817 25S rRNA binding site [nucleotide binding]; other site 123214000818 PIN (PilT N terminus) domain: Superfamily; Region: PIN_SF; cl14812 123214000819 PLD-like domain; Region: PLDc_2; pfam13091 123214000820 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cd00138 123214000821 putative active site [active] 123214000822 catalytic site [active] 123214000823 Domain of unknown function (DUF1998); Region: DUF1998; pfam09369 123214000824 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 123214000825 nucleotide binding region [chemical binding]; other site 123214000826 ATP-binding site [chemical binding]; other site 123214000827 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 123214000828 endonuclease III; Region: ENDO3c; smart00478 123214000829 minor groove reading motif; other site 123214000830 helix-hairpin-helix signature motif; other site 123214000831 substrate binding pocket [chemical binding]; other site 123214000832 active site 123214000833 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; cl15754 123214000834 C-5 cytosine-specific DNA methylase; Region: DNA_methylase; pfam00145 123214000835 cofactor binding site; other site 123214000836 DNA binding site [nucleotide binding] 123214000837 substrate interaction site [chemical binding]; other site 123214000838 Uncharacterized conserved protein [Function unknown]; Region: COG3287 123214000839 FIST N domain; Region: FIST; cl10701 123214000840 FIST C domain; Region: FIST_C; pfam10442 123214000841 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214000842 metal binding site [ion binding]; metal-binding site 123214000843 active site 123214000844 I-site; other site 123214000845 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 123214000846 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 123214000847 ABC (ATP-binding cassette) transport system involved in resistant to organic solvents; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex...; Region: ABC_Org_Solvent_Resistant; cd03261 123214000848 Walker A/P-loop; other site 123214000849 ATP binding site [chemical binding]; other site 123214000850 Q-loop/lid; other site 123214000851 ABC transporter signature motif; other site 123214000852 Walker B; other site 123214000853 D-loop; other site 123214000854 H-loop/switch region; other site 123214000855 threonine synthase; Reviewed; Region: PRK06721 123214000856 Threonine synthase is a pyridoxal phosphate (PLP) dependent enzyme that catalyses the last reaction in the synthesis of threonine from aspartate. It proceeds by converting O-phospho-L-homoserine (OPH) into threonine and inorganic phosphate. In plants; Region: Thr-synth_1; cd01563 123214000857 homodimer interface [polypeptide binding]; other site 123214000858 pyridoxal 5'-phosphate binding site [chemical binding]; other site 123214000859 catalytic residue [active] 123214000860 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214000861 2-dehydropantoate 2-reductase; Region: apbA_panE; TIGR00745 123214000862 Ketopantoate reductase PanE/ApbA C terminal; Region: ApbA_C; pfam08546 123214000863 ribonuclease PH; Reviewed; Region: rph; PRK00173 123214000864 Ribonuclease PH; Region: RNase_PH_bact; cd11362 123214000865 hexamer interface [polypeptide binding]; other site 123214000866 active site 123214000867 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 123214000868 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 123214000869 GDP-binding site [chemical binding]; other site 123214000870 ACT binding site; other site 123214000871 IMP binding site; other site 123214000872 YjeF-related protein N-terminus; Region: YjeF_N; cl00318 123214000873 putative carbohydrate kinase; Provisional; Region: PRK10565 123214000874 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 123214000875 putative substrate binding site [chemical binding]; other site 123214000876 putative ATP binding site [chemical binding]; other site 123214000877 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 123214000878 active site 123214000879 intersubunit interface [polypeptide binding]; other site 123214000880 zinc binding site [ion binding]; other site 123214000881 Na+ binding site [ion binding]; other site 123214000882 Fructose-1,6-bisphosphatase, an enzyme that catalyzes the hydrolysis of fructose-1,6-biphosphate into fructose-6-phosphate and is critical in gluconeogenesis pathway. The alignment model also includes chloroplastic FBPases and sedoheptulose-1; Region: FBPase; cd00354 123214000883 AMP binding site [chemical binding]; other site 123214000884 metal binding site [ion binding]; metal-binding site 123214000885 active site 123214000886 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214000887 metal binding site [ion binding]; metal-binding site 123214000888 active site 123214000889 I-site; other site 123214000890 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 123214000891 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214000892 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 123214000893 NAD(P) binding site [chemical binding]; other site 123214000894 CrcB-like protein; Region: CRCB; cl09114 123214000895 Uncharacterized ACR, COG1993; Region: DUF190; cl00872 123214000896 Alpha-crystallin domain (ACD) of alpha-crystallin-type small(s) heat shock proteins (Hsps). sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is the Alpha-crystallin domain (ACD). sHsps are generally...; Region: ACD_sHsps-like; cd06464 123214000897 putative dimer interface [polypeptide binding]; other site 123214000898 anthranilate synthase component I; Provisional; Region: PRK13565 123214000899 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 123214000900 chorismate binding enzyme; Region: Chorismate_bind; cl10555 123214000901 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK08651 123214000902 M20 Peptidase actinobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_actinobac; cd05647 123214000903 metal binding site [ion binding]; metal-binding site 123214000904 putative dimer interface [polypeptide binding]; other site 123214000905 Transcriptional regulator [Transcription]; Region: IclR; COG1414 123214000906 Bacterial transcriptional regulator; Region: IclR; pfam01614 123214000907 Radical SAM superfamily; Region: Radical_SAM; pfam04055 123214000908 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 123214000909 FeS/SAM binding site; other site 123214000910 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 123214000911 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 123214000912 motif 1; other site 123214000913 active site 123214000914 motif 2; other site 123214000915 motif 3; other site 123214000916 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 123214000917 DHHA1 domain; Region: DHHA1; pfam02272 123214000918 Domain of unknown function (DUF296); Region: DUF296; cl00720 123214000919 Uncharacterized protein family, UPF0114; Region: UPF0114; cl01078 123214000920 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 123214000921 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 123214000922 active site 123214000923 Predicted amidohydrolase [General function prediction only]; Region: COG0388 123214000924 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cl11424 123214000925 active site 123214000926 catalytic triad [active] 123214000927 dimer interface [polypeptide binding]; other site 123214000928 phosphoribosylformylglycinamidine synthase II; Provisional; Region: PRK01213 123214000929 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 123214000930 dimerization interface [polypeptide binding]; other site 123214000931 ATP binding site [chemical binding]; other site 123214000932 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 123214000933 dimerization interface [polypeptide binding]; other site 123214000934 ATP binding site [chemical binding]; other site 123214000935 Heme/copper-type cytochrome/quinol oxidases, subunit 2 [Energy production and conversion]; Region: CyoA; COG1622 123214000936 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 123214000937 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 123214000938 D-pathway; other site 123214000939 Low-spin heme binding site [chemical binding]; other site 123214000940 Putative water exit pathway; other site 123214000941 Binuclear center (active site) [active] 123214000942 K-pathway; other site 123214000943 Putative proton exit pathway; other site 123214000944 ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]; Region: RecB; COG1074 123214000945 Family description; Region: UvrD_C_2; cl15862 123214000946 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 123214000947 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 123214000948 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 123214000949 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 123214000950 ligand binding site [chemical binding]; other site 123214000951 flexible hinge region; other site 123214000952 Helix-turn-helix domains; Region: HTH; cl00088 123214000953 anaerobic ribonucleoside-triphosphate reductase activating protein; Region: NrdG2; TIGR02495 123214000954 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 123214000955 FeS/SAM binding site; other site 123214000956 Anaerobic ribonucleoside-triphosphate reductase; Region: NRDD; pfam13597 123214000957 Class III ribonucleotide reductase; Region: RNR_III; cd01675 123214000958 effector binding site; other site 123214000959 active site 123214000960 Zn binding site [ion binding]; other site 123214000961 glycine loop; other site 123214000962 nitrate reductase catalytic subunit; Provisional; Region: PRK13532 123214000963 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 123214000964 molybdopterin cofactor binding site; other site 123214000965 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 123214000966 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 123214000967 Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol...; Region: MopB_CT_Nitrate-R-NapA-like; cd02791 123214000968 molybdopterin cofactor binding site; other site 123214000969 quinol dehydrogenase periplasmic component; Provisional; Region: napG; PRK09476 123214000970 quinol dehydrogenase membrane component; Provisional; Region: napH; PRK09477 123214000971 4Fe-4S binding domain; Region: Fer4_5; pfam12801 123214000972 4Fe-4S binding domain; Region: Fer4_5; pfam12801 123214000973 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 123214000974 Nitrate reductase cytochrome c-type subunit (NapB); Region: NapB; cl01153 123214000975 quinol dehydrogenase periplasmic component; Provisional; Region: napG; PRK09476 123214000976 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 123214000977 4Fe-4S binding domain; Region: Fer4; cl02805 123214000978 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 123214000979 structural tetrad; other site 123214000980 NapD protein; Region: NapD; cl01163 123214000981 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 123214000982 Cytochrome c; Region: Cytochrom_C; cl11414 123214000983 Cytochrome D1 heme domain; Region: Cytochrom_D1; pfam02239 123214000984 Cytochrome c; Region: Cytochrom_C; cl11414 123214000985 Cytochrome D1 heme domain; Region: Cytochrom_D1; pfam02239 123214000986 Cytochrome c; Region: Cytochrom_C; cl11414 123214000987 heme d1 biosynthesis radical SAM protein NirJ; Region: rSAM_NirJ; TIGR04051 123214000988 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 123214000989 FeS/SAM binding site; other site 123214000990 Domain of unknown function (DUF4008); Region: DUF4008; cl14869 123214000991 Cytochrome D1 heme domain; Region: Cytochrom_D1; pfam02239 123214000992 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 123214000993 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 123214000994 Tetrapyrrole (Corrin/Porphyrin) Methylases; Region: TP_methylase; pfam00590 123214000995 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 123214000996 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 123214000997 Predicted hydrocarbon binding protein (contains V4R domain) [General function prediction only]; Region: COG1719 123214000998 Heme NO binding; Region: HNOB; cl15268 123214000999 Nitric oxide reductase large subunit [Inorganic ion transport and metabolism]; Region: NorB; COG3256 123214001000 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 123214001001 Binuclear center (active site) [active] 123214001002 K-pathway; other site 123214001003 Putative proton exit pathway; other site 123214001004 Putative water exit pathway; other site 123214001005 Cupin domain; Region: Cupin_2; cl09118 123214001006 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3399 123214001007 Predicted transcriptional regulator [Transcription]; Region: COG1959 123214001008 Helix-turn-helix domains; Region: HTH; cl00088 123214001009 Copper resistance protein D; Region: CopD; cl00563 123214001010 Type I 3-dehydroquinase, (3-dehydroquinate dehydratase or DHQase); Region: DHQase_I; cd00502 123214001011 3-dehydroquinate dehydratase, type I; Region: aroD; TIGR01093 123214001012 active site 123214001013 catalytic residue [active] 123214001014 dimer interface [polypeptide binding]; other site 123214001015 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 123214001016 Nicotinamidase/pyrazinamidase (PZase). Nicotinamidase, a ubiquitous enzyme in prokaryotes, converts nicotinamide to nicotinic acid (niacin) and ammonia, which in turn can be recycled to make nicotinamide adenine dinucleotide (NAD). The same enzyme is...; Region: nicotinamidase; cd01011 123214001017 Isochorismatase family; Region: Isochorismatase; pfam00857 123214001018 catalytic triad [active] 123214001019 metal binding site [ion binding]; metal-binding site 123214001020 conserved cis-peptide bond; other site 123214001021 Putative heavy-metal-binding; Region: YbjQ_1; cl00426 123214001022 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional; Region: PRK14975 123214001023 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 123214001024 catalytic site [active] 123214001025 putative active site [active] 123214001026 putative substrate binding site [chemical binding]; other site 123214001027 Phylum Aquificae Pol A is different from Escherichia coli Pol A by three signature sequences; Region: DNA_pol_A_Aquificae_like; cd08639 123214001028 active site 123214001029 DNA binding site [nucleotide binding] 123214001030 catalytic site [active] 123214001031 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 123214001032 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 123214001033 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 123214001034 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 123214001035 Recombination protein O N terminal; Region: RecO_N; cl15812 123214001036 Recombination protein O C terminal; Region: RecO_C; pfam02565 123214001037 Predicted transcriptional regulators [Transcription]; Region: COG1318 123214001038 probable regulatory domain; Region: near_KaiC_dom; TIGR03879 123214001039 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]; Region: RAD55; COG0467 123214001040 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 123214001041 Walker A motif; other site 123214001042 ATP binding site [chemical binding]; other site 123214001043 Walker B motif; other site 123214001044 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 123214001045 active site 123214001046 Selenophosphate synthase [Amino acid transport and metabolism]; Region: SelD; COG0709 123214001047 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK13581 123214001048 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214001049 ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH); Region: ACT_3PGDH-like; cd04879 123214001050 L-serine binding site [chemical binding]; other site 123214001051 Myo-inositol-1-phosphate synthase; Region: NAD_binding_5; cl00554 123214001052 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cl00235 123214001053 active site 1 [active] 123214001054 dimer interface [polypeptide binding]; other site 123214001055 hexamer interface [polypeptide binding]; other site 123214001056 active site 2 [active] 123214001057 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 123214001058 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 123214001059 active site 123214001060 phosphorylation site [posttranslational modification] 123214001061 intermolecular recognition site; other site 123214001062 dimerization interface [polypeptide binding]; other site 123214001063 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 123214001064 Walker A motif; other site 123214001065 ATP binding site [chemical binding]; other site 123214001066 Walker B motif; other site 123214001067 arginine finger; other site 123214001068 Helix-turn-helix domains; Region: HTH; cl00088 123214001069 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 123214001070 alanine racemase; Reviewed; Region: alr; PRK00053 123214001071 active site 123214001072 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 123214001073 dimer interface [polypeptide binding]; other site 123214001074 substrate binding site [chemical binding]; other site 123214001075 catalytic residues [active] 123214001076 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 123214001077 metal-binding site [ion binding] 123214001078 copper-(or silver)-translocating P-type ATPase; Region: ATPase-IB1_Cu; TIGR01511 123214001079 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 123214001080 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 123214001081 motif II; other site 123214001082 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 123214001083 Glycerophosphodiester phosphodiesterase domain as found in prokaryota and eukaryota, and similar proteins; Region: GDPD; cd08556 123214001084 active site 123214001085 catalytic site [active] 123214001086 metal binding site [ion binding]; metal-binding site 123214001087 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]; Region: COG0075 123214001088 Alanine-glyoxylate aminotransferase (AGAT) family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to alanine-glyoxylate aminotransferase (AGAT); Region: AGAT_like; cd06451 123214001089 homodimer interface [polypeptide binding]; other site 123214001090 pyridoxal 5'-phosphate binding site [chemical binding]; other site 123214001091 catalytic residue [active] 123214001092 Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP_PGM_like; cd07067 123214001093 catalytic core [active] 123214001094 ATP phosphoribosyltransferase regulatory subunit; Provisional; Region: hisZ; PRK12292 123214001095 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 123214001096 dimer interface [polypeptide binding]; other site 123214001097 motif 1; other site 123214001098 active site 123214001099 motif 2; other site 123214001100 motif 3; other site 123214001101 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 123214001102 Lysine 2,3-aminomutase [Amino acid transport and metabolism]; Region: KamA; COG1509 123214001103 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 123214001104 FeS/SAM binding site; other site 123214001105 Lysine-2,3-aminomutase; Region: LAM_C; pfam12544 123214001106 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 123214001107 hydrogenase nickel incorporation protein; Provisional; Region: hypA; cl00418 123214001108 Hydrogenase expression/synthesis hypA family; Region: HypA; pfam01155 123214001109 Polyferredoxin [Energy production and conversion]; Region: NapH; COG0348 123214001110 TonB-dependent siderophore receptor; Region: TonB-siderophor; TIGR01783 123214001111 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 123214001112 N-terminal plug; other site 123214001113 ligand-binding site [chemical binding]; other site 123214001114 Protein of unknown function (DUF1009); Region: DUF1009; cl09182 123214001115 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 123214001116 UDP-N-acetylglucosamine O-acyltransferase (UDP-GlcNAc acyltransferase): Proteins in this family catalyze the transfer of (R)-3-hydroxymyristic acid from its acyl carrier protein thioester to UDP-GlcNAc. It is the first enzyme in the lipid A biosynthetic...; Region: LbH_UDP-GlcNAc_AT; cd03351 123214001117 active site 123214001118 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 123214001119 catalytic residues [active] 123214001120 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 123214001121 dimerization interface [polypeptide binding]; other site 123214001122 putative DNA binding site [nucleotide binding]; other site 123214001123 putative Zn2+ binding site [ion binding]; other site 123214001124 Heterodisulfide reductase, subunit B [Energy production and conversion]; Region: HdrB; COG2048 123214001125 Cysteine-rich domain; Region: CCG; pfam02754 123214001126 Cysteine-rich domain; Region: CCG; pfam02754 123214001127 Succinate dehydrogenase/fumarate reductase, Fe-S protein subunit [Energy production and conversion]; Region: FrdB; COG0479 123214001128 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 123214001129 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 123214001130 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 123214001131 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 123214001132 substrate binding pocket [chemical binding]; other site 123214001133 chain length determination region; other site 123214001134 substrate-Mg2+ binding site; other site 123214001135 catalytic residues [active] 123214001136 aspartate-rich region 1; other site 123214001137 active site lid residues [active] 123214001138 aspartate-rich region 2; other site 123214001139 Restriction endonuclease; Region: Mrr_cat; cl00516 123214001140 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 123214001141 RNA/DNA hybrid binding site [nucleotide binding]; other site 123214001142 active site 123214001143 Ribosomal protein L19; Region: Ribosomal_L19; cl00406 123214001144 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 123214001145 catalytic triad [active] 123214001146 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase protein; Reviewed; Region: PRK02759 123214001147 Phosphoribosyl-AMP cyclohydrolase; Region: PRA-CH; cl00344 123214001148 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00345 123214001149 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 123214001150 Thiamine pyrophosphate (TPP) family, DXS subfamily, TPP-binding module; 1-Deoxy-D-xylulose-5-phosphate synthase (DXS) is a regulatory enzyme of the mevalonate-independent pathway involved in terpenoid biosynthesis. Terpeniods are plant natural products...; Region: TPP_DXS; cd02007 123214001151 TPP-binding site; other site 123214001152 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 123214001153 PYR/PP interface [polypeptide binding]; other site 123214001154 dimer interface [polypeptide binding]; other site 123214001155 TPP binding site [chemical binding]; other site 123214001156 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 123214001157 Uncharacterized conserved protein (DUF2203); Region: DUF2203; cl02056 123214001158 Bifunctional nuclease; Region: DNase-RNase; cl00553 123214001159 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 123214001160 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 123214001161 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 123214001162 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 123214001163 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 123214001164 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 123214001165 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 123214001166 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 123214001167 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 123214001168 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; cl02529 123214001169 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 123214001170 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 123214001171 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 123214001172 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 123214001173 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 123214001174 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 123214001175 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 123214001176 Ankyrin repeats (many copies); Region: Ank_5; pfam13857 123214001177 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 123214001178 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214001179 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 123214001180 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1729 123214001181 Tetratricopeptide repeat; Region: TPR_6; pfam13174 123214001182 Tetratricopeptide repeat; Region: TPR_6; pfam13174 123214001183 Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl...; Region: CIS_IPPS; cl00230 123214001184 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 123214001185 catalytic residue [active] 123214001186 putative FPP diphosphate binding site; other site 123214001187 putative FPP binding hydrophobic cleft; other site 123214001188 dimer interface [polypeptide binding]; other site 123214001189 putative IPP diphosphate binding site; other site 123214001190 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 123214001191 menaquinone biosynthesis protein, SCO4550 family; Region: mena_SCO4550; TIGR03699 123214001192 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; cl15377 123214001193 FeS/SAM binding site; other site 123214001194 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 123214001195 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 123214001196 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 123214001197 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 123214001198 Bacitracin resistance protein BacA; Region: BacA; cl00858 123214001199 radical SAM protein, TIGR01212 family; Region: TIGR01212 123214001200 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 123214001201 FeS/SAM binding site; other site 123214001202 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214001203 metal binding site [ion binding]; metal-binding site 123214001204 active site 123214001205 I-site; other site 123214001206 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 123214001207 Cytochrome c peroxidase [Inorganic ion transport and metabolism]; Region: MauG; COG1858 123214001208 tartrate dehydrogenase; Provisional; Region: PRK08194 123214001209 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 123214001210 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 123214001211 nicotinate-nucleotide pyrophosphorylase; Region: nadC; TIGR00078 123214001212 dimerization interface [polypeptide binding]; other site 123214001213 active site 123214001214 Uncharacterized protein family (UPF0093); Region: UPF0093; cl00863 123214001215 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 123214001216 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 123214001217 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 123214001218 tandem repeat interface [polypeptide binding]; other site 123214001219 oligomer interface [polypeptide binding]; other site 123214001220 active site residues [active] 123214001221 Ribosome-binding factor A; Region: RBFA; cl00542 123214001222 Protein of unknown function (DUF503); Region: DUF503; cl00669 123214001223 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 123214001224 active site 123214001225 FtsH Extracellular; Region: FtsH_ext; pfam06480 123214001226 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 123214001227 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 123214001228 Walker A motif; other site 123214001229 ATP binding site [chemical binding]; other site 123214001230 Walker B motif; other site 123214001231 arginine finger; other site 123214001232 Peptidase family M41; Region: Peptidase_M41; pfam01434 123214001233 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 123214001234 Ligand Binding Site [chemical binding]; other site 123214001235 B3/4 domain; Region: B3_4; cl11458 123214001236 Ribosomal protein S20; Region: Ribosomal_S20p; cl00384 123214001237 S-adenosylmethionine synthetase; Provisional; Region: PRK04439 123214001238 Nitrate and nitrite sensing; Region: NIT; pfam08376 123214001239 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 123214001240 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 123214001241 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 123214001242 dimer interface [polypeptide binding]; other site 123214001243 putative CheW interface [polypeptide binding]; other site 123214001244 reverse gyrase; Reviewed; Region: PRK09401 123214001245 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 123214001246 ATP binding site [chemical binding]; other site 123214001247 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 123214001248 Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from...; Region: TOPRIM; cl00718 123214001249 active site 123214001250 metal binding site [ion binding]; metal-binding site 123214001251 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 123214001252 domain I; other site 123214001253 DNA binding groove [nucleotide binding] 123214001254 phosphate binding site [ion binding]; other site 123214001255 domain II; other site 123214001256 domain III; other site 123214001257 nucleotide binding site [chemical binding]; other site 123214001258 catalytic site [active] 123214001259 domain IV; other site 123214001260 UDP glucuronic acid epimerase, extended (e) SDRs; Region: UDP_GE_SDE_e; cd05253 123214001261 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 123214001262 putative NAD(P) binding site [chemical binding]; other site 123214001263 active site 123214001264 putative substrate binding site [chemical binding]; other site 123214001265 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 123214001266 This family is most closely related to the GT1 family of glycosyltransferases. WabH in Klebsiella pneumoniae has been shown to transfer a GlcNAc residue from UDP-GlcNAc onto the acceptor GalUA residue in the cellular outer core; Region: GT1_WabH_like; cd03811 123214001267 putative ADP-binding pocket [chemical binding]; other site 123214001268 dihydroorotate dehydrogenase (subfamily 1) family protein; Region: pyrD_sub1_fam; TIGR01037 123214001269 Dihydroorotate dehydrogenase (DHOD) class 1B FMN-binding domain. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine...; Region: DHOD_1B_like; cd04740 123214001270 heterodimer interface [polypeptide binding]; other site 123214001271 active site 123214001272 FMN binding site [chemical binding]; other site 123214001273 homodimer interface [polypeptide binding]; other site 123214001274 substrate binding site [chemical binding]; other site 123214001275 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 123214001276 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 123214001277 active site 123214001278 Zn binding site [ion binding]; other site 123214001279 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 123214001280 2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Reviewed; Region: mtnW; PRK09549 123214001281 Ribulose bisphosphate carboxylase large chain; Region: RuBisCO_large; cl08232 123214001282 dimer interface [polypeptide binding]; other site 123214001283 catalytic residue [active] 123214001284 metal binding site [ion binding]; metal-binding site 123214001285 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 123214001286 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 123214001287 Cytochrome c; Region: Cytochrom_C; cl11414 123214001288 Cytochrome c; Region: Cytochrom_C; cl11414 123214001289 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 123214001290 Low-spin heme binding site [chemical binding]; other site 123214001291 D-pathway; other site 123214001292 Binuclear center (active site) [active] 123214001293 K-pathway; other site 123214001294 Putative proton exit pathway; other site 123214001295 Putative water exit pathway; other site 123214001296 Cytochrome C oxidase, mono-heme subunit/FixO; Region: FixO; cl01130 123214001297 Rhomboid family; Region: Rhomboid; cl11446 123214001298 Fibronectin type 3 domain-containing protein [General function prediction only]; Region: COG3401 123214001299 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cl00065 123214001300 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 123214001301 NeuB family; Region: NeuB; cl00496 123214001302 SprA-related family; Region: SprA-related; pfam12118 123214001303 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 123214001304 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 123214001305 Cu(I) binding site [ion binding]; other site 123214001306 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 123214001307 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 123214001308 Gram-negative bacterial tonB protein; Region: TonB; cl10048 123214001309 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 123214001310 RNA/DNA hybrid binding site [nucleotide binding]; other site 123214001311 active site 123214001312 DNA repair protein RadA; Provisional; Region: PRK11823 123214001313 Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of...; Region: Sms; cd01121 123214001314 Walker A motif/ATP binding site; other site 123214001315 ATP binding site [chemical binding]; other site 123214001316 Walker B motif; other site 123214001317 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 123214001318 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 123214001319 Fe-S cluster binding site [ion binding]; other site 123214001320 active site 123214001321 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 123214001322 active site 123214001323 dimer interface [polypeptide binding]; other site 123214001324 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 123214001325 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 123214001326 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 123214001327 RaiA ('ribosome-associated inhibitor A', also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal A site; Region: RaiA; cd00552 123214001328 30S subunit binding site; other site 123214001329 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 123214001330 23S rRNA interface [nucleotide binding]; other site 123214001331 L3 interface [polypeptide binding]; other site 123214001332 Ribosomal protein S9/S16; Region: Ribosomal_S9; cl00334 123214001333 N-acetyl-gamma-glutamyl-phosphate reductase; Validated; Region: argC; PRK00436 123214001334 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214001335 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 123214001336 RfaE encodes a bifunctional ADP-heptose synthase involved in the biosynthesis of the lipopolysaccharide (LPS) core precursor ADP-L-glycero-D-manno-heptose. LPS plays an important role in maintaining the structural integrity of the bacterial outer...; Region: RfaE_like; cd01172 123214001337 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 123214001338 putative ribose interaction site [chemical binding]; other site 123214001339 putative ADP binding site [chemical binding]; other site 123214001340 Phosphoribosylformylglycinamidine (FGAM) synthase; Region: PurS; cl00789 123214001341 Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase; Region: GATase1_FGAR_AT; cd01740 123214001342 putative active site [active] 123214001343 catalytic triad [active] 123214001344 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 123214001345 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 123214001346 catalytic residues [active] 123214001347 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 123214001348 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 123214001349 Zn2+ binding site [ion binding]; other site 123214001350 Mg2+ binding site [ion binding]; other site 123214001351 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 123214001352 Spore Coat Protein U domain; Region: SCPU; cl02253 123214001353 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 123214001354 Sporulation related domain; Region: SPOR; cl10051 123214001355 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 123214001356 Spore Coat Protein U domain; Region: SCPU; cl02253 123214001357 Spore Coat Protein U domain; Region: SCPU; cl02253 123214001358 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3677 123214001359 Helix-turn-helix domains; Region: HTH; cl00088 123214001360 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 123214001361 Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12. HMBS catalyzes the conversion of...; Region: HMBS; cd00494 123214001362 domain interfaces; other site 123214001363 active site 123214001364 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 123214001365 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl15769 123214001366 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 123214001367 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 123214001368 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 123214001369 Walker A/P-loop; other site 123214001370 ATP binding site [chemical binding]; other site 123214001371 Q-loop/lid; other site 123214001372 ABC transporter signature motif; other site 123214001373 Walker B; other site 123214001374 D-loop; other site 123214001375 H-loop/switch region; other site 123214001376 DNA polymerase alpha chain like domain; Region: POLIIIAc; smart00481 123214001377 PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid...; Region: PAP2_like; cl00474 123214001378 active site 123214001379 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 123214001380 active site 123214001381 hydrophilic channel; other site 123214001382 dimerization interface [polypeptide binding]; other site 123214001383 catalytic residues [active] 123214001384 active site lid [active] 123214001385 AMIN domain; Region: AMIN; pfam11741 123214001386 N-acetylmuramoyl-L-alanine amidase or MurNAc-LAA (also known as peptidoglycan aminohydrolase, NAMLA amidase, NAMLAA, Amidase 3, and peptidoglycan amidase; EC 3.5.1.28) is an autolysin that hydrolyzes the amide bond between N-acetylmuramoyl and L-amino...; Region: MurNAc-LAA; cd02696 123214001387 active site 123214001388 metal binding site [ion binding]; metal-binding site 123214001389 Type III pantothenate kinase; Region: Pan_kinase; cl09130 123214001390 dihydrodipicolinate reductase; Provisional; Region: PRK00048 123214001391 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214001392 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 123214001393 Putative F0F1-ATPase subunit (ATPase_gene1); Region: ATPase_gene1; cl09754 123214001394 Exopolyphosphatase-related proteins [General function prediction only]; Region: COG0618 123214001395 DHH family; Region: DHH; pfam01368 123214001396 DHHA1 domain; Region: DHHA1; pfam02272 123214001397 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 123214001398 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 123214001399 minor groove reading motif; other site 123214001400 helix-hairpin-helix signature motif; other site 123214001401 substrate binding pocket [chemical binding]; other site 123214001402 active site 123214001403 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 123214001404 5'-3' exonuclease; Region: 53EXOc; smart00475 123214001405 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 123214001406 active site 123214001407 metal binding site 1 [ion binding]; metal-binding site 123214001408 putative 5' ssDNA interaction site; other site 123214001409 metal binding site 3; metal-binding site 123214001410 metal binding site 2 [ion binding]; metal-binding site 123214001411 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 123214001412 putative DNA binding site [nucleotide binding]; other site 123214001413 putative metal binding site [ion binding]; other site 123214001414 Peptidase family M23; Region: Peptidase_M23; pfam01551 123214001415 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; cd00384 123214001416 dimer interface [polypeptide binding]; other site 123214001417 active site 123214001418 Schiff base residues; other site 123214001419 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385; cl00611 123214001420 RNA methyltransferase; Region: Methyltrans_RNA; pfam04452 123214001421 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 123214001422 ABC-ATPase subunit interface; other site 123214001423 dimer interface [polypeptide binding]; other site 123214001424 putative PBP binding regions; other site 123214001425 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 123214001426 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 123214001427 Alcohol dehydrogenases of the MDR family; Region: Zn_ADH_like1; cd08266 123214001428 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 123214001429 putative NAD(P) binding site [chemical binding]; other site 123214001430 structural Zn binding site [ion binding]; other site 123214001431 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 123214001432 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 123214001433 G1 box; other site 123214001434 GTP/Mg2+ binding site [chemical binding]; other site 123214001435 Switch I region; other site 123214001436 G2 box; other site 123214001437 G3 box; other site 123214001438 Switch II region; other site 123214001439 G4 box; other site 123214001440 G5 box; other site 123214001441 Nucleoside recognition; Region: Gate; cl00486 123214001442 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 123214001443 Nucleoside recognition; Region: Gate; cl00486 123214001444 FeoA domain; Region: FeoA; cl00838 123214001445 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the...; Region: S2P-M50_like_1; cd06158 123214001446 active site 123214001447 putative substrate binding region [chemical binding]; other site 123214001448 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Region: murF; TIGR01143 123214001449 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 123214001450 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 123214001451 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 123214001452 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214001453 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 123214001454 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 123214001455 PIN domain of ribonucleases (toxins), VapC and FitB, of prokaryotic toxin/antitoxin operons, Pyrococcus horikoshii protein PH0500, and other similar bacterial and archaeal homologs; Region: PIN_VapC-FitB; cd09881 123214001456 homodimer interface [polypeptide binding]; other site 123214001457 putative active site [active] 123214001458 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 123214001459 HIGH motif; other site 123214001460 dimer interface [polypeptide binding]; other site 123214001461 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 123214001462 active site 123214001463 KMSKS motif; other site 123214001464 helicase/secretion neighborhood putative DEAH-box helicase; Region: DECH_helic; TIGR03817 123214001465 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 123214001466 ATP binding site [chemical binding]; other site 123214001467 putative Mg++ binding site [ion binding]; other site 123214001468 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 123214001469 nucleotide binding region [chemical binding]; other site 123214001470 ATP-binding site [chemical binding]; other site 123214001471 Domain of unknown function (DUF1998); Region: DUF1998; pfam09369 123214001472 SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+; Region: SIR2; cl00195 123214001473 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 123214001474 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 123214001475 N-acetyl-D-glucosamine binding site [chemical binding]; other site 123214001476 catalytic residue [active] 123214001477 TPR repeat; Region: TPR_11; pfam13414 123214001478 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 123214001479 binding surface 123214001480 TPR repeat; Region: TPR_11; pfam13414 123214001481 TPR motif; other site 123214001482 TPR repeat; Region: TPR_11; pfam13414 123214001483 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 123214001484 binding surface 123214001485 TPR motif; other site 123214001486 TPR repeat; Region: TPR_11; pfam13414 123214001487 CHAT domain; Region: CHAT; pfam12770 123214001488 chaperone protein DnaJ; Provisional; Region: PRK14282 123214001489 bifunctional 3-deoxy-7-phosphoheptulonate synthase/chorismate mutase; Reviewed; Region: PRK12595 123214001490 Creatinine amidohydrolase; Region: Creatininase; cl00618 123214001491 comEA protein; Region: comE; TIGR01259 123214001492 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl14786 123214001493 NurA domain; Region: NurA; cl09134 123214001494 Obg family GTPase CgtA; Region: Obg_CgtA; TIGR02729 123214001495 GTP1/OBG; Region: GTP1_OBG; pfam01018 123214001496 Obg GTPase; Region: Obg; cd01898 123214001497 G1 box; other site 123214001498 GTP/Mg2+ binding site [chemical binding]; other site 123214001499 Switch I region; other site 123214001500 G2 box; other site 123214001501 G3 box; other site 123214001502 Switch II region; other site 123214001503 G4 box; other site 123214001504 G5 box; other site 123214001505 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 123214001506 PLD-like domain; Region: PLDc_2; pfam13091 123214001507 putative active site [active] 123214001508 catalytic site [active] 123214001509 HerA helicase [Replication, recombination, and repair]; Region: COG0433 123214001510 Domain of unknown function DUF87; Region: DUF87; pfam01935 123214001511 Ribosomal L28 family; Region: Ribosomal_L28; cl00367 123214001512 FOG: CBS domain [General function prediction only]; Region: COG0517 123214001513 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cd02205 123214001514 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214001515 metal binding site [ion binding]; metal-binding site 123214001516 active site 123214001517 I-site; other site 123214001518 ribosomal protein S12 methylthiotransferase RimO; Region: TIGR01125 123214001519 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 123214001520 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 123214001521 FeS/SAM binding site; other site 123214001522 methylthioribose-1-phosphate isomerase; Reviewed; Region: mtnA; PRK05720 123214001523 Predicted translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis]; Region: COG0182; cl00348 123214001524 family of mostly uncharacterized proteins similar to B.subtilis YvcK; Region: YvcK_like; cd07187 123214001525 Uncharacterized protein family UPF0052; Region: UPF0052; pfam01933 123214001526 putative substrate binding pocket [chemical binding]; other site 123214001527 dimer interface [polypeptide binding]; other site 123214001528 phosphate binding site [ion binding]; other site 123214001529 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214001530 Aspartate oxidase [Coenzyme metabolism]; Region: NadB; COG0029 123214001531 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 123214001532 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 123214001533 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 123214001534 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 123214001535 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 123214001536 Phosphoribosylanthranilate isomerase (PRAI) catalyzes the fourth step of the tryptophan biosynthesis, the conversion of N-(5'- phosphoribosyl)-anthranilate (PRA) to 1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate (CdRP). Most PRAIs are monomeric; Region: PRAI; cd00405 123214001537 active site 123214001538 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1729 123214001539 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 123214001540 binding surface 123214001541 TPR motif; other site 123214001542 Tetratricopeptide repeat; Region: TPR_12; pfam13424 123214001543 TPR repeat; Region: TPR_11; pfam13414 123214001544 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 123214001545 binding surface 123214001546 TPR motif; other site 123214001547 TPR repeat; Region: TPR_11; pfam13414 123214001548 Tetratricopeptide repeat; Region: TPR_16; pfam13432 123214001549 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 123214001550 Tetratricopeptide repeat; Region: TPR_16; pfam13432 123214001551 TPR motif; other site 123214001552 binding surface 123214001553 Tetratricopeptide repeat; Region: TPR_16; pfam13432 123214001554 TPR repeat; Region: TPR_11; pfam13414 123214001555 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 123214001556 binding surface 123214001557 TPR motif; other site 123214001558 type IV pilus biogenesis/stability protein PilW; Region: type_IV_pilW; TIGR02521 123214001559 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 123214001560 Ligand Binding Site [chemical binding]; other site 123214001561 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 123214001562 Ligand Binding Site [chemical binding]; other site 123214001563 Aconatase-like swivel domain of 3-isopropylmalate dehydratase and related uncharacterized proteins. 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate...; Region: IPMI_Swivel; cd01577 123214001564 substrate binding site [chemical binding]; other site 123214001565 Lactate dehydrogenase and related dehydrogenases [Energy production and conversion / Coenzyme metabolism / General function prediction only]; Region: LdhA; COG1052 123214001566 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214001567 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 123214001568 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 123214001569 NAD(P) binding site [chemical binding]; other site 123214001570 homotetramer interface [polypeptide binding]; other site 123214001571 homodimer interface [polypeptide binding]; other site 123214001572 active site 123214001573 Phosphopantetheine attachment site; Region: PP-binding; cl09936 123214001574 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 123214001575 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 123214001576 dimer interface [polypeptide binding]; other site 123214001577 active site 123214001578 ribonuclease III, bacterial; Region: RNaseIII; TIGR02191 123214001579 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 123214001580 dimerization interface [polypeptide binding]; other site 123214001581 active site 123214001582 metal binding site [ion binding]; metal-binding site 123214001583 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 123214001584 dsRNA binding site [nucleotide binding]; other site 123214001585 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 123214001586 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl15769 123214001587 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 123214001588 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 123214001589 Walker A motif; other site 123214001590 ATP binding site [chemical binding]; other site 123214001591 Walker B motif; other site 123214001592 arginine finger; other site 123214001593 Helix-turn-helix domains; Region: HTH; cl00088 123214001594 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 123214001595 Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]; Region: NarQ; COG3850 123214001596 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 123214001597 dimerization interface [polypeptide binding]; other site 123214001598 Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism]; Region: CysI; COG0155 123214001599 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 123214001600 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 123214001601 SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this...; Region: SirA_YedF_YeeD; cd00291 123214001602 CPxP motif; other site 123214001603 Anthranilate phosphoribosyltransferase [Amino acid transport and metabolism]; Region: TrpD; COG0547 123214001604 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 123214001605 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes [Amino acid transport and metabolism / Coenzyme metabolism]; Region: CysH; COG0175 123214001606 This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. A highly...; Region: PAPS_reductase; cd01713 123214001607 Active Sites [active] 123214001608 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 123214001609 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214001610 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 123214001611 active site 123214001612 tetramer interface; other site 123214001613 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 123214001614 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 123214001615 ATP binding site [chemical binding]; other site 123214001616 active site 123214001617 substrate binding site [chemical binding]; other site 123214001618 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2976 123214001619 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 123214001620 Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from...; Region: GT1_LPS_heptosyltransferase; cd03789 123214001621 putative active site [active] 123214001622 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 123214001623 TPR motif; other site 123214001624 TPR repeat; Region: TPR_11; pfam13414 123214001625 binding surface 123214001626 pyruvate ferredoxin oxidoreductase subunit beta; Provisional; Region: PRK11865 123214001627 Thiamine pyrophosphate (TPP family), PFOR porB-like subfamily, TPP-binding module; composed of proteins similar to the beta subunit (porB) of the Helicobacter pylori four-subunit pyruvate ferredoxin oxidoreductase (PFOR), which are also found in archaea...; Region: TPP_PFOR_porB_like; cd03376 123214001628 TPP-binding site [chemical binding]; other site 123214001629 putative dimer interface [polypeptide binding]; other site 123214001630 pyruvate flavodoxin oxidoreductase subunit alpha; Reviewed; Region: porA; PRK09622 123214001631 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 123214001632 dimer interface [polypeptide binding]; other site 123214001633 PYR/PP interface [polypeptide binding]; other site 123214001634 TPP binding site [chemical binding]; other site 123214001635 substrate binding site [chemical binding]; other site 123214001636 2-oxoacid:acceptor oxidoreductase, delta subunit, pyruvate/2-ketoisovalerate family; Region: PorD_KorD; TIGR02179 123214001637 4Fe-4S binding domain; Region: Fer4; cl02805 123214001638 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 123214001639 pyruvate/ketoisovalerate ferredoxin oxidoreductase subunit gamma; Provisional; Region: PRK14029 123214001640 recombination protein RecR; Reviewed; Region: recR; PRK00076 123214001641 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 123214001642 putative active site [active] 123214001643 putative metal-binding site [ion binding]; other site 123214001644 tetramer interface [polypeptide binding]; other site 123214001645 YbaB/EbfC DNA-binding family; Region: YbaB_DNA_bd; cl00494 123214001646 DNA polymerase III subunits gamma and tau; Provisional; Region: PRK14953 123214001647 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 123214001648 Walker A motif; other site 123214001649 ATP binding site [chemical binding]; other site 123214001650 Walker B motif; other site 123214001651 arginine finger; other site 123214001652 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 123214001653 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 123214001654 ribosome biogenesis GTP-binding protein YlqF; Region: GTPase_YlqF; TIGR03596 123214001655 GTP/Mg2+ binding site [chemical binding]; other site 123214001656 G4 box; other site 123214001657 G5 box; other site 123214001658 G1 box; other site 123214001659 Switch I region; other site 123214001660 G2 box; other site 123214001661 G3 box; other site 123214001662 Switch II region; other site 123214001663 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 123214001664 OstA-like protein; Region: OstA; cl00844 123214001665 Organic solvent tolerance protein; Region: OstA_C; pfam04453 123214001666 Transcriptional regulator [Transcription]; Region: IclR; COG1414 123214001667 Helix-turn-helix domains; Region: HTH; cl00088 123214001668 Bacterial transcriptional regulator; Region: IclR; pfam01614 123214001669 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 123214001670 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 123214001671 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of...; Region: Sm_like; cl00259 123214001672 Sm1 motif; other site 123214001673 D1 - D2 interaction site; other site 123214001674 D3 - B interaction site; other site 123214001675 Hfq - Hfq interaction site; other site 123214001676 RNA binding pocket [nucleotide binding]; other site 123214001677 Sm2 motif; other site 123214001678 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 123214001679 HflX GTPase family; Region: HflX; cd01878 123214001680 Elongation factor Tu GTP binding domain; Region: GTP_EFTU; pfam00009 123214001681 G1 box; other site 123214001682 GTP/Mg2+ binding site [chemical binding]; other site 123214001683 Switch I region; other site 123214001684 G2 box; other site 123214001685 G3 box; other site 123214001686 Switch II region; other site 123214001687 G4 box; other site 123214001688 G5 box; other site 123214001689 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 123214001690 nucleotide binding site/active site [active] 123214001691 HIT family signature motif; other site 123214001692 catalytic residue [active] 123214001693 SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this...; Region: SirA_YedF_YeeD; cd00291 123214001694 CPxP motif; other site 123214001695 Protein of unknown function (DUF3343); Region: DUF3343; pfam11823 123214001696 Helix-turn-helix domains; Region: HTH; cl00088 123214001697 NosL; Region: NosL; cl01769 123214001698 imidazoleglycerol-phosphate dehydratase; Validated; Region: hisB; PRK00951 123214001699 Imidazoleglycerol-phosphate dehydratase; Region: IGPD; cd07914 123214001700 putative active site pocket [active] 123214001701 4-fold oligomerization interface [polypeptide binding]; other site 123214001702 metal binding residues [ion binding]; metal-binding site 123214001703 3-fold/trimer interface [polypeptide binding]; other site 123214001704 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 123214001705 Walker A motif; other site 123214001706 ATP binding site [chemical binding]; other site 123214001707 Walker B motif; other site 123214001708 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 123214001709 Helix-turn-helix domains; Region: HTH; cl00088 123214001710 YsiA-like protein, C-terminal region; Region: TetR_C_4; pfam08359 123214001711 DHH family; Region: DHH; pfam01368 123214001712 Predicted phosphohydrolase (DHH superfamily) [General function prediction only]; Region: COG2404 123214001713 DHHA1 domain; Region: DHHA1; pfam02272 123214001714 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 123214001715 dimer interface [polypeptide binding]; other site 123214001716 putative radical transfer pathway; other site 123214001717 diiron center [ion binding]; other site 123214001718 tyrosyl radical; other site 123214001719 ATP cone domain; Region: ATP-cone; pfam03477 123214001720 Class I ribonucleotide reductase; Region: RNR_I; cd01679 123214001721 active site 123214001722 dimer interface [polypeptide binding]; other site 123214001723 Ribonucleotide reductase, barrel domain; Region: Ribonuc_red_lgC; pfam02867 123214001724 catalytic residues [active] 123214001725 effector binding site; other site 123214001726 R2 peptide binding site; other site 123214001727 Outer membrane protein family (DUF1597); Region: DUF1597; pfam07642 123214001728 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor...; Region: Ribosomal_L24e_L24; cl00909 123214001729 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 123214001730 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 123214001731 GatB domain; Region: GatB_Yqey; cl11497 123214001732 S-adenosyl-L-homocysteine hydrolase; Provisional; Region: PRK05476 123214001733 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214001734 oligomerization interface [polypeptide binding]; other site 123214001735 active site 123214001736 NAD+ binding site [chemical binding]; other site 123214001737 Dehydratase family; Region: ILVD_EDD; cl00340 123214001738 S-adenosylmethionine synthetase; Validated; Region: PRK05250 123214001739 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 123214001740 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 123214001741 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 123214001742 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214001743 I-site; other site 123214001744 metal binding site [ion binding]; metal-binding site 123214001745 dihydrolipoamide dehydrogenase; Region: lipoamide_DH; TIGR01350 123214001746 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 123214001747 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 123214001748 general secretion pathway protein D; Region: type_II_gspD; TIGR02517 123214001749 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 123214001750 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 123214001751 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 123214001752 Fimbrial assembly protein (PilN); Region: PilN; pfam05137 123214001753 Tfp pilus assembly protein, ATPase PilM [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilM; COG4972 123214001754 phosphoenolpyruvate synthase; Validated; Region: PRK06464 123214001755 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 123214001756 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 123214001757 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 123214001758 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 123214001759 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 123214001760 Class II Glycyl-tRNA synthetase (GlyRS) alpha subunit core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes and in arabidopsis. It is responsible for the...; Region: GlyRS_alpha_core; cd00733 123214001761 dimer interface [polypeptide binding]; other site 123214001762 motif 1; other site 123214001763 active site 123214001764 motif 2; other site 123214001765 motif 3; other site 123214001766 tRNA pseudouridine synthase D; Reviewed; Region: truD; PRK00984 123214001767 PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of...; Region: PseudoU_synth; cl00130 123214001768 active site 123214001769 PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of...; Region: PseudoU_synth; cl00130 123214001770 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 123214001771 Transglycosylase; Region: Transgly; cl07896 123214001772 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 123214001773 Tryptophan synthase-beta: Trptophan synthase is a bifunctional enzyme that catalyses the last two steps in the biosynthesis of L-tryptophan via its alpha and beta reactions. In the alpha reaction, indole 3-glycerol phosphate is cleaved reversibly to...; Region: Trp-synth_B; cd06446 123214001774 Pyridoxal-phosphate dependent enzyme; Region: PALP; pfam00291 123214001775 pyridoxal 5'-phosphate binding site [chemical binding]; other site 123214001776 catalytic residue [active] 123214001777 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK14467 123214001778 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 123214001779 FeS/SAM binding site; other site 123214001780 Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is...; Region: MopB_Formate-Dh-H; cd02753 123214001781 formate dehydrogenase, alpha subunit, archaeal-type; Region: Fdh-alpha; TIGR01591 123214001782 [4Fe-4S] binding site [ion binding]; other site 123214001783 molybdopterin cofactor binding site; other site 123214001784 Molybdopterin-Binding, C-terminal (MopB_CT) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum-...; Region: MopB_CT; cl09929 123214001785 molybdopterin cofactor binding site; other site 123214001786 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214001787 metal binding site [ion binding]; metal-binding site 123214001788 active site 123214001789 I-site; other site 123214001790 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 123214001791 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl00284 123214001792 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 123214001793 Ligand binding site; other site 123214001794 oligomer interface; other site 123214001795 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 123214001796 ThiS interaction site; other site 123214001797 putative active site [active] 123214001798 tetramer interface [polypeptide binding]; other site 123214001799 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 123214001800 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 123214001801 Beta-Casp domain; Region: Beta-Casp; cl12567 123214001802 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 123214001803 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 123214001804 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 123214001805 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 123214001806 putative active site [active] 123214001807 substrate binding site [chemical binding]; other site 123214001808 putative cosubstrate binding site; other site 123214001809 catalytic site [active] 123214001810 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 123214001811 substrate binding site [chemical binding]; other site 123214001812 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 123214001813 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; cl06870 123214001814 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 123214001815 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 123214001816 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 123214001817 [2Fe-2S] cluster binding site [ion binding]; other site 123214001818 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 123214001819 Qi binding site; other site 123214001820 intrachain domain interface; other site 123214001821 interchain domain interface [polypeptide binding]; other site 123214001822 cytochrome b; Provisional; Region: CYTB; MTH00191 123214001823 heme bH binding site [chemical binding]; other site 123214001824 heme bL binding site [chemical binding]; other site 123214001825 Qo binding site; other site 123214001826 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; cl00193 123214001827 intrachain domain interface; other site 123214001828 Qo binding site; other site 123214001829 Cytochrome c1 [Energy production and conversion]; Region: CYT1; COG2857 123214001830 Cytochrome c; Region: Cytochrom_C; cl11414 123214001831 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 123214001832 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214001833 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 123214001834 active site 123214001835 catalytic site [active] 123214001836 substrate binding site [chemical binding]; other site 123214001837 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 123214001838 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 123214001839 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 123214001840 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214001841 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl15357 123214001842 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4641 123214001843 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 123214001844 Sporulation related domain; Region: SPOR; cl10051 123214001845 arginyl-tRNA synthetase; Reviewed; Region: argS; PRK01611 123214001846 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; cl04104 123214001847 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 123214001848 active site 123214001849 HIGH motif; other site 123214001850 KMSK motif region; other site 123214001851 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 123214001852 tRNA binding surface [nucleotide binding]; other site 123214001853 anticodon binding site; other site 123214001854 CTP synthetase; Validated; Region: pyrG; PRK05380 123214001855 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 123214001856 Catalytic site [active] 123214001857 active site 123214001858 UTP binding site [chemical binding]; other site 123214001859 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 123214001860 active site 123214001861 putative oxyanion hole; other site 123214001862 catalytic triad [active] 123214001863 acetyl-CoA synthetase; Provisional; Region: PRK00174 123214001864 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 123214001865 AMP-binding enzyme; Region: AMP-binding; cl15778 123214001866 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 123214001867 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 123214001868 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 123214001869 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 123214001870 Walker A motif; other site 123214001871 ATP binding site [chemical binding]; other site 123214001872 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 123214001873 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 123214001874 alanyl-tRNA synthetase; Provisional; Region: alaS; PRK13902 123214001875 Helix-turn-helix domains; Region: HTH; cl00088 123214001876 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 123214001877 SmpB-tmRNA interface; other site 123214001878 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 123214001879 Zn binding site [ion binding]; other site 123214001880 Protein of unknown function, DUF399; Region: DUF399; cl01139 123214001881 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 123214001882 adenylosuccinate lyase; Provisional; Region: PRK07492 123214001883 Adenylsuccinate lyase (ASL)_subgroup 1; Region: Adenylsuccinate_lyase_1; cd01360 123214001884 tetramer interface [polypeptide binding]; other site 123214001885 active site 123214001886 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 123214001887 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 123214001888 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 123214001889 minor groove reading motif; other site 123214001890 helix-hairpin-helix signature motif; other site 123214001891 substrate binding pocket [chemical binding]; other site 123214001892 active site 123214001893 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 123214001894 NAD synthetase; Provisional; Region: PRK13981 123214001895 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 123214001896 multimer interface [polypeptide binding]; other site 123214001897 active site 123214001898 catalytic triad [active] 123214001899 protein interface 1 [polypeptide binding]; other site 123214001900 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 123214001901 homodimer interface [polypeptide binding]; other site 123214001902 NAD binding pocket [chemical binding]; other site 123214001903 ATP binding pocket [chemical binding]; other site 123214001904 Mg binding site [ion binding]; other site 123214001905 active-site loop [active] 123214001906 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cl00290 123214001907 HDOD domain; Region: HDOD; pfam08668 123214001908 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 123214001909 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 123214001910 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 123214001911 synthetase active site [active] 123214001912 NTP binding site [chemical binding]; other site 123214001913 metal binding site [ion binding]; metal-binding site 123214001914 TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named after...; Region: TGS_RelA_SpoT; cd01668 123214001915 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 123214001916 Glycerol-3-phosphate acyltransferase; Region: G3P_acyltransf; cl00410 123214001917 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 123214001918 cell division protein FtsZ; Validated; Region: PRK09330 123214001919 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 123214001920 nucleotide binding site [chemical binding]; other site 123214001921 SulA interaction site; other site 123214001922 cell division protein FtsA; Region: ftsA; TIGR01174 123214001923 Cell division protein FtsA; Region: FtsA; cl11496 123214001924 Cell division protein FtsA; Region: FtsA; cl11496 123214001925 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 123214001926 Cell division protein FtsQ; Region: FtsQ; pfam03799 123214001927 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 123214001928 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 123214001929 ATP-grasp domain; Region: ATP-grasp_4; cl03087 123214001930 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 123214001931 FAD binding domain; Region: FAD_binding_4; pfam01565 123214001932 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 123214001933 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 123214001934 MurG is an N-acetylglucosaminyltransferase, the last enzyme involved in the intracellular phase of peptidoglycan biosynthesis. It transfers N-acetyl-D-glucosamine (GlcNAc) from UDP-GlcNAc to the C4 hydroxyl of a lipid-linked N-acetylmuramoyl pentapeptide...; Region: GT1_MurG; cd03785 123214001935 active site 123214001936 homodimer interface [polypeptide binding]; other site 123214001937 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 123214001938 UDP-N-acetylmuramoylalanine--D-glutamate ligase; Region: murD; TIGR01087 123214001939 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 123214001940 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 123214001941 pyruvate carboxylase subunit B; Validated; Region: PRK09282 123214001942 Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain; Region: DRE_TIM_PC_TC_5S; cd07937 123214001943 active site 123214001944 catalytic residues [active] 123214001945 metal binding site [ion binding]; metal-binding site 123214001946 homodimer binding site [polypeptide binding]; other site 123214001947 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 123214001948 carboxyltransferase (CT) interaction site; other site 123214001949 biotinylation site [posttranslational modification]; other site 123214001950 Uncharacterized conserved protein (DUF2173); Region: DUF2173; cl01994 123214001951 dihydropyrimidine dehydrogenase subunit A; Provisional; Region: PRK11749 123214001952 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214001953 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214001954 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 123214001955 ornithine carbamoyltransferase; Provisional; Region: PRK00779 123214001956 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 123214001957 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214001958 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 123214001959 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 123214001960 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214001961 PAS domain S-box; Region: sensory_box; TIGR00229 123214001962 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 123214001963 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214001964 metal binding site [ion binding]; metal-binding site 123214001965 active site 123214001966 I-site; other site 123214001967 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 123214001968 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK00130 123214001969 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 123214001970 RNA binding site [nucleotide binding]; other site 123214001971 active site 123214001972 folylpolyglutamate synthase/dihydrofolate synthase; Region: folC; TIGR01499 123214001973 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 123214001974 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 123214001975 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 123214001976 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 123214001977 active site 123214001978 catalytic residues [active] 123214001979 metal binding site [ion binding]; metal-binding site 123214001980 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 123214001981 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 123214001982 substrate binding site [chemical binding]; other site 123214001983 hexamer interface [polypeptide binding]; other site 123214001984 metal binding site [ion binding]; metal-binding site 123214001985 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 123214001986 Domain of unknown function DUF59; Region: DUF59; cl00941 123214001987 dihydroorotase; Validated; Region: pyrC; PRK09357 123214001988 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 123214001989 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 123214001990 active site 123214001991 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 123214001992 Catalytic site [active] 123214001993 Signal peptidase, peptidase S26; Region: Peptidase_S26; pfam10502 123214001994 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 123214001995 Staphylococcal nuclease homologues; Region: SNc; smart00318 123214001996 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cd00175 123214001997 Catalytic site; other site 123214001998 AIR carboxylase; Region: AIRC; cl00310 123214001999 glutamate synthase subunit alpha; Provisional; Region: gltB; PRK11750 123214002000 Glutamine amidotransferases class-II (Gn-AT), glutamate synthase (GltS)-type. GltS is a homodimer that synthesizes L-glutamate from 2-oxoglutarate and L-glutamine, an important step in ammonia assimilation in bacteria, cyanobacteria and plants. The...; Region: GltS; cd00713 123214002001 active site 123214002002 dimer interface [polypeptide binding]; other site 123214002003 Glutamate synthase central domain; Region: Glu_syn_central; pfam04898 123214002004 Glutamate synthase (GltS) FMN-binding domain. GltS is a complex iron-sulfur flavoprotein that catalyzes the reductive synthesis of L-glutamate from 2-oxoglutarate and L-glutamine via intramolecular channelling of ammonia, a reaction in the plant, yeast...; Region: GltS_FMN; cd02808 123214002005 active site 123214002006 FMN binding site [chemical binding]; other site 123214002007 substrate binding site [chemical binding]; other site 123214002008 3Fe-4S cluster binding site [ion binding]; other site 123214002009 gltb_C. This domain is found at the C-terminus of the large subunit (gltB) of glutamate synthase (GltS). GltS encodes a complex iron-sulfur flavoprotein that catalyzes the synthesis of L-glutamate from L-glutamine and 2-oxoglutarate. It requires the...; Region: gltB_C; cd00982 123214002010 domain interface; other site 123214002011 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 123214002012 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 123214002013 dimerization interface 3.5A [polypeptide binding]; other site 123214002014 active site 123214002015 GTPase Era; Reviewed; Region: era; PRK00089 123214002016 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 123214002017 G1 box; other site 123214002018 GTP/Mg2+ binding site [chemical binding]; other site 123214002019 Switch I region; other site 123214002020 G2 box; other site 123214002021 Switch II region; other site 123214002022 G3 box; other site 123214002023 G4 box; other site 123214002024 G5 box; other site 123214002025 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that...; Region: KH-I; cl00098 123214002026 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 123214002027 MgtE intracellular N domain; Region: MgtE_N; cl15244 123214002028 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 123214002029 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cl15354 123214002030 Divalent cation transporter; Region: MgtE; cl00786 123214002031 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 123214002032 dimer interface [polypeptide binding]; other site 123214002033 putative CheW interface [polypeptide binding]; other site 123214002034 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 123214002035 Tryptophan synthase-beta: Trptophan synthase is a bifunctional enzyme that catalyses the last two steps in the biosynthesis of L-tryptophan via its alpha and beta reactions. In the alpha reaction, indole 3-glycerol phosphate is cleaved reversibly to...; Region: Trp-synth_B; cd06446 123214002036 Pyridoxal-phosphate dependent enzyme; Region: PALP; pfam00291 123214002037 pyridoxal 5'-phosphate binding site [chemical binding]; other site 123214002038 catalytic residue [active] 123214002039 Acyl transferase domain; Region: Acyl_transf_1; cl08282 123214002040 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 123214002041 AAA domain; Region: AAA_26; pfam13500 123214002042 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 123214002043 Protein of unknown function DUF72; Region: DUF72; cl00777 123214002044 MgtC family; Region: MgtC; pfam02308 123214002045 Predicted membrane protein [Function unknown]; Region: COG3174 123214002046 Domain of unknown function (DUF4010); Region: DUF4010; pfam13194 123214002047 Endodeoxyribonuclease RusA; Region: RusA; cl01885 123214002048 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 123214002049 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 123214002050 active site residue [active] 123214002051 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 123214002052 active site residue [active] 123214002053 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 123214002054 DMSO reductase family type II enzyme, molybdopterin subunit; Region: DMSO_red_II_alp; TIGR03479 123214002055 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 123214002056 molybdopterin cofactor binding site; other site 123214002057 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 123214002058 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 123214002059 Molybdopterin-Binding, C-terminal (MopB_CT) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum-...; Region: MopB_CT; cl09929 123214002060 molybdopterin cofactor binding site; other site 123214002061 DMSO reductase family type II enzyme, iron-sulfur subunit; Region: DMSO_red_II_bet; TIGR03478 123214002062 4Fe-4S binding domain; Region: Fer4; cl02805 123214002063 Heme-binding domain of bacterial ethylbenzene dehydrogenase; Region: DOMON_EBDH; cd09623 123214002064 heme binding site [chemical binding]; other site 123214002065 beta subunit binding site [polypeptide binding]; other site 123214002066 putative heme-binding domain, Pirellula/Verrucomicrobium type; Region: CxxCH_TIGR02603 123214002067 Cytochrome c; Region: Cytochrom_C; cl11414 123214002068 Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]; Region: HybA; COG0437 123214002069 4Fe-4S binding domain; Region: Fer4; cl02805 123214002070 Formate-dependent nitrite reductase, membrane component [Inorganic ion transport and metabolism]; Region: NrfD; COG3301 123214002071 Polysulphide reductase, NrfD; Region: NrfD; cl01295 123214002072 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 123214002073 molybdopterin cofactor binding site; other site 123214002074 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 123214002075 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 123214002076 Molybdopterin-Binding, C-terminal (MopB_CT) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum-...; Region: MopB_CT; cl09929 123214002077 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 123214002078 ferredoxin; Validated; Region: PRK07118 123214002079 4Fe-4S binding domain; Region: Fer4; cl02805 123214002080 MinD superfamily P-loop ATPase containing an inserted ferredoxin domain [Energy production and conversion]; Region: COG1149 123214002081 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 123214002082 SCP-2 sterol transfer family; Region: SCP2; cl01225 123214002083 Conserved hypothetical protein 698; Region: Cons_hypoth698; cl01075 123214002084 Predicted CRISPR-associated nuclease, contains McrA/HNH-nuclease and RuvC-like nuclease domain [Defense mechanisms]; Region: COG3513 123214002085 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cl00083 123214002086 HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the basis...; Region: HIT_like; cl00228 123214002087 nucleotide binding site/active site [active] 123214002088 HIT family signature motif; other site 123214002089 catalytic residue [active] 123214002090 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cd03440 123214002091 active site 2 [active] 123214002092 active site 1 [active] 123214002093 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 123214002094 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 123214002095 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 123214002096 Septum formation initiator; Region: DivIC; cl11433 123214002097 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG0275 123214002098 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214002099 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 123214002100 SurA N-terminal domain; Region: SurA_N_3; cl07813 123214002101 PPIC-type PPIASE domain; Region: Rotamase; cl08278 123214002102 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 123214002103 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 123214002104 Walker A/P-loop; other site 123214002105 ATP binding site [chemical binding]; other site 123214002106 Q-loop/lid; other site 123214002107 ABC transporter signature motif; other site 123214002108 Walker B; other site 123214002109 D-loop; other site 123214002110 H-loop/switch region; other site 123214002111 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 123214002112 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 123214002113 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 123214002114 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 123214002115 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 123214002116 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 123214002117 active site 123214002118 HIGH motif; other site 123214002119 nucleotide binding site [chemical binding]; other site 123214002120 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 123214002121 active site 123214002122 KMSKS motif; other site 123214002123 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 123214002124 tRNA binding surface [nucleotide binding]; other site 123214002125 anticodon binding site; other site 123214002126 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 123214002127 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 123214002128 IHF dimer interface [polypeptide binding]; other site 123214002129 IHF - DNA interface [nucleotide binding]; other site 123214002130 D,D-heptose 1,7-bisphosphate phosphatase; Validated; Region: PRK08942 123214002131 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 123214002132 active site 123214002133 motif I; other site 123214002134 motif II; other site 123214002135 Ferredoxin thioredoxin reductase catalytic beta chain; Region: FeThRed_B; cl01977 123214002136 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; cl00417 123214002137 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl15792 123214002138 anaerobic sulfite reductase subunit B; Provisional; Region: PRK08221 123214002139 Anaerobic sulfite reductase contains an FAD and NADPH binding module with structural similarity to ferredoxin reductase and sequence similarity to dihydroorotate dehydrogenases. Clostridium pasteurianum inducible dissimilatory type sulfite reductase is...; Region: sulfite_reductase_like; cd06221 123214002140 FAD binding pocket [chemical binding]; other site 123214002141 FAD binding motif [chemical binding]; other site 123214002142 phosphate binding motif [ion binding]; other site 123214002143 beta-alpha-beta structure motif; other site 123214002144 NAD binding pocket [chemical binding]; other site 123214002145 Iron coordination center [ion binding]; other site 123214002146 sulfite reductase, subunit A; Region: sulfite_red_A; TIGR02910 123214002147 hydrogenase (NiFe) small subunit (hydA); Region: hydA; TIGR00391 123214002148 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl15792 123214002149 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; cl00417 123214002150 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cl00859 123214002151 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 123214002152 metal ion-dependent adhesion site (MIDAS); other site 123214002153 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cd00198 123214002154 metal ion-dependent adhesion site (MIDAS); other site 123214002155 MoxR-like ATPases [General function prediction only]; Region: COG0714 123214002156 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 123214002157 Walker A motif; other site 123214002158 ATP binding site [chemical binding]; other site 123214002159 Walker B motif; other site 123214002160 arginine finger; other site 123214002161 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 123214002162 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 123214002163 Acylphosphatase; Region: Acylphosphatase; cl00551 123214002164 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypF; COG0068 123214002165 HypF finger; Region: zf-HYPF; pfam07503 123214002166 HypF finger; Region: zf-HYPF; pfam07503 123214002167 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 123214002168 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 123214002169 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257; cl15822 123214002170 Bacterial export proteins, family 1; Region: Bac_export_1; cl00734 123214002171 Bacterial export proteins, family 3; Region: Bac_export_3; cl00867 123214002172 FliP family; Region: FliP; cl00593 123214002173 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 123214002174 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 123214002175 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 123214002176 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 123214002177 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 123214002178 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 123214002179 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 123214002180 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 123214002181 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 123214002182 FlgD Ig-like domain; Region: FlgD_ig; cl15790 123214002183 flagellar protein export ATPase FliI; Region: FliI_clade1; TIGR03496 123214002184 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 123214002185 Flagellum-specific ATPase/type III secretory pathway virulence-related protein. This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they...; Region: ATPase_flagellum-secretory_path_III; cd01136 123214002186 Walker A motif/ATP binding site; other site 123214002187 Walker B motif; other site 123214002188 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 123214002189 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 123214002190 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 123214002191 Flagellar hook-basal body complex protein FliE; Region: FliE; cl09139 123214002192 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 123214002193 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 123214002194 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 123214002195 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK05680 123214002196 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 123214002197 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1729 123214002198 RNA polymerase sigma factor, FliA/WhiG family; Region: FliA_WhiG; TIGR02479 123214002199 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 123214002200 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 123214002201 DNA binding residues [nucleotide binding] 123214002202 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 123214002203 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 123214002204 FleN is a member of the Fer4_NifH superfamily. It shares the common function as an ATPase, with the ATP-binding domain at the N-terminus. In Pseudomonas aeruginosa, FleN gene is involved in regulating the number of flagella and chemotactic motility by...; Region: FleN-like; cd02038 123214002205 flagellar biosynthetic protein FlhF; Region: FlhF; TIGR03499 123214002206 SRP54-type protein, GTPase domain; Region: SRP54; smart00962 123214002207 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 123214002208 flagellar biosynthesis protein FlhA; Validated; Region: flhA; cl07980 123214002209 FHIPEP family; Region: FHIPEP; pfam00771 123214002210 Rod binding protein; Region: Rod-binding; cl01626 123214002211 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 123214002212 Flagellar P-ring protein; Region: FlgI; pfam02119 123214002213 Flagellar L-ring protein; Region: FlgH; cl00905 123214002214 SAF-like; Region: SAF_2; pfam13144 123214002215 SAF domain; Region: SAF; cl00555 123214002216 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 123214002217 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 123214002218 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 123214002219 Flagellar basal body rod protein [Cell motility and secretion]; Region: FlgG; COG4786 123214002220 Flagella basal body rod protein; Region: Flg_bb_rod; cl15793 123214002221 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 123214002222 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 123214002223 flagellar motor switch protein FliM; Region: fliM_switch; TIGR01397 123214002224 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 123214002225 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 123214002226 FliG C-terminal domain; Region: FliG_C; pfam01706 123214002227 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 123214002228 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 123214002229 dimerization interface [polypeptide binding]; other site 123214002230 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 123214002231 dimer interface [polypeptide binding]; other site 123214002232 putative CheW interface [polypeptide binding]; other site 123214002233 PAS domain; Region: PAS_9; pfam13426 123214002234 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 123214002235 dimer interface [polypeptide binding]; other site 123214002236 putative CheW interface [polypeptide binding]; other site 123214002237 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 123214002238 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 123214002239 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 123214002240 active site 123214002241 phosphorylation site [posttranslational modification] 123214002242 intermolecular recognition site; other site 123214002243 dimerization interface [polypeptide binding]; other site 123214002244 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 123214002245 Response regulator receiver domain; Region: Response_reg; pfam00072 123214002246 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 123214002247 active site 123214002248 phosphorylation site [posttranslational modification] 123214002249 intermolecular recognition site; other site 123214002250 dimerization interface [polypeptide binding]; other site 123214002251 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cl00256 123214002252 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cd00088 123214002253 putative binding surface; other site 123214002254 active site 123214002255 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 123214002256 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 123214002257 ATP binding site [chemical binding]; other site 123214002258 Mg2+ binding site [ion binding]; other site 123214002259 G-X-G motif; other site 123214002260 CheA regulatory domain; CheA is a histidine protein kinase present in bacteria and archea. Activated by the chemotaxis receptor a histidine phosphoryl group from CheA is passed directly to an aspartate in the response regulator CheY. This signalling...; Region: CheA_reg; cd00731 123214002261 Chemotaxis phosphatase, CheZ; Region: CheZ; cl01219 123214002262 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 123214002263 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 123214002264 active site 123214002265 phosphorylation site [posttranslational modification] 123214002266 intermolecular recognition site; other site 123214002267 dimerization interface [polypeptide binding]; other site 123214002268 CheB methylesterase; Region: CheB_methylest; pfam01339 123214002269 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 123214002270 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214002271 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 123214002272 Permease P (pink-eyed dilution). Mutations in the human melanosomal P gene were responsible for classic phenotype of oculocutaneous albinism type 2 (OCA2). Although the precise function of the P protein is unknown, it was predicted to regulate the...; Region: P_permease; cd01116 123214002273 transmembrane helices; other site 123214002274 histidinol dehydrogenase; Region: hisD; TIGR00069 123214002275 Peptidase family M48; Region: Peptidase_M48; cl12018 123214002276 PAS domain S-box; Region: sensory_box; TIGR00229 123214002277 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 123214002278 putative active site [active] 123214002279 heme pocket [chemical binding]; other site 123214002280 Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]; Region: RocR; COG3829 123214002281 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 123214002282 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 123214002283 PAS domain; Region: PAS_9; pfam13426 123214002284 putative active site [active] 123214002285 heme pocket [chemical binding]; other site 123214002286 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214002287 metal binding site [ion binding]; metal-binding site 123214002288 active site 123214002289 I-site; other site 123214002290 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 123214002291 FGGY family of carbohydrate kinases; Region: FGGY; cl08364 123214002292 SNF2 family N-terminal domain; Region: SNF2_N; pfam00176 123214002293 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 123214002294 ATP binding site [chemical binding]; other site 123214002295 putative Mg++ binding site [ion binding]; other site 123214002296 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 123214002297 nucleotide binding region [chemical binding]; other site 123214002298 ATP-binding site [chemical binding]; other site 123214002299 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 123214002300 PAS domain; Region: PAS_9; pfam13426 123214002301 putative active site [active] 123214002302 heme pocket [chemical binding]; other site 123214002303 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 123214002304 CutA1 divalent ion tolerance protein; Region: CutA1; cl00584 123214002305 Band_7_stomatin_like: A subgroup of the band 7 domain of flotillin (reggie) like proteins similar to stomatin and podicin (two lipid raft-associated integral membrane proteins). Individual proteins of this band 7 domain family may cluster to form...; Region: Band_7_stomatin_like; cd03403 123214002306 Clp amino terminal domain; Region: Clp_N; pfam02861 123214002307 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 123214002308 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 123214002309 Walker A motif; other site 123214002310 ATP binding site [chemical binding]; other site 123214002311 Walker B motif; other site 123214002312 arginine finger; other site 123214002313 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 123214002314 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 123214002315 Walker A motif; other site 123214002316 ATP binding site [chemical binding]; other site 123214002317 Walker B motif; other site 123214002318 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 123214002319 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 123214002320 MutS domain I; Region: MutS_I; pfam01624 123214002321 MutS domain II; Region: MutS_II; pfam05188 123214002322 MutS family domain IV; Region: MutS_IV; pfam05190 123214002323 MutS1 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal...; Region: ABC_MutS1; cd03284 123214002324 Walker A/P-loop; other site 123214002325 ATP binding site [chemical binding]; other site 123214002326 Q-loop/lid; other site 123214002327 ABC transporter signature motif; other site 123214002328 Walker B; other site 123214002329 D-loop; other site 123214002330 H-loop/switch region; other site 123214002331 Peptidase family M23; Region: Peptidase_M23; pfam01551 123214002332 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14331 123214002333 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 123214002334 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 123214002335 FeS/SAM binding site; other site 123214002336 TRAM domain; Region: TRAM; cl01282 123214002337 Bifunctional nuclease; Region: DNase-RNase; cl00553 123214002338 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 123214002339 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 123214002340 dimer interface [polypeptide binding]; other site 123214002341 active site 123214002342 CoA binding pocket [chemical binding]; other site 123214002343 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 123214002344 Ribosomal L32p protein family; Region: Ribosomal_L32p; cl09115 123214002345 LL-diaminopimelate aminotransferase; Provisional; Region: PRK09276 123214002346 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 123214002347 pyridoxal 5'-phosphate binding site [chemical binding]; other site 123214002348 homodimer interface [polypeptide binding]; other site 123214002349 catalytic residue [active] 123214002350 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 123214002351 AAA domain; Region: AAA_33; pfam13671 123214002352 Short-chain dehydrogenases of various substrate specificities [General function prediction only]; Region: DltE; COG0300 123214002353 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 123214002354 NADP binding site [chemical binding]; other site 123214002355 active site 123214002356 steroid binding site; other site 123214002357 Virulence factor BrkB; Region: Virul_fac_BrkB; cl07918 123214002358 OsmC-like protein; Region: OsmC; cl00767 123214002359 HflC protein; Region: hflC; TIGR01932 123214002360 The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. Many of these band 7 domain-containing proteins are lipid raft-associated. Individual proteins of this...; Region: Band_7; cl02525 123214002361 excinuclease ABC subunit B; Provisional; Region: PRK05298 123214002362 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 123214002363 ATP binding site [chemical binding]; other site 123214002364 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 123214002365 nucleotide binding region [chemical binding]; other site 123214002366 ATP-binding site [chemical binding]; other site 123214002367 Ultra-violet resistance protein B; Region: UvrB; pfam12344 123214002368 UvrB/uvrC motif; Region: UVR; pfam02151 123214002369 Predicted O-methyltransferase [General function prediction only]; Region: COG4122 123214002370 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214002371 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 123214002372 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cd00761 123214002373 active site 123214002374 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 123214002375 putative metal binding site; other site 123214002376 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 123214002377 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 123214002378 FeS/SAM binding site; other site 123214002379 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 123214002380 Predicted methyltransferases [General function prediction only]; Region: COG0313 123214002381 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 123214002382 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 123214002383 HIGH motif; other site 123214002384 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 123214002385 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 123214002386 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 123214002387 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1672 123214002388 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 123214002389 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 123214002390 active site 123214002391 KMSKS motif; other site 123214002392 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 123214002393 tRNA binding surface [nucleotide binding]; other site 123214002394 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 123214002395 Ligand Binding Site [chemical binding]; other site 123214002396 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 123214002397 CAAX protease self-immunity; Region: Abi; cl00558 123214002398 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 123214002399 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214002400 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214002401 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 123214002402 Outer membrane protein family (DUF1597); Region: DUF1597; pfam07642 123214002403 Protein of unknown function (DUF501); Region: DUF501; cl00652 123214002404 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: VicK; COG5002 123214002405 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214002406 metal binding site [ion binding]; metal-binding site 123214002407 active site 123214002408 I-site; other site 123214002409 2'-5' RNA ligase [Translation, ribosomal structure and biogenesis]; Region: LigT; COG1514 123214002410 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 123214002411 LigT like Phosphoesterase; Region: LigT_PEase; pfam02834 123214002412 ThiC family; Region: ThiC; cl08031 123214002413 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 123214002414 Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]; Region: NtrB; COG3852 123214002415 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 123214002416 dimer interface [polypeptide binding]; other site 123214002417 phosphorylation site [posttranslational modification] 123214002418 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 123214002419 ATP binding site [chemical binding]; other site 123214002420 Mg2+ binding site [ion binding]; other site 123214002421 G-X-G motif; other site 123214002422 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 123214002423 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 123214002424 active site 123214002425 phosphorylation site [posttranslational modification] 123214002426 intermolecular recognition site; other site 123214002427 dimerization interface [polypeptide binding]; other site 123214002428 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 123214002429 Walker A motif; other site 123214002430 ATP binding site [chemical binding]; other site 123214002431 Walker B motif; other site 123214002432 arginine finger; other site 123214002433 Helix-turn-helix domains; Region: HTH; cl00088 123214002434 TPR repeat; Region: TPR_11; pfam13414 123214002435 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 123214002436 binding surface 123214002437 TPR motif; other site 123214002438 Tetratricopeptide repeat; Region: TPR_12; pfam13424 123214002439 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 123214002440 binding surface 123214002441 TPR motif; other site 123214002442 TPR repeat; Region: TPR_11; pfam13414 123214002443 Sporulation related domain; Region: SPOR; cl10051 123214002444 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional; Region: PRK10714 123214002445 Bacterial DPM1_like enzymes are related to eukaryotic DPM1; Region: DPM1_like_bac; cd04187 123214002446 Ligand binding site; other site 123214002447 Putative Catalytic site; other site 123214002448 DXD motif; other site 123214002449 Uncharacterized protein family (UPF0104); Region: UPF0104; cl04219 123214002450 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 123214002451 Helix-turn-helix domains; Region: HTH; cl00088 123214002452 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 123214002453 efflux pump membrane protein (multidrug resistance protein A); Region: 8a0101; TIGR00998 123214002454 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 123214002455 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 123214002456 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 123214002457 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 123214002458 putative substrate translocation pore; other site 123214002459 putative efflux pump membrane fusion protein; Provisional; Region: PRK03598 123214002460 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 123214002461 Mechanosensitive ion channel; Region: MS_channel; pfam00924 123214002462 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 123214002463 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 123214002464 Walker A/P-loop; other site 123214002465 ATP binding site [chemical binding]; other site 123214002466 Q-loop/lid; other site 123214002467 ABC transporter signature motif; other site 123214002468 Walker B; other site 123214002469 D-loop; other site 123214002470 H-loop/switch region; other site 123214002471 This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity. In bacteria and archaea, these transporters usually include an ATP-binding...; Region: ABC_DR_subfamily_A; cd03230 123214002472 Walker A/P-loop; other site 123214002473 ATP binding site [chemical binding]; other site 123214002474 Q-loop/lid; other site 123214002475 ABC transporter signature motif; other site 123214002476 Walker B; other site 123214002477 D-loop; other site 123214002478 H-loop/switch region; other site 123214002479 Low molecular weight phosphatase family; Region: LMWPc; cd00115 123214002480 Low molecular weight phosphotyrosine protein phosphatase; Region: LMWPc; pfam01451 123214002481 active site 123214002482 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 123214002483 ABC-type multidrug transport system, permease component [Defense mechanisms]; Region: COG0842 123214002484 ABC-2 type transporter; Region: ABC2_membrane; cl11417 123214002485 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 123214002486 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 123214002487 P-loop; other site 123214002488 Magnesium ion binding site [ion binding]; other site 123214002489 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 123214002490 Magnesium ion binding site [ion binding]; other site 123214002491 ParB-like nuclease domain; Region: ParBc; cl02129 123214002492 general secretion pathway protein G; Region: typeII_sec_gspG; TIGR01710 123214002493 Type II secretion system (T2SS), protein G; Region: T2SG; pfam08334 123214002494 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; cl06830 123214002495 general secretion pathway protein I; Region: gspI; TIGR01707 123214002496 Type II secretion system (T2SS), protein K; Region: T2SK; pfam03934 123214002497 Peptidase S8 family domain in Subtilisin-like proteins; Region: Peptidases_S8_Subtilisin_like; cd07473 123214002498 catalytic triad [active] 123214002499 putative active site [active] 123214002500 general secretion pathway protein C; Region: typeII_sec_gspC; TIGR01713 123214002501 Type IV pilus biogenesis; Region: Pilus_PilP; cl11837 123214002502 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 123214002503 general secretion pathway protein D; Region: type_II_gspD; TIGR02517 123214002504 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 123214002505 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 123214002506 Bacterial type II/III secretion system short domain; Region: Secretin_N; pfam03958 123214002507 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 123214002508 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 123214002509 general secretory pathway protein E; Region: type_II_gspE; TIGR02533 123214002510 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 123214002511 Walker A motif; other site 123214002512 ATP binding site [chemical binding]; other site 123214002513 Walker B motif; other site 123214002514 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 123214002515 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 123214002516 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 123214002517 Methyltransferase domain; Region: Methyltransf_31; pfam13847 123214002518 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 123214002519 S-adenosylmethionine binding site [chemical binding]; other site 123214002520 Rubredoxin; Region: Rubredoxin; pfam00301 123214002521 Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are...; Region: rubredoxin; cd00730 123214002522 iron binding site [ion binding]; other site 123214002523 Predicted enolase-phosphatase [Energy production and conversion]; Region: COG4229 123214002524 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 123214002525 motif II; other site 123214002526 Cobalt uptake substrate-specific transmembrane region; Region: CbiM; cl00397 123214002527 Putative MetA-pathway of phenol degradation; Region: Phenol_MetA_deg; cl01768 123214002528 Domain of unknown function (DUF4198); Region: DUF4198; pfam10670 123214002529 Transcriptional regulator [Transcription]; Region: IclR; COG1414 123214002530 Helix-turn-helix domains; Region: HTH; cl00088 123214002531 Phosphate-selective porin O and P; Region: Porin_O_P; cl01524 123214002532 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 123214002533 acetyl-CoA synthetase; Provisional; Region: PRK00174 123214002534 Domain of unknown function (DUF3448); Region: DUF3448; pfam11930 123214002535 AMP-binding enzyme; Region: AMP-binding; cl15778 123214002536 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 123214002537 Protein of unknown function, DUF485; Region: DUF485; cl01231 123214002538 Sodium:solute symporter family; Region: SSF; cl00456 123214002539 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 123214002540 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]; Region: COG2905 123214002541 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 123214002542 ligand binding site [chemical binding]; other site 123214002543 flexible hinge region; other site 123214002544 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with either the CAP_ED (cAMP receptor protein effector domain) family of transcription factors and the DUF294 domain or the PB1 (Phox and Bem1p) domain; Region: CBS_pair_CAP-ED_DUF294_PBI_assoc2; cd04800 123214002545 Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins; Region: NT_GlnE_GlnD_like; cd05401 123214002546 metal binding triad; other site 123214002547 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 123214002548 active site 123214002549 catalytic site [active] 123214002550 substrate binding site [chemical binding]; other site 123214002551 Archaeal ATPase; Region: Arch_ATPase; pfam01637 123214002552 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 123214002553 Acylphosphatase; Region: Acylphosphatase; cl00551 123214002554 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypF; COG0068 123214002555 HypF finger; Region: zf-HYPF; pfam07503 123214002556 HypF finger; Region: zf-HYPF; pfam07503 123214002557 hypothetical protein; Reviewed; Region: PRK09588 123214002558 Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein; Region: Hint; cl15780 123214002559 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 123214002560 Mechanosensitive ion channel; Region: MS_channel; pfam00924 123214002561 FixH; Region: FixH; cl01254 123214002562 Helix-turn-helix domains; Region: HTH; cl00088 123214002563 Peptidase family M48; Region: Peptidase_M48; cl12018 123214002564 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 123214002565 Dehydroquinate synthase-like (DHQ-like) and iron-containing alcohol dehydrogenases (Fe-ADH); Region: DHQ_Fe-ADH; cl02872 123214002566 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 123214002567 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 123214002568 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 123214002569 Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, chaperones]; Region: PflA; COG1180 123214002570 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 123214002571 FeS/SAM binding site; other site 123214002572 C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some...; Region: Peptidase_C1; cl00298 123214002573 active site 123214002574 C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some...; Region: Peptidase_C1; cl00298 123214002575 active site 123214002576 Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus; Region: E_set; cl09101 123214002577 Carbamoylphosphate synthase large subunit (split gene in MJ) [Amino acid transport and metabolism / Nucleotide transport and metabolism]; Region: CarB; COG0458 123214002578 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 123214002579 ATP-grasp domain; Region: ATP-grasp_4; cl03087 123214002580 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 123214002581 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; smart01096 123214002582 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK06406 123214002583 ATP cone domain; Region: ATP-cone; pfam03477 123214002584 Ribonucleotide reductase, all-alpha domain; Region: Ribonuc_red_lgN; pfam00317 123214002585 Class II ribonucleotide reductase, dimeric form; Region: RNR_II_dimer; cd02888 123214002586 active site 123214002587 dimer interface [polypeptide binding]; other site 123214002588 effector binding site; other site 123214002589 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 123214002590 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK08665 123214002591 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 123214002592 Walker A motif; other site 123214002593 ATP binding site [chemical binding]; other site 123214002594 Walker B motif; other site 123214002595 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 123214002596 Helix-turn-helix domains; Region: HTH; cl00088 123214002597 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; cl09905 123214002598 Cytochrome c554 and c-prime; Region: Cytochrome_C554; pfam13435 123214002599 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; cl09905 123214002600 aromatic acid decarboxylase; Validated; Region: PRK05920 123214002601 Flavoprotein; Region: Flavoprotein; cl08021 123214002602 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 123214002603 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 123214002604 active site 123214002605 DNA binding site [nucleotide binding] 123214002606 Int/Topo IB signature motif; other site 123214002607 The cyclase subunit of imidazoleglycerol phosphate synthase (HisF). Imidazole glycerol phosphate synthase (IGPS) catalyzes the fifth step of histidine biosynthesis, the formation of the imidazole ring. IGPS converts N1-(5'-phosphoribulosyl)...; Region: HisF; cd04731 123214002608 Histidine biosynthesis protein; Region: His_biosynth; pfam00977 123214002609 substrate binding site [chemical binding]; other site 123214002610 glutamase interaction surface [polypeptide binding]; other site 123214002611 Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from...; Region: TOPRIM; cd00188 123214002612 active site 123214002613 metal binding site [ion binding]; metal-binding site 123214002614 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 123214002615 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 123214002616 active site 123214002617 phosphorylation site [posttranslational modification] 123214002618 intermolecular recognition site; other site 123214002619 dimerization interface [polypeptide binding]; other site 123214002620 NMT1-like family; Region: NMT1_2; cl15260 123214002621 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 123214002622 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; cl09940 123214002623 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 123214002624 active site 123214002625 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 123214002626 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 123214002627 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 123214002628 putative menaquinone biosynthesis protein, SCO4494 family; Region: mena_SCO4494; TIGR03700 123214002629 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 123214002630 FeS/SAM binding site; other site 123214002631 Cation efflux family; Region: Cation_efflux; cl00316 123214002632 pseudouridine synthase, RluA family; Region: rluA_subfam; TIGR00005 123214002633 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 123214002634 RNA binding surface [nucleotide binding]; other site 123214002635 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 123214002636 active site 123214002637 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 123214002638 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 123214002639 Walker A/P-loop; other site 123214002640 ATP binding site [chemical binding]; other site 123214002641 Q-loop/lid; other site 123214002642 RecN ATPase involved in DNA repair; ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and...; Region: ABC_RecN; cd03241 123214002643 ABC transporter signature motif; other site 123214002644 Walker B; other site 123214002645 D-loop; other site 123214002646 H-loop/switch region; other site 123214002647 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 123214002648 dihydrolipoamide acetyltransferase; Reviewed; Region: PRK11855 123214002649 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 123214002650 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 123214002651 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 123214002652 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 123214002653 Predicted membrane protein (DUF2231); Region: DUF2231; cl01730 123214002654 CCC1-related family of proteins; Region: CCC1_like; cl00278 123214002655 carbamoyl phosphate synthase-like protein; Provisional; Region: PRK12767 123214002656 ATP-grasp domain; Region: ATP-grasp_4; cl03087 123214002657 diaminopimelate decarboxylase; Region: lysA; TIGR01048 123214002658 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme MccE; Region: PLPDE_III_MccE_like; cd06841 123214002659 dimer interface [polypeptide binding]; other site 123214002660 active site 123214002661 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 123214002662 catalytic residues [active] 123214002663 substrate binding site [chemical binding]; other site 123214002664 Urea transporter; Region: UT; cl01829 123214002665 Peptidase family M23; Region: Peptidase_M23; pfam01551 123214002666 Tetratricopeptide repeat; Region: TPR_16; pfam13432 123214002667 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 123214002668 binding surface 123214002669 TPR motif; other site 123214002670 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: COG4235 123214002671 GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is...; Region: GGCT_like; cd06661 123214002672 putative active site pocket [active] 123214002673 dimerization interface [polypeptide binding]; other site 123214002674 putative catalytic residue [active] 123214002675 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 123214002676 Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol...; Region: MopB_Nitrate-R-NapA-like; cd02754 123214002677 [4Fe-4S] binding site [ion binding]; other site 123214002678 molybdopterin cofactor binding site; other site 123214002679 Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol...; Region: MopB_CT_Nitrate-R-NapA-like; cd02791 123214002680 molybdopterin cofactor binding site; other site 123214002681 Nitrate/nitrite transporter [Inorganic ion transport and metabolism]; Region: NarK; COG2223 123214002682 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 123214002683 putative substrate translocation pore; other site 123214002684 ferredoxin-nitrite reductase; Reviewed; Region: nirA; PRK09566 123214002685 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 123214002686 Nitrite/Sulfite reductase ferredoxin-like half domain; Region: NIR_SIR_ferr; pfam03460 123214002687 serine/threonine-protein kinase; Reviewed; Region: pknD; PRK13184 123214002688 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 123214002689 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 123214002690 catalytic triad [active] 123214002691 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214002692 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 123214002693 substrate binding site [chemical binding]; other site 123214002694 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 123214002695 substrate binding site [chemical binding]; other site 123214002696 Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II); Region: Aldolase_II; cl00214 123214002697 intersubunit interface [polypeptide binding]; other site 123214002698 active site 123214002699 Zn2+ binding site [ion binding]; other site 123214002700 Peroxiredoxin (PRX) family, Atypical 2-cys PRX subfamily; composed of PRXs containing peroxidatic and resolving cysteines, similar to the homodimeric thiol specific antioxidant (TSA) protein also known as TRX-dependent thiol peroxidase (Tpx). Tpx is a...; Region: PRX_Atyp2cys; cd03014 123214002701 dimer interface [polypeptide binding]; other site 123214002702 catalytic triad [active] 123214002703 peroxidatic and resolving cysteines [active] 123214002704 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 123214002705 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214002706 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK06916 123214002707 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 123214002708 inhibitor-cofactor binding pocket; inhibition site 123214002709 pyridoxal 5'-phosphate binding site [chemical binding]; other site 123214002710 catalytic residue [active] 123214002711 Uncharacterized conserved protein (DUF2267); Region: DUF2267; cl02314 123214002712 PHP domain; Region: PHP; pfam02811 123214002713 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 123214002714 Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein; Region: Hint; cd00081 123214002715 protein-splicing catalytic site; other site 123214002716 thioester formation/cholesterol transfer; other site 123214002717 Intein/homing endonuclease [DNA replication, recombination, and repair]; Region: COG1372 123214002718 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 123214002719 Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein; Region: Hint; cl15780 123214002720 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 123214002721 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 123214002722 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 123214002723 generic binding surface II; other site 123214002724 generic binding surface I; other site 123214002725 GTP cyclohydrolase I (GTP-CH-I) catalyzes the conversion of GTP into dihydroneopterin triphosphate. The enzyme product is the precursor of tetrahydrofolate in eubacteria, fungi, and plants and of the folate analogs in methanogenic bacteria. In...; Region: GTP_cyclohydro1; cd00642 123214002726 homodecamer interface [polypeptide binding]; other site 123214002727 GTP cyclohydrolase I; Provisional; Region: PLN03044 123214002728 active site 123214002729 putative catalytic site residues [active] 123214002730 zinc binding site [ion binding]; other site 123214002731 GTP-CH-I/GFRP interaction surface; other site 123214002732 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214002733 lipoyl synthase; Provisional; Region: PRK05481 123214002734 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 123214002735 FeS/SAM binding site; other site 123214002736 DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif; Region: DEADc; cd00268 123214002737 DEAD-like helicases superfamily; Region: DEXDc; smart00487 123214002738 ATP binding site [chemical binding]; other site 123214002739 Mg++ binding site [ion binding]; other site 123214002740 motif III; other site 123214002741 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 123214002742 nucleotide binding region [chemical binding]; other site 123214002743 ATP-binding site [chemical binding]; other site 123214002744 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 123214002745 DnaA N-terminal domain; Region: DnaA_N; pfam11638 123214002746 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 123214002747 Walker A motif; other site 123214002748 ATP binding site [chemical binding]; other site 123214002749 Walker B motif; other site 123214002750 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 123214002751 arginine finger; other site 123214002752 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 123214002753 DnaA box-binding interface [nucleotide binding]; other site 123214002754 Predicted metal-binding protein (DUF2103); Region: DUF2103; cl01651 123214002755 Transaldolase-like fructose-6-phosphate aldolases (FSA) found in bacteria and archaea; Region: Transaldolase_FSA; cd00956 123214002756 active site 123214002757 intersubunit interactions; other site 123214002758 catalytic residue [active] 123214002759 Peptidase family M23; Region: Peptidase_M23; pfam01551 123214002760 2-isopropylmalate synthase; Validated; Region: PRK00915 123214002761 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 123214002762 active site 123214002763 catalytic residues [active] 123214002764 metal binding site [ion binding]; metal-binding site 123214002765 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; cl07212 123214002766 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; cl00417 123214002767 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl15792 123214002768 Helix-turn-helix domains; Region: HTH; cl00088 123214002769 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 123214002770 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cl14632 123214002771 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 123214002772 active site 123214002773 metal binding site [ion binding]; metal-binding site 123214002774 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 123214002775 nickel responsive regulator; Provisional; Region: PRK00630 123214002776 NikR C terminal nickel binding domain; Region: NikR_C; pfam08753 123214002777 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 123214002778 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC...; Region: ABC_cobalt_CbiO_domain1; cd03225 123214002779 Walker A/P-loop; other site 123214002780 ATP binding site [chemical binding]; other site 123214002781 Q-loop/lid; other site 123214002782 ABC transporter signature motif; other site 123214002783 Walker B; other site 123214002784 D-loop; other site 123214002785 H-loop/switch region; other site 123214002786 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 123214002787 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 123214002788 Cysteine-rich domain; Region: CCG; pfam02754 123214002789 Cysteine-rich domain; Region: CCG; pfam02754 123214002790 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 123214002791 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 123214002792 Walker A motif; other site 123214002793 ATP binding site [chemical binding]; other site 123214002794 Walker B motif; other site 123214002795 arginine finger; other site 123214002796 Helix-turn-helix domains; Region: HTH; cl00088 123214002797 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4399 123214002798 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4399 123214002799 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 123214002800 GTP-binding protein TypA/BipA; Region: TypA_BipA; TIGR01394 123214002801 G1 box; other site 123214002802 putative GEF interaction site [polypeptide binding]; other site 123214002803 GTP/Mg2+ binding site [chemical binding]; other site 123214002804 Switch I region; other site 123214002805 G2 box; other site 123214002806 G3 box; other site 123214002807 Switch II region; other site 123214002808 G4 box; other site 123214002809 G5 box; other site 123214002810 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 123214002811 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 123214002812 excinuclease ABC subunit C; Provisional; Region: uvrC; PRK14667 123214002813 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 123214002814 GIY-YIG motif/motif A; other site 123214002815 active site 123214002816 catalytic site [active] 123214002817 putative DNA binding site [nucleotide binding]; other site 123214002818 metal binding site [ion binding]; metal-binding site 123214002819 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 123214002820 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 123214002821 PAS domain; Region: PAS_9; pfam13426 123214002822 putative active site [active] 123214002823 heme pocket [chemical binding]; other site 123214002824 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 123214002825 putative CheW interface [polypeptide binding]; other site 123214002826 HAD-superfamily subfamily IIA hydrolase, TIGR01458; Region: HAD-SF-IIA-hyp3 123214002827 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 123214002828 active site 123214002829 motif I; other site 123214002830 motif II; other site 123214002831 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 123214002832 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 123214002833 acetolactate synthase; Reviewed; Region: PRK08617 123214002834 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214002835 metal binding site [ion binding]; metal-binding site 123214002836 active site 123214002837 I-site; other site 123214002838 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 123214002839 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 123214002840 Peptidase family U32; Region: Peptidase_U32; cl03113 123214002841 Indole-3-glycerol phosphate synthase (IGPS); an enzyme in the tryptophan biosynthetic pathway, catalyzing the ring closure reaction of 1-(o-carboxyphenylamino)-1-deoxyribulose-5-phosphate (CdRP) to indole-3-glycerol phosphate (IGP), accompanied by the...; Region: IGPS; cd00331 123214002842 active site 123214002843 ribulose/triose binding site [chemical binding]; other site 123214002844 phosphate binding site [ion binding]; other site 123214002845 substrate (anthranilate) binding pocket [chemical binding]; other site 123214002846 product (indole) binding pocket [chemical binding]; other site 123214002847 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 123214002848 bis(5'-nucleosyl)-tetraphosphatase (symmetrical); Region: apaH; TIGR00668 123214002849 active site 123214002850 metal binding site [ion binding]; metal-binding site 123214002851 Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which...; Region: ZnMc; cl00064 123214002852 polycystin cation channel protein; Region: PCC; TIGR00864 123214002853 Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus; Region: E_set; cl09101 123214002854 Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus; Region: E_set; cl09101 123214002855 GTPase RsgA; Reviewed; Region: PRK00098 123214002856 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 123214002857 GTPase/Zn-binding domain interface [polypeptide binding]; other site 123214002858 GTP/Mg2+ binding site [chemical binding]; other site 123214002859 G4 box; other site 123214002860 G5 box; other site 123214002861 G1 box; other site 123214002862 Switch I region; other site 123214002863 G2 box; other site 123214002864 G3 box; other site 123214002865 Switch II region; other site 123214002866 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between...; Region: TroA-like; cl00262 123214002867 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 123214002868 intersubunit interface [polypeptide binding]; other site 123214002869 nicotinate phosphoribosyltransferase; Validated; Region: PRK09243 123214002870 Nicotinate phosphoribosyltransferase (NAPRTase), subgroup A. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting, reaction...; Region: NAPRTase_A; cd01570 123214002871 active site 123214002872 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 123214002873 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 123214002874 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 123214002875 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 123214002876 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 123214002877 Putative catalytic NodB homology domain of uncharacterized bacterial polysaccharide deacetylases which consist of a 5-stranded beta/alpha barrel; Region: CE4_DAC_u4_5s; cd10973 123214002878 putative active site [active] 123214002879 putative metal binding site [ion binding]; other site 123214002880 Predicted membrane protein [Function unknown]; Region: COG2860 123214002881 UPF0126 domain; Region: UPF0126; pfam03458 123214002882 UPF0126 domain; Region: UPF0126; pfam03458 123214002883 Sugar fermentation stimulation protein; Region: SfsA; cl00647 123214002884 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 123214002885 substrate binding site [chemical binding]; other site 123214002886 active site 123214002887 Cytochrome c; Region: Cytochrom_C; cl11414 123214002888 Cytochrome c; Region: Cytochrom_C; cl11414 123214002889 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 123214002890 dimer interface [polypeptide binding]; other site 123214002891 phosphorylation site [posttranslational modification] 123214002892 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 123214002893 ATP binding site [chemical binding]; other site 123214002894 Mg2+ binding site [ion binding]; other site 123214002895 G-X-G motif; other site 123214002896 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 123214002897 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 123214002898 active site 123214002899 phosphorylation site [posttranslational modification] 123214002900 intermolecular recognition site; other site 123214002901 dimerization interface [polypeptide binding]; other site 123214002902 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 123214002903 DNA binding site [nucleotide binding] 123214002904 Exopolyphosphatase-related proteins [General function prediction only]; Region: COG0618 123214002905 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cl15354 123214002906 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 123214002907 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 123214002908 active site 123214002909 NTP binding site [chemical binding]; other site 123214002910 metal binding triad [ion binding]; metal-binding site 123214002911 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 123214002912 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 123214002913 active site 123214002914 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 123214002915 This PGM-like (phosphoglucomutase-like) protein of unknown function belongs to the alpha-D-phosphohexomutase superfamily and is found in both archaea and bacteria. The alpha-D-phosphohexomutases include several related enzymes that catalyze a reversible...; Region: PGM_like2; cd05800 123214002916 active site 123214002917 substrate binding site [chemical binding]; other site 123214002918 metal binding site [ion binding]; metal-binding site 123214002919 methionyl-tRNA synthetase; Reviewed; Region: PRK12267 123214002920 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 123214002921 active site 123214002922 HIGH motif; other site 123214002923 KMSKS motif; other site 123214002924 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 123214002925 tRNA binding surface [nucleotide binding]; other site 123214002926 anticodon binding site; other site 123214002927 tRNA-binding-domain-containing Escherichia coli methionyl-tRNA synthetase (EcMetRS)-like proteins. This family includes EcMetRS and Aquifex aeolicus Trbp111 (AaTrbp111). This domain has general tRNA binding properties. MetRS aminoacylates methionine...; Region: tRNA_bind_EcMetRS_like; cd02800 123214002928 dimer interface [polypeptide binding]; other site 123214002929 putative tRNA-binding site [nucleotide binding]; other site 123214002930 NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]; Region: NuoE; COG1905 123214002931 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 123214002932 putative dimer interface [polypeptide binding]; other site 123214002933 [2Fe-2S] cluster binding site [ion binding]; other site 123214002934 NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]; Region: NuoF; COG1894 123214002935 Respiratory-chain NADH dehydrogenase 51 Kd subunit; Region: Complex1_51K; pfam01512 123214002936 SLBB domain; Region: SLBB; pfam10531 123214002937 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; cl11211 123214002938 catalase/hydroperoxidase HPI(I); Provisional; Region: PRK15061 123214002939 N-terminal catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_1; cd00649 123214002940 dimer interface [polypeptide binding]; other site 123214002941 active site 123214002942 heme binding site [chemical binding]; other site 123214002943 C-terminal non-catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_2; cd08200 123214002944 aspartate aminotransferase; Provisional; Region: PRK05764 123214002945 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 123214002946 pyridoxal 5'-phosphate binding site [chemical binding]; other site 123214002947 homodimer interface [polypeptide binding]; other site 123214002948 catalytic residue [active] 123214002949 glycine oxidase ThiO; Region: thiamin_ThiO; TIGR02352 123214002950 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214002951 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 123214002952 pteridine reductase; Provisional; Region: PRK09135 123214002953 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214002954 NAD(P) binding site [chemical binding]; other site 123214002955 active site 123214002956 AAA domain; Region: AAA_22; pfam13401 123214002957 Sporulation related domain; Region: SPOR; cl10051 123214002958 putative secretion ATPase, PEP-CTERM locus subfamily; Region: pepcterm_ATPase; TIGR03015 123214002959 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 123214002960 Bacterial SH3 domain; Region: SH3_3; cl02551 123214002961 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214002962 metal binding site [ion binding]; metal-binding site 123214002963 active site 123214002964 I-site; other site 123214002965 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 123214002966 Tetratricopeptide repeat; Region: TPR_15; pfam13429 123214002967 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 123214002968 Secretin and TonB N terminus short domain; Region: STN; cl06624 123214002969 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 123214002970 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 123214002971 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 123214002972 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 123214002973 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 123214002974 Walker A motif; other site 123214002975 ATP binding site [chemical binding]; other site 123214002976 Walker B motif; other site 123214002977 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 123214002978 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 123214002979 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 123214002980 Patatin-like phospholipase domain containing protein 6, protein 7, and fungal NTE1; Region: Pat_PNPLA6_PNPLA7_NTE1_like; cd07205 123214002981 active site 123214002982 nucleophile elbow; other site 123214002983 chaperone protein DnaJ; Region: DnaJ_bact; TIGR02349 123214002984 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 123214002985 HSP70 interaction site [polypeptide binding]; other site 123214002986 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 123214002987 Zn binding sites [ion binding]; other site 123214002988 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 123214002989 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 123214002990 dimer interface [polypeptide binding]; other site 123214002991 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 123214002992 LabA_like proteins; Region: LabA; cd10911 123214002993 putative metal binding site [ion binding]; other site 123214002994 Mre11 nuclease, N-terminal metallophosphatase domain; Region: MPP_Mre11_N; cd00840 123214002995 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 123214002996 active site 123214002997 metal binding site [ion binding]; metal-binding site 123214002998 DNA binding site [nucleotide binding] 123214002999 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]; Region: Tas; COG0667 123214003000 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 123214003001 active site 123214003002 catalytic tetrad [active] 123214003003 FOG: GAF domain [Signal transduction mechanisms]; Region: FhlA; COG2203 123214003004 GAF domain; Region: GAF; cl15785 123214003005 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 123214003006 Zn2+ binding site [ion binding]; other site 123214003007 Mg2+ binding site [ion binding]; other site 123214003008 FecR protein; Region: FecR; pfam04773 123214003009 CHASE2 domain; Region: CHASE2; cl01732 123214003010 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 123214003011 cyclase homology domain; Region: CHD; cd07302 123214003012 nucleotidyl binding site; other site 123214003013 metal binding site [ion binding]; metal-binding site 123214003014 dimer interface [polypeptide binding]; other site 123214003015 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 123214003016 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 123214003017 Protein of unknown function (DUF3365); Region: DUF3365; pfam11845 123214003018 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214003019 metal binding site [ion binding]; metal-binding site 123214003020 active site 123214003021 I-site; other site 123214003022 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 123214003023 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 123214003024 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 123214003025 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 123214003026 Walker A/P-loop; other site 123214003027 ATP binding site [chemical binding]; other site 123214003028 Q-loop/lid; other site 123214003029 ABC transporter signature motif; other site 123214003030 Walker B; other site 123214003031 D-loop; other site 123214003032 H-loop/switch region; other site 123214003033 ATP-dependent DNA helicase PcrA; Region: pcrA; TIGR01073 123214003034 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 123214003035 Family description; Region: UvrD_C_2; cl15862 123214003036 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 123214003037 Oligomerisation domain; Region: Oligomerisation; cl00519 123214003038 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 123214003039 ribonuclease, Rne/Rng family; Region: RNaseEG; TIGR00757 123214003040 S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and...; Region: S1_RNase_E; cd04453 123214003041 homodimer interface [polypeptide binding]; other site 123214003042 oligonucleotide binding site [chemical binding]; other site 123214003043 Polyferredoxin [Energy production and conversion]; Region: NapH; COG0348 123214003044 4Fe-4S binding domain; Region: Fer4_5; pfam12801 123214003045 4Fe-4S binding domain; Region: Fer4_5; pfam12801 123214003046 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 123214003047 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 123214003048 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 123214003049 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 123214003050 structural tetrad; other site 123214003051 amidophosphoribosyltransferase; Region: purF; TIGR01134 123214003052 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 123214003053 active site 123214003054 tetramer interface [polypeptide binding]; other site 123214003055 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 123214003056 active site 123214003057 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 123214003058 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 123214003059 Similar to Prolidase and Aminopeptidase P. The members of this subfamily presumably catalyse hydrolysis of Xaa-Pro dipeptides and/or release of any N-terminal amino acid, including proline, that is linked with proline; Region: APP-like; cd01092 123214003060 active site 123214003061 superfamily containing globins and truncated hemoglobins; Region: globin_like; cl00280 123214003062 heme-binding site [chemical binding]; other site 123214003063 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 123214003064 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 123214003065 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 123214003066 PilZ domain; Region: PilZ; cl01260 123214003067 This family is the oxydase domain of NRPS (non-ribosomal peptide synthetase) and other proteins that modify polypeptides by cyclizing a thioester to form a ring. These include epoB, part of the epothilone biosynthesis pathway; tubD, part of the tubulysin...; Region: mcbC-like_oxidoreductase; cd02142 123214003068 putative FMN binding site [chemical binding]; other site 123214003069 NADPH bind site [chemical binding]; other site 123214003070 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 123214003071 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 123214003072 S-adenosylmethionine binding site [chemical binding]; other site 123214003073 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 123214003074 active site 123214003075 catalytic site [active] 123214003076 substrate binding site [chemical binding]; other site 123214003077 HupF/HypC family; Region: HupF_HypC; cl00394 123214003078 PIN domain of ribonucleases (toxins), VapC, FitB, and PAE0151 of bacterial and archaeal toxin/antitoxin-like operons, and other similar homologs; Region: PIN_VapC-like; cd09861 123214003079 putative active site [active] 123214003080 Hydrogenase formation hypA family; Region: HypD; cl12072 123214003081 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypD; COG0409 123214003082 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 123214003083 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; cl02930 123214003084 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 123214003085 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 123214003086 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 123214003087 motif II; other site 123214003088 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 123214003089 Ca2+/Na+ antiporter [Inorganic ion transport and metabolism]; Region: ECM27; COG0530 123214003090 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 123214003091 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 123214003092 HypE (Hydrogenase expression/formation protein). HypE is involved in Ni-Fe hydrogenase biosynthesis. HypE dehydrates its own carbamoyl moiety in an ATP-dependent process to yield the enzyme thiocyanate. The N-terminal domain of HypE is related to the...; Region: HypE; cd02197 123214003093 dimerization interface [polypeptide binding]; other site 123214003094 hydrogenase expression/formation protein HypE; Region: hypE; TIGR02124 123214003095 ATP binding site [chemical binding]; other site 123214003096 coenzyme F420-reducing hydrogenase delta subunit (putative coenzyme F420 hydrogenase processing subunit); Region: frhD; TIGR00130 123214003097 Endopeptidases belonging to membrane-bound hydrogenases group. These hydrogenases transfer electrons from H2 to a cytochrome that is bound to a membrane-located complex coupling electron transfer to transmembrane proton translocation. Endopeptidase HybD...; Region: H2MP_MemB-H2up; cd06062 123214003098 putative substrate-binding site; other site 123214003099 nickel binding site [ion binding]; other site 123214003100 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]; Region: COG1579 123214003101 Putative zinc ribbon domain; Region: DUF164; pfam02591 123214003102 diaminopimelate epimerase; Provisional; Region: PRK13577 123214003103 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 123214003104 Diaminopimelate epimerase; Region: DAP_epimerase; cl14668 123214003105 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 123214003106 metal binding site 2 [ion binding]; metal-binding site 123214003107 putative DNA binding helix; other site 123214003108 metal binding site 1 [ion binding]; metal-binding site 123214003109 dimer interface [polypeptide binding]; other site 123214003110 structural Zn2+ binding site [ion binding]; other site 123214003111 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 123214003112 Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); Region: MPN_like; cd08070 123214003113 MPN+ (JAMM) motif; other site 123214003114 Zinc-binding site [ion binding]; other site 123214003115 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 123214003116 DNA-binding site [nucleotide binding]; DNA binding site 123214003117 RNA-binding motif; other site 123214003118 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 123214003119 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; cl09940 123214003120 Pseudouridine synthases are responsible for the synthesis of pseudouridine from uracil in ribosomal RNA. The RsuA subfamily includes Pseudouridine Synthase similar to Ribosomal small subunit pseudouridine 516 synthase. Most of the proteins in this...; Region: PseudoU_synth_RsuA_like; cd02870 123214003121 active site 123214003122 Putative MetA-pathway of phenol degradation; Region: Phenol_MetA_deg; cl01768 123214003123 A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the 'double-glycine' leader peptides from the precursors of various bacteriocins; Region: Peptidase_C39G; cd02423 123214003124 Peptidase_C39 like family; Region: Peptidase_C39_2; pfam13529 123214003125 putative active site [active] 123214003126 dipeptide transporter; Provisional; Region: PRK10913 123214003127 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 123214003128 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 123214003129 dimer interface [polypeptide binding]; other site 123214003130 conserved gate region; other site 123214003131 ABC-ATPase subunit interface; other site 123214003132 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 123214003133 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 123214003134 dimer interface [polypeptide binding]; other site 123214003135 conserved gate region; other site 123214003136 putative PBP binding loops; other site 123214003137 ABC-ATPase subunit interface; other site 123214003138 Citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CCL cleaves citryl-CoA (CiCoA) to acetyl-CoA (AcCoA) and oxaloacetate (OAA); Region: CCL_ACL-C; cd06100 123214003139 active site 123214003140 oxalacetate binding site [chemical binding]; other site 123214003141 citrylCoA binding site [chemical binding]; other site 123214003142 coenzyme A binding site [chemical binding]; other site 123214003143 catalytic triad [active] 123214003144 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 123214003145 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 123214003146 dimerization interface [polypeptide binding]; other site 123214003147 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 123214003148 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 123214003149 dimer interface [polypeptide binding]; other site 123214003150 phosphorylation site [posttranslational modification] 123214003151 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 123214003152 ATP binding site [chemical binding]; other site 123214003153 Mg2+ binding site [ion binding]; other site 123214003154 G-X-G motif; other site 123214003155 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 123214003156 Phospho-N-acetylmuramoyl-pentapeptide-transferase (mraY) is an enzyme responsible for the formation of the first lipid intermediate in the synthesis of bacterial cell wall peptidoglycan. It catalyzes the formation of...; Region: GT_MraY; cd06852 123214003157 Mg++ binding site [ion binding]; other site 123214003158 putative catalytic motif [active] 123214003159 putative substrate binding site [chemical binding]; other site 123214003160 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 123214003161 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 123214003162 substrate binding site [chemical binding]; other site 123214003163 dimer interface [polypeptide binding]; other site 123214003164 catalytic triad [active] 123214003165 Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP_PGM_like; cd07067 123214003166 catalytic core [active] 123214003167 Domain of unknown function (DUF3817); Region: DUF3817; cl14844 123214003168 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 123214003169 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214003170 ATP synthase, Delta/Epsilon chain, beta-sandwich domain; Region: ATP-synt_DE_N; cl10033 123214003171 isoprenoid biosynthesis protein with amidotransferase-like domain; Provisional; Region: PRK11780 123214003172 Type 1 glutamine amidotransferase (GATase1)-like domain found in zebrafish ES1; Region: GATase1_ES1; cd03133 123214003173 conserved cys residue [active] 123214003174 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 123214003175 trimer interface [polypeptide binding]; other site 123214003176 active site 123214003177 homoserine dehydrogenase; Provisional; Region: PRK06349 123214003178 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214003179 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 123214003180 ACT_HSDH_Hom CD includes the C-terminal ACT domain of the NAD(P)H-dependent, homoserine dehydrogenase (HSDH) and related domains; Region: ACT_HSDH-Hom; cd04881 123214003181 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 123214003182 Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is...; Region: SLC13_permease; cd01115 123214003183 transmembrane helices; other site 123214003184 Diadenosine hexaphosphate (Ap6A) hydrolase is a member of the Nudix hydrolase superfamily. Ap6A hydrolase specifically hydrolyzes diadenosine polyphosphates, but not ATP or diadenosine triphosphate, and it generates ATP as the product. Ap6A, the most...; Region: Ap6A_hydrolase; cd03673 123214003185 active site 123214003186 Ap6A binding site [chemical binding]; other site 123214003187 nudix motif; other site 123214003188 metal binding site [ion binding]; metal-binding site 123214003189 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 123214003190 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 123214003191 putative acyl-acceptor binding pocket; other site 123214003192 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 123214003193 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 123214003194 inhibitor-cofactor binding pocket; inhibition site 123214003195 pyridoxal 5'-phosphate binding site [chemical binding]; other site 123214003196 catalytic residue [active] 123214003197 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 123214003198 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 123214003199 ATP cone domain; Region: ATP-cone; pfam03477 123214003200 Domain of unknown function (DUF1931); Region: DUF1931; pfam09123 123214003201 cell division ATPase MinD, archaeal; Region: minD_arch; TIGR01969 123214003202 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 123214003203 Walker A motif; other site 123214003204 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 123214003205 cysteine desulfurase DndA; Region: DNA_S_dndA; TIGR03235 123214003206 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 123214003207 catalytic residue [active] 123214003208 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 123214003209 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 123214003210 trimerization site [polypeptide binding]; other site 123214003211 active site 123214003212 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 123214003213 ThiI is required for thiazole synthesis in the thiamine biosynthesis pathway. It belongs to the Adenosine Nucleotide Hydrolysis suoerfamily and predicted to bind to Adenosine nucleotide; Region: ThiI; cd01712 123214003214 Ligand Binding Site [chemical binding]; other site 123214003215 SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this...; Region: SirA_YedF_YeeD; cd00291 123214003216 CPxP motif; other site 123214003217 Domain of unknown function (DUF1858); Region: DUF1858; cl14817 123214003218 NifU-like domain; Region: NifU; cl00484 123214003219 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 123214003220 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 123214003221 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 123214003222 shikimate binding site; other site 123214003223 NAD(P) binding site [chemical binding]; other site 123214003224 Uncharacterized protein family UPF0047; Region: UPF0047; cl00439 123214003225 Endonuclease_V, a DNA repair enzyme that initiates repair of nitrosative deaminated purine bases; Region: Endonuclease_V; cd06559 123214003226 Active_site [active] 123214003227 gamma-glutamyl kinase; Provisional; Region: PRK05429 123214003228 AAK_G5K_ProB: Glutamate-5-kinase (G5K) catalyzes glutamate-dependent ATP cleavage; G5K transfers the terminal phosphoryl group of ATP to the gamma-carboxyl group of glutamate, in the first and controlling step of proline (and, in mammals, ornithine)...; Region: AAK_G5K_ProB; cd04242 123214003229 nucleotide binding site [chemical binding]; other site 123214003230 homotetrameric interface [polypeptide binding]; other site 123214003231 putative phosphate binding site [ion binding]; other site 123214003232 putative allosteric binding site; other site 123214003233 PUA domain; Region: PUA; cl00607 123214003234 tRNA(1-methyladenosine) methyltransferase and related methyltransferases [Translation, ribosomal structure and biogenesis]; Region: GCD14; COG2519 123214003235 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214003236 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 123214003237 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214003238 putative alpha-isopropylmalate/homocitrate synthase family transferase; Provisional; Region: PRK12344 123214003239 Desulfobacterium autotrophicum LeuA3 and related proteins, N-terminal catalytic TIM barrel domain; Region: DRE_TIM_LeuA3; cd07941 123214003240 active site 123214003241 catalytic residues [active] 123214003242 metal binding site [ion binding]; metal-binding site 123214003243 LeuA allosteric (dimerisation) domain; Region: LeuA_dimer; cl07212 123214003244 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 123214003245 thiamine-monophosphate kinase; Region: thiL; TIGR01379 123214003246 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 123214003247 ATP binding site [chemical binding]; other site 123214003248 dimerization interface [polypeptide binding]; other site 123214003249 elongation factor P; Validated; Region: PRK00529 123214003250 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 123214003251 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 123214003252 RNA binding site [nucleotide binding]; other site 123214003253 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 123214003254 RNA binding site [nucleotide binding]; other site 123214003255 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 123214003256 carboxyltransferase (CT) interaction site; other site 123214003257 biotinylation site [posttranslational modification]; other site 123214003258 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214003259 ADP-L-glycero-D-manno-heptose-6-epimerase; Region: heptose_epim; TIGR02197 123214003260 NAD(P) binding site [chemical binding]; other site 123214003261 active site 123214003262 homoserine kinase; Provisional; Region: PRK01212 123214003263 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 123214003264 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 123214003265 CarD-like/TRCF domain; Region: CarD_CdnL_TRCF; cl00588 123214003266 DEAD-like helicases superfamily; Region: DEXDc; smart00487 123214003267 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 123214003268 ATP binding site [chemical binding]; other site 123214003269 putative Mg++ binding site [ion binding]; other site 123214003270 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 123214003271 nucleotide binding region [chemical binding]; other site 123214003272 ATP-binding site [chemical binding]; other site 123214003273 TRCF domain; Region: TRCF; cl04088 123214003274 Phosphate-starvation-inducible E; Region: PsiE; cl01264 123214003275 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 123214003276 N-acetyl-D-glucosamine binding site [chemical binding]; other site 123214003277 catalytic residue [active] 123214003278 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 123214003279 putative peptidoglycan binding site; other site 123214003280 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 123214003281 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 123214003282 putative peptidoglycan binding site; other site 123214003283 FOG: LysM repeat [Cell envelope biogenesis, outer membrane]; Region: LytE; COG1388 123214003284 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 123214003285 putative peptidoglycan binding site; other site 123214003286 Fe-S oxidoreductases [Energy production and conversion]; Region: COG0731 123214003287 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 123214003288 FeS/SAM binding site; other site 123214003289 CRISPR/Cas system-associated RAMP superfamily protein Cas6; Region: Cas6-I-III; cd09652 123214003290 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 123214003291 Flavoprotein; Region: Flavoprotein; cl08021 123214003292 DNA / pantothenate metabolism flavoprotein; Region: DFP; cl04410 123214003293 Putative regulatory, ligand-binding protein related to C-terminal domains of K+ channels [Inorganic ion transport and metabolism]; Region: COG0490 123214003294 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl15357 123214003295 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 123214003296 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 123214003297 poxB regulator PoxA; Provisional; Region: PRK09350 123214003298 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 123214003299 motif 1; other site 123214003300 dimer interface [polypeptide binding]; other site 123214003301 active site 123214003302 motif 2; other site 123214003303 motif 3; other site 123214003304 Ion channel; Region: Ion_trans_2; cl11596 123214003305 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214003306 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 123214003307 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 123214003308 active site 123214003309 UDP-3-O-acyl-N-acetylglucosamine deacetylase [Cell envelope biogenesis, outer membrane]; Region: LpxC; cl00512 123214003310 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 123214003311 Protein of unknown function DUF86; Region: DUF86; cl01031 123214003312 Protein of unknown function DUF86; Region: DUF86; cl01031 123214003313 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 123214003314 nickel import ATP-binding protein NikD; Region: nickel_nikD; TIGR02770 123214003315 Walker A/P-loop; other site 123214003316 ATP binding site [chemical binding]; other site 123214003317 Q-loop/lid; other site 123214003318 ABC transporter signature motif; other site 123214003319 Walker B; other site 123214003320 D-loop; other site 123214003321 H-loop/switch region; other site 123214003322 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 123214003323 DsbA family, DsbC and DsbG subfamily; V-shaped homodimeric proteins containing a redox active CXXC motif imbedded in a TRX fold. They function as protein disulfide isomerases and chaperones in the bacterial periplasm to correct non-native disulfide bonds...; Region: DsbA_DsbC_DsbG; cd03020 123214003324 dimerization domain [polypeptide binding]; other site 123214003325 dimer interface [polypeptide binding]; other site 123214003326 catalytic residues [active] 123214003327 Ribose/Galactose Isomerase; Region: LacAB_rpiB; cl00485 123214003328 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 123214003329 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 123214003330 dimer interface [polypeptide binding]; other site 123214003331 active site 123214003332 glycine-pyridoxal phosphate binding site [chemical binding]; other site 123214003333 folate binding site [chemical binding]; other site 123214003334 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 123214003335 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 123214003336 homotrimer interaction site [polypeptide binding]; other site 123214003337 zinc binding site [ion binding]; other site 123214003338 CDP-binding sites; other site 123214003339 Domain of unknown function (DUF1858); Region: DUF1858; cl14817 123214003340 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 123214003341 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 123214003342 ssDNA binding site; other site 123214003343 generic binding surface II; other site 123214003344 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 123214003345 ATP binding site [chemical binding]; other site 123214003346 putative Mg++ binding site [ion binding]; other site 123214003347 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 123214003348 nucleotide binding region [chemical binding]; other site 123214003349 ATP-binding site [chemical binding]; other site 123214003350 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428; cl00437 123214003351 PAS fold; Region: PAS_4; pfam08448 123214003352 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 123214003353 putative active site [active] 123214003354 heme pocket [chemical binding]; other site 123214003355 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214003356 metal binding site [ion binding]; metal-binding site 123214003357 active site 123214003358 I-site; other site 123214003359 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 123214003360 putative monovalent cation/H+ antiporter subunit A; Reviewed; Region: PRK12649 123214003361 PAS domain S-box; Region: sensory_box; TIGR00229 123214003362 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 123214003363 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 123214003364 putative active site [active] 123214003365 heme pocket [chemical binding]; other site 123214003366 PAS domain S-box; Region: sensory_box; TIGR00229 123214003367 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 123214003368 putative active site [active] 123214003369 heme pocket [chemical binding]; other site 123214003370 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 123214003371 PAS domain; Region: PAS_9; pfam13426 123214003372 putative active site [active] 123214003373 heme pocket [chemical binding]; other site 123214003374 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214003375 metal binding site [ion binding]; metal-binding site 123214003376 active site 123214003377 I-site; other site 123214003378 Domain of unknown function (DUF3488); Region: DUF3488; pfam11992 123214003379 Transglutaminase-like superfamily; Region: Transglut_core; cl10469 123214003380 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 123214003381 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 123214003382 MoxR-like ATPases [General function prediction only]; Region: COG0714 123214003383 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 123214003384 Walker A motif; other site 123214003385 ATP binding site [chemical binding]; other site 123214003386 Walker B motif; other site 123214003387 arginine finger; other site 123214003388 Pantoate-beta-alanine ligase; Region: PanC; cd00560 123214003389 pantoate--beta-alanine ligase; Region: panC; TIGR00018 123214003390 active site 123214003391 ATP-binding site [chemical binding]; other site 123214003392 pantoate-binding site; other site 123214003393 HXXH motif; other site 123214003394 PAS domain S-box; Region: sensory_box; TIGR00229 123214003395 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 123214003396 PAS domain; Region: PAS_9; pfam13426 123214003397 putative active site [active] 123214003398 heme pocket [chemical binding]; other site 123214003399 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214003400 metal binding site [ion binding]; metal-binding site 123214003401 active site 123214003402 I-site; other site 123214003403 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 123214003404 histidinol-phosphate aminotransferase; Validated; Region: PRK02731 123214003405 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 123214003406 pyridoxal 5'-phosphate binding site [chemical binding]; other site 123214003407 homodimer interface [polypeptide binding]; other site 123214003408 catalytic residue [active] 123214003409 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 123214003410 MoeA family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF), an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoeA; cd00887 123214003411 dimer interface [polypeptide binding]; other site 123214003412 putative functional site; other site 123214003413 putative MPT binding site; other site 123214003414 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 123214003415 Carbamoylphosphate synthase large subunit (split gene in MJ) [Amino acid transport and metabolism / Nucleotide transport and metabolism]; Region: CarB; COG0458 123214003416 ATP-grasp domain; Region: ATP-grasp_4; cl03087 123214003417 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 123214003418 IMP binding site; other site 123214003419 dimer interface [polypeptide binding]; other site 123214003420 interdomain contacts; other site 123214003421 partial ornithine binding site; other site 123214003422 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 123214003423 thiamine phosphate binding site [chemical binding]; other site 123214003424 active site 123214003425 pyrophosphate binding site [ion binding]; other site 123214003426 Trm112p-like protein; Region: Trm112p; cl01066 123214003427 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 123214003428 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_4; cd08500 123214003429 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 123214003430 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214003431 metal binding site [ion binding]; metal-binding site 123214003432 active site 123214003433 I-site; other site 123214003434 uncharacterized peroxidase-related enzyme; Region: peroxid_rel; TIGR01926 123214003435 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 123214003436 malate dehydrogenase; Reviewed; Region: PRK06223 123214003437 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 123214003438 NAD(P) binding site [chemical binding]; other site 123214003439 dimer interface [polypeptide binding]; other site 123214003440 tetramer (dimer of dimers) interface [polypeptide binding]; other site 123214003441 substrate binding site [chemical binding]; other site 123214003442 Fumarate hydratase (Fumerase); Region: Fumerase; cl00851 123214003443 Fumarase C-terminus; Region: Fumerase_C; cl00795 123214003444 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 123214003445 ATP-grasp domain; Region: ATP-grasp_4; cl03087 123214003446 CoA-ligase; Region: Ligase_CoA; cl02894 123214003447 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 123214003448 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214003449 CoA-ligase; Region: Ligase_CoA; cl02894 123214003450 2-oxoacid:acceptor oxidoreductase, alpha subunit; Region: OAFO_sf; TIGR03710 123214003451 Pyruvate ferredoxin/flavodoxin oxidoreductase; Region: POR; cl00546 123214003452 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 123214003453 dimer interface [polypeptide binding]; other site 123214003454 PYR/PP interface [polypeptide binding]; other site 123214003455 TPP binding site [chemical binding]; other site 123214003456 substrate binding site [chemical binding]; other site 123214003457 2-oxoglutarate ferredoxin oxidoreductase subunit beta; Reviewed; Region: PRK11867 123214003458 Thiamine pyrophosphate (TPP family), 2-oxoglutarate ferredoxin oxidoreductase (OGFOR) subfamily, TPP-binding module; OGFOR catalyzes the oxidative decarboxylation of 2-oxo-acids, with ferredoxin acting as an electron acceptor. In the TCA cycle, OGFOR...; Region: TPP_OGFOR; cd03375 123214003459 TPP-binding site [chemical binding]; other site 123214003460 Pyruvate ferredoxin oxidoreductase beta subunit C terminal; Region: PFO_beta_C; pfam12367 123214003461 Domain of unknown function (DUF4323); Region: DUF4323; pfam14211 123214003462 Domain of unknown function (DUF4324); Region: DUF4324; pfam14212 123214003463 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 123214003464 MatE; Region: MatE; cl10513 123214003465 MatE; Region: MatE; cl10513 123214003466 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor...; Region: Ribosomal_L24e_L24; cl00909 123214003467 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 123214003468 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 123214003469 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 123214003470 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cd00158 123214003471 active site residue [active] 123214003472 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 123214003473 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 123214003474 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 123214003475 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 123214003476 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 123214003477 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 123214003478 Type II secretory pathway, component PulJ [Intracellular trafficking and secretion]; Region: PulJ; COG4795 123214003479 Neisseria PilC beta-propeller domain; Region: Neisseria_PilC; pfam05567 123214003480 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 123214003481 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 123214003482 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 123214003483 active site 123214003484 phosphorylation site [posttranslational modification] 123214003485 intermolecular recognition site; other site 123214003486 dimerization interface [polypeptide binding]; other site 123214003487 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 123214003488 DNA binding site [nucleotide binding] 123214003489 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 123214003490 substrate binding site; other site 123214003491 dimer interface; other site 123214003492 Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP_PGM_like; cd07067 123214003493 catalytic core [active] 123214003494 bifunctional argininosuccinate lyase/N-acetylglutamate synthase; Provisional; Region: PRK12308 123214003495 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 123214003496 Coenzyme A binding pocket [chemical binding]; other site 123214003497 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 123214003498 Found in ATP-dependent protease La (LON); Region: LON; smart00464 123214003499 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 123214003500 Walker A motif; other site 123214003501 ATP binding site [chemical binding]; other site 123214003502 Walker B motif; other site 123214003503 arginine finger; other site 123214003504 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 123214003505 Alpha-crystallin domain (ACD) of alpha-crystallin-type small(s) heat shock proteins (Hsps). sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is the Alpha-crystallin domain (ACD). sHsps are generally...; Region: ACD_sHsps-like; cd06464 123214003506 putative dimer interface [polypeptide binding]; other site 123214003507 tRNA (Guanine-1)-methyltransferase; Region: tRNA_m1G_MT; cl00407 123214003508 Outer membrane protein (OmpH-like); Region: OmpH; pfam03938 123214003509 Uncharacterized conserved protein [Function unknown]; Region: COG1912 123214003510 S-adenosyl-l-methionine hydroxide adenosyltransferase; Region: SAM_adeno_trans; pfam01887 123214003511 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]; Region: FAA1; COG1022 123214003512 AMP-binding enzyme; Region: AMP-binding; cl15778 123214003513 Phosphopantetheine attachment site; Region: PP-binding; cl09936 123214003514 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 123214003515 putative acyl-acceptor binding pocket; other site 123214003516 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 123214003517 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 123214003518 catalytic triad [active] 123214003519 Uncharacterized protein family (UPF0227); Region: UPF0227; cl14886 123214003520 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 123214003521 elongation factor Tu; Reviewed; Region: PRK00049 123214003522 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 123214003523 G1 box; other site 123214003524 GEF interaction site [polypeptide binding]; other site 123214003525 GTP/Mg2+ binding site [chemical binding]; other site 123214003526 Switch I region; other site 123214003527 G2 box; other site 123214003528 G3 box; other site 123214003529 Switch II region; other site 123214003530 G4 box; other site 123214003531 G5 box; other site 123214003532 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 123214003533 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 123214003534 Antibiotic Binding Site [chemical binding]; other site 123214003535 Ribosomal protein L33; Region: Ribosomal_L33; cl00383 123214003536 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 123214003537 N-Utilization Substance G (NusG) N-terminal (NGN) domain Superfamily; Region: NGN; cl02766 123214003538 NGN-insert domain found between N-terminal domain (D1) and C-terminal KOW domain (DIII) repeats of some N-Utilization Substance G (NusG) N-terminal (NGN); Region: NGN-insert_like; cd09910 123214003539 transcriptional activator RfaH; Region: RfaH; TIGR01955 123214003540 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 123214003541 putative homodimer interface [polypeptide binding]; other site 123214003542 KOW motif; Region: KOW; cl00354 123214003543 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 123214003544 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 123214003545 23S rRNA interface [nucleotide binding]; other site 123214003546 L7/L12 interface [polypeptide binding]; other site 123214003547 putative thiostrepton binding site; other site 123214003548 L25 interface [polypeptide binding]; other site 123214003549 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 123214003550 mRNA/rRNA interface [nucleotide binding]; other site 123214003551 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 123214003552 23S rRNA interface [nucleotide binding]; other site 123214003553 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 123214003554 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 123214003555 core dimer interface [polypeptide binding]; other site 123214003556 peripheral dimer interface [polypeptide binding]; other site 123214003557 L10 interface [polypeptide binding]; other site 123214003558 L11 interface [polypeptide binding]; other site 123214003559 putative EF-Tu interaction site [polypeptide binding]; other site 123214003560 putative EF-G interaction site [polypeptide binding]; other site 123214003561 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 123214003562 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 123214003563 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 123214003564 RPB11 interaction site [polypeptide binding]; other site 123214003565 RPB12 interaction site [polypeptide binding]; other site 123214003566 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 123214003567 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 123214003568 RPB1 interaction site [polypeptide binding]; other site 123214003569 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 123214003570 RNA polymerase Rpb1, domain 2; Region: RNA_pol_Rpb1_2; cl11591 123214003571 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 123214003572 DNA-directed RNA polymerase subunit beta'; Provisional; Region: rpoC2; PRK02597 123214003573 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 123214003574 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 123214003575 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 123214003576 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed; Region: PRK09603 123214003577 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 123214003578 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 123214003579 DNA binding site [nucleotide binding] 123214003580 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 123214003581 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 123214003582 S17 interaction site [polypeptide binding]; other site 123214003583 S8 interaction site; other site 123214003584 16S rRNA interaction site [nucleotide binding]; other site 123214003585 streptomycin interaction site [chemical binding]; other site 123214003586 23S rRNA interaction site [nucleotide binding]; other site 123214003587 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 123214003588 Ribosomal protein S7p/S5e; Region: Ribosomal_S7; cl00313 123214003589 elongation factor G; Reviewed; Region: PRK00007 123214003590 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 123214003591 G1 box; other site 123214003592 putative GEF interaction site [polypeptide binding]; other site 123214003593 GTP/Mg2+ binding site [chemical binding]; other site 123214003594 Switch I region; other site 123214003595 G2 box; other site 123214003596 G3 box; other site 123214003597 Switch II region; other site 123214003598 G4 box; other site 123214003599 G5 box; other site 123214003600 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 123214003601 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 123214003602 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 123214003603 elongation factor Tu; Reviewed; Region: PRK00049 123214003604 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 123214003605 G1 box; other site 123214003606 GEF interaction site [polypeptide binding]; other site 123214003607 GTP/Mg2+ binding site [chemical binding]; other site 123214003608 Switch I region; other site 123214003609 G2 box; other site 123214003610 G3 box; other site 123214003611 Switch II region; other site 123214003612 G4 box; other site 123214003613 G5 box; other site 123214003614 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 123214003615 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 123214003616 Antibiotic Binding Site [chemical binding]; other site 123214003617 Ribosomal protein S10p/S20e; Region: Ribosomal_S10; cl00314 123214003618 Ribosomal protein L3; Region: Ribosomal_L3; cl00324 123214003619 Ribosomal protein L4/L1 family; Region: Ribosomal_L4; cl00325 123214003620 Ribosomal protein L23; Region: Ribosomal_L23; cl00326 123214003621 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 123214003622 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 123214003623 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 123214003624 Ribosomal protein S19; Region: Ribosomal_S19; cl00350 123214003625 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 123214003626 putative translocon binding site; other site 123214003627 protein-rRNA interface [nucleotide binding]; other site 123214003628 ribosomal protein S3, bacterial type; Region: rpsC_bact; TIGR01009 123214003629 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 123214003630 G-X-X-G motif; other site 123214003631 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 123214003632 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 123214003633 23S rRNA interface [nucleotide binding]; other site 123214003634 5S rRNA interface [nucleotide binding]; other site 123214003635 putative antibiotic binding site [chemical binding]; other site 123214003636 L25 interface [polypeptide binding]; other site 123214003637 L27 interface [polypeptide binding]; other site 123214003638 Ribosomal L29 protein/HIP. L29 is a protein of the large ribosomal Subunit. A homolog, called heparin/heparan sulfate interacting protein (HIP), has also been identified in mammals. L29 is located on the surface of the large ribosomal subunit, where it...; Region: Ribosomal_L29_HIP; cd00427 123214003639 L23 interface [polypeptide binding]; other site 123214003640 signal recognition particle (SRP54) interaction site; other site 123214003641 trigger factor interaction site; other site 123214003642 23S rRNA interface [nucleotide binding]; other site 123214003643 Ribosomal protein S17; Region: Ribosomal_S17; cl00351 123214003644 Ribosomal protein L14p/L23e; Region: Ribosomal_L14; cl00328 123214003645 KOW motif; Region: KOW; cl00354 123214003646 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 123214003647 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 123214003648 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 123214003649 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 123214003650 Ribosomal protein S14p/S29e; Region: Ribosomal_S14; cl00355 123214003651 Ribosomal protein S8; Region: Ribosomal_S8; cl00330 123214003652 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 123214003653 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 123214003654 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 123214003655 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 123214003656 23S rRNA interface [nucleotide binding]; other site 123214003657 5S rRNA interface [nucleotide binding]; other site 123214003658 L27 interface [polypeptide binding]; other site 123214003659 L5 interface [polypeptide binding]; other site 123214003660 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 123214003661 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 123214003662 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 123214003663 Ribosomal protein L30, which is found in eukaryotes and prokaryotes but not in archaea, is one of the smallest ribosomal proteins with a molecular mass of about 7kDa. L30 binds the 23SrRNA as well as the 5S rRNA and is one of five ribosomal proteins that...; Region: Ribosomal_L30; cd01658 123214003664 23S rRNA binding site [nucleotide binding]; other site 123214003665 Ribosomal protein L18e/L15; Region: Ribosomal_L18e; cl12022 123214003666 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 123214003667 SecY translocase; Region: SecY; pfam00344 123214003668 adenylate kinase; Reviewed; Region: adk; PRK00279 123214003669 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 123214003670 AMP-binding site [chemical binding]; other site 123214003671 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 123214003672 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 123214003673 active site 123214003674 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 123214003675 rRNA binding site [nucleotide binding]; other site 123214003676 predicted 30S ribosome binding site; other site 123214003677 Ribosomal protein L36; Region: Ribosomal_L36; cl00380 123214003678 Ribosomal protein S13/S18; Region: Ribosomal_S13; cl00331 123214003679 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 123214003680 Ribosomal protein S11; Region: Ribosomal_S11; cl00332 123214003681 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 123214003682 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 123214003683 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 123214003684 RNA binding surface [nucleotide binding]; other site 123214003685 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 123214003686 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 123214003687 alphaNTD homodimer interface [polypeptide binding]; other site 123214003688 alphaNTD - beta interaction site [polypeptide binding]; other site 123214003689 alphaNTD - beta' interaction site [polypeptide binding]; other site 123214003690 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; cl11613 123214003691 Ribosomal protein L17; Region: Ribosomal_L17; cl00356 123214003692 YGGT family; Region: YGGT; cl00508 123214003693 BCAT_beta_family: Branched-chain aminotransferase catalyses the transamination of the branched-chain amino acids leusine, isoleucine and valine to their respective alpha-keto acids, alpha-ketoisocaproate, alpha-keto-beta-methylvalerate and...; Region: BCAT_beta_family; cd01557 123214003694 homodimer interface [polypeptide binding]; other site 123214003695 substrate-cofactor binding pocket; other site 123214003696 catalytic residue [active] 123214003697 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 123214003698 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 123214003699 substrate-cofactor binding pocket; other site 123214003700 pyridoxal 5'-phosphate binding site [chemical binding]; other site 123214003701 catalytic residue [active] 123214003702 2-hydroxyacid dehydrogenase; Provisional; Region: PRK08410 123214003703 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214003704 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cd00143 123214003705 active site 123214003706 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 123214003707 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214003708 metal binding site [ion binding]; metal-binding site 123214003709 active site 123214003710 I-site; other site 123214003711 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 123214003712 NMT1-like family; Region: NMT1_2; cl15260 123214003713 NMT1/THI5 like; Region: NMT1; pfam09084 123214003714 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cl00528 123214003715 Helix-turn-helix domains; Region: HTH; cl00088 123214003716 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional; Region: PRK11886 123214003717 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 123214003718 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 123214003719 Anthranilate phosphoribosyltransferase [Amino acid transport and metabolism]; Region: TrpD; COG0547 123214003720 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 123214003721 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 123214003722 GTP-binding protein LepA; Provisional; Region: PRK05433 123214003723 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 123214003724 G1 box; other site 123214003725 putative GEF interaction site [polypeptide binding]; other site 123214003726 GTP/Mg2+ binding site [chemical binding]; other site 123214003727 Switch I region; other site 123214003728 G2 box; other site 123214003729 G3 box; other site 123214003730 Switch II region; other site 123214003731 G4 box; other site 123214003732 G5 box; other site 123214003733 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 123214003734 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 123214003735 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 123214003736 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 123214003737 catalytic residues [active] 123214003738 Cupin domain; Region: Cupin_2; cl09118 123214003739 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 123214003740 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]; Region: COG3118 123214003741 ybbN protein family; ybbN is a hypothetical protein containing a redox-inactive TRX-like domain. Its gene has been sequenced from several gammaproteobacteria and actinobacteria; Region: ybbN; cd02956 123214003742 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 123214003743 binding surface 123214003744 TPR motif; other site 123214003745 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 123214003746 This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This subfamily; Region: Alpha_ANH_like_II; cd01993 123214003747 Ligand Binding Site [chemical binding]; other site 123214003748 TIGR00269 family protein; Region: TIGR00269 123214003749 Ubiquitin-like proteins; Region: UBQ; cl00155 123214003750 N-formylglutamate amidohydrolase; Region: FGase; cl01522 123214003751 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; cl08040 123214003752 Gamma-glutamyltranspeptidase; Region: G_glu_transpept; pfam01019 123214003753 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 123214003754 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 123214003755 ATP-grasp domain; Region: ATP-grasp_4; cl03087 123214003756 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cl00447 123214003757 nudix motif; other site 123214003758 Cytochrome c; Region: Cytochrom_C; cl11414 123214003759 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 123214003760 ligand binding site [chemical binding]; other site 123214003761 flexible hinge region; other site 123214003762 Helix-turn-helix domains; Region: HTH; cl00088 123214003763 Cytochrome c; Region: Cytochrom_C; cl11414 123214003764 nitrous-oxide reductase; Validated; Region: PRK02888 123214003765 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 123214003766 NosL; Region: NosL; cl01769 123214003767 Pectinesterase; Region: Pectinesterase; cl01911 123214003768 Nitrous oxidase accessory protein [Inorganic ion transport and metabolism]; Region: NosD; COG3420 123214003769 parallel beta-helix repeat (two copies); Region: para_beta_helix; TIGR03804 123214003770 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 123214003771 This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity. In bacteria and archaea, these transporters usually include an ATP-binding...; Region: ABC_DR_subfamily_A; cd03230 123214003772 Walker A/P-loop; other site 123214003773 ATP binding site [chemical binding]; other site 123214003774 Q-loop/lid; other site 123214003775 ABC transporter signature motif; other site 123214003776 Walker B; other site 123214003777 D-loop; other site 123214003778 H-loop/switch region; other site 123214003779 ABC-2 type transporter; Region: ABC2_membrane; cl11417 123214003780 Cytochrome c; Region: Cytochrom_C; cl11414 123214003781 Protein of unknown function (DUF461); Region: DUF461; cl01071 123214003782 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 123214003783 Cu(I) binding site [ion binding]; other site 123214003784 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 123214003785 N-terminal plug; other site 123214003786 TonB-dependent copper receptor; Region: TonB-copper; TIGR01778 123214003787 ligand-binding site [chemical binding]; other site 123214003788 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214003789 metal binding site [ion binding]; metal-binding site 123214003790 active site 123214003791 I-site; other site 123214003792 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; cl03652 123214003793 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 123214003794 ScpA/B protein; Region: ScpA_ScpB; cl00598 123214003795 CLC voltage-gated chloride channel. The ClC chloride channels catalyse the selective flow of Cl- ions across cell membranes, thereby regulating electrical excitation in skeletal muscle and the flow of salt and water across epithelial barriers. This...; Region: Voltage_gated_ClC; cd00400 123214003796 Voltage gated chloride channel; Region: Voltage_CLC; pfam00654 123214003797 Cl- selectivity filter; other site 123214003798 Cl- binding residues [ion binding]; other site 123214003799 pore gating glutamate residue; other site 123214003800 dimer interface [polypeptide binding]; other site 123214003801 FOG: CBS domain [General function prediction only]; Region: COG0517 123214003802 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cl15354 123214003803 Cation transport protein; Region: TrkH; cl10514 123214003804 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 123214003805 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 123214003806 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214003807 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl15357 123214003808 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214003809 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl15357 123214003810 Radical SAM superfamily; Region: Radical_SAM; pfam04055 123214003811 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 123214003812 FeS/SAM binding site; other site 123214003813 FMN-binding domain; Region: FMN_bind; cl01081 123214003814 ApbE family; Region: ApbE; cl00643 123214003815 Outer membrane protein family (DUF1597); Region: DUF1597; pfam07642 123214003816 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214003817 Prephenate dehydrogenase; Region: PDH; pfam02153 123214003818 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 123214003819 Ligand Binding Site [chemical binding]; other site 123214003820 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 123214003821 Ligand Binding Site [chemical binding]; other site 123214003822 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 123214003823 Cation efflux family; Region: Cation_efflux; cl00316 123214003824 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 123214003825 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; cl03056 123214003826 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 123214003827 catalytic site [active] 123214003828 subunit interface [polypeptide binding]; other site 123214003829 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: PRK14611 123214003830 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 123214003831 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 123214003832 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 123214003833 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 123214003834 active site 123214003835 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 123214003836 ribosomal protein L25, Ctc-form; Region: ctc_TL5; TIGR00731 123214003837 5S rRNA interface [nucleotide binding]; other site 123214003838 CTC domain interface [polypeptide binding]; other site 123214003839 L16 interface [polypeptide binding]; other site 123214003840 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 123214003841 putative active site [active] 123214003842 catalytic residue [active] 123214003843 Ribosomal protein S6; Region: Ribosomal_S6; cl00414 123214003844 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 123214003845 dimer interface [polypeptide binding]; other site 123214003846 ssDNA binding site [nucleotide binding]; other site 123214003847 tetramer (dimer of dimers) interface [polypeptide binding]; other site 123214003848 Ribosomal protein S18; Region: Ribosomal_S18; cl00373 123214003849 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 123214003850 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 123214003851 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 123214003852 replicative DNA helicase; Region: DnaB; TIGR00665 123214003853 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 123214003854 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 123214003855 Walker A motif; other site 123214003856 ATP binding site [chemical binding]; other site 123214003857 Walker B motif; other site 123214003858 DNA binding loops [nucleotide binding] 123214003859 Permease; Region: Permease; cl00510 123214003860 Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate. The members belong to PFK family that includes ATP- and pyrophosphate (PPi)- dependent phosphofructokinases; Region: PFK; cl00204 123214003861 active site 123214003862 ADP/pyrophosphate binding site [chemical binding]; other site 123214003863 dimerization interface [polypeptide binding]; other site 123214003864 allosteric effector site; other site 123214003865 fructose-1,6-bisphosphate binding site; other site 123214003866 SpoVG; Region: SpoVG; cl00915 123214003867 Protein of unknown function, DUF481; Region: DUF481; cl01213 123214003868 4Fe-4S single cluster domain; Region: Fer4_15; pfam13459 123214003869 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 123214003870 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 123214003871 putative active site [active] 123214003872 catalytic triad [active] 123214003873 putative dimer interface [polypeptide binding]; other site 123214003874 Protein of unknown function DUF45; Region: DUF45; cl00636 123214003875 type I site-specific deoxyribonuclease, HsdR family; Region: hsdR; TIGR00348 123214003876 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl14958 123214003877 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 123214003878 ATP binding site [chemical binding]; other site 123214003879 putative Mg++ binding site [ion binding]; other site 123214003880 AAA domain; Region: AAA_13; pfam13166 123214003881 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 123214003882 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 123214003883 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 123214003884 Protein of unknown function (DUF3644); Region: DUF3644; pfam12358 123214003885 Protein of unknown function (Hypoth_ymh); Region: Hypoth_Ymh; cl09741 123214003886 HsdM N-terminal domain; Region: HsdM_N; pfam12161 123214003887 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 123214003888 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214003889 TniQ; Region: TniQ; pfam06527 123214003890 Protein present in Fab1, YOTB, Vac1, and EEA1; Region: FYVE; smart00064 123214003891 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 123214003892 AAA domain; Region: AAA_22; pfam13401 123214003893 Helix-turn-helix domains; Region: HTH; cl00088 123214003894 Helix-turn-helix domains; Region: HTH; cl00088 123214003895 Integrase core domain; Region: rve; cl01316 123214003896 Mu transposase, C-terminal; Region: Mu-transpos_C; pfam09299 123214003897 TnsA endonuclease N terminal; Region: Tn7_Tnp_TnsA_N; cl07370 123214003898 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 123214003899 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 123214003900 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 123214003901 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 123214003902 FeS/SAM binding site; other site 123214003903 trigger factor; Provisional; Region: tig; PRK01490 123214003904 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 123214003905 Clp protease; Region: CLP_protease; pfam00574 123214003906 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 123214003907 oligomer interface [polypeptide binding]; other site 123214003908 active site residues [active] 123214003909 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 123214003910 ClpX C4-type zinc finger; Region: zf-C4_ClpX; cl05964 123214003911 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 123214003912 Walker A motif; other site 123214003913 ATP binding site [chemical binding]; other site 123214003914 Walker B motif; other site 123214003915 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 123214003916 Predicted GTPase [General function prediction only]; Region: COG0218 123214003917 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 123214003918 G1 box; other site 123214003919 GTP/Mg2+ binding site [chemical binding]; other site 123214003920 Switch I region; other site 123214003921 G2 box; other site 123214003922 G3 box; other site 123214003923 Switch II region; other site 123214003924 G4 box; other site 123214003925 G5 box; other site 123214003926 tryptophan synthase subunit alpha; Provisional; Region: trpA; PRK13111 123214003927 Ttryptophan synthase (TRPS) alpha subunit (TSA). TPRS is a bifunctional tetrameric enzyme (2 alpha and 2 beta subunits) that catalyzes the last two steps of L-tryptophan biosynthesis. Alpha and beta subunit catalyze two distinct reactions which are both...; Region: Tryptophan_synthase_alpha; cd04724 123214003928 substrate binding site [chemical binding]; other site 123214003929 active site 123214003930 catalytic residues [active] 123214003931 heterodimer interface [polypeptide binding]; other site 123214003932 imidazole glycerol phosphate synthase subunit HisH; Provisional; Region: hisH; PRK13141 123214003933 Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS); Region: GATase1_IGP_Synthase; cd01748 123214003934 putative active site [active] 123214003935 oxyanion strand; other site 123214003936 catalytic triad [active] 123214003937 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 123214003938 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 123214003939 FeS/SAM binding site; other site 123214003940 HemN C-terminal domain; Region: HemN_C; pfam06969 123214003941 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 123214003942 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 123214003943 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 123214003944 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 123214003945 CRISPR/Cas system-associated RAMP superfamily protein Cas6; Region: Cas6-I-III; cd09652 123214003946 CRISPR/Cas system-associated protein Cas8a1; Region: Cas8a1_I-A; cd09665 123214003947 CRISPR/Cas system-associated RAMP superfamily protein Cas7; Region: Cas7_I-C; cd09687 123214003948 CRISPR-associated protein Cas5, subtype I-B/TNEAP; Region: cas_Cas5t; TIGR01895 123214003949 CRISPR/Cas system-associated RAMP superfamily protein Cas5; Region: Cas5_I-B; cd09658 123214003950 CRISPR/Cas system-associated protein Cas3''; Region: Cas3''_I; cd09641 123214003951 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 123214003952 CRISPR-associated helicase Cas3; Region: cas3_core; TIGR01587 123214003953 Predicted nucleotidyltransferase; Region: Nuc-transf; cl01417 123214003954 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 123214003955 GTPase subunit of restriction endonuclease [Defense mechanisms]; Region: McrB; COG1401 123214003956 Domain of unknown function (DUF2357); Region: DUF2357; pfam09823 123214003957 Protein of unknown function (DUF524); Region: DUF524; pfam04411 123214003958 CRISPR/Cas system-associated protein Cas1; Region: Cas1_I-B; cd09722 123214003959 CRISPR/Cas system-associated protein Cas2; Region: Cas2_I_II_III; cd09725 123214003960 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 123214003961 Methyltransferase domain; Region: Methyltransf_31; pfam13847 123214003962 S-adenosylmethionine binding site [chemical binding]; other site 123214003963 hypothetical protein; Provisional; Region: PRK11820 123214003964 YicC-like family, N-terminal region; Region: YicC_N; pfam03755 123214003965 Domain of unknown function (DUF1732); Region: DUF1732; pfam08340 123214003966 Ferritin-CCC1, N-terminal ferritin-like diiron-binding domain; Region: Ferritin_CCC1_N; cd01044 123214003967 diiron binding motif [ion binding]; other site 123214003968 CCC1-related domain of ferritin; Region: Ferritin_CCC1_C; cd02431 123214003969 3-deoxy-D-manno-octulosonic-acid transferase [Cell envelope biogenesis, outer membrane]; Region: KdtA; COG1519 123214003970 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 123214003971 Uncharacterized protein family (UPF0014); Region: UPF0014; cl00424 123214003972 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 123214003973 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 123214003974 biotin synthase; Region: bioB; TIGR00433 123214003975 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 123214003976 FeS/SAM binding site; other site 123214003977 Biotin and Thiamin Synthesis associated domain; Region: BATS; cl06149 123214003978 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214003979 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 123214003980 NAD(P) binding site [chemical binding]; other site 123214003981 active site 123214003982 Tetratricopeptide repeat; Region: TPR_15; pfam13429 123214003983 TM1410 hypothetical-related protein; Region: DUF297; cl00997 123214003984 C-terminal Putative NodB-like catalytic domain of PelA-like uncharacterized hypothetical proteins found in bacteria; Region: CE4_PelA_like_C; cd10922 123214003985 putative active site [active] 123214003986 Predicted membrane protein [Function unknown]; Region: COG4267 123214003987 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can...; Region: GT1_like_3; cd03813 123214003988 Domain of unknown function (DUF4118); Region: DUF4118; pfam13493 123214003989 TPR/MLP1/MLP2-like protein; Region: TPR_MLP1_2; pfam07926 123214003990 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 123214003991 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 123214003992 MazG nucleotide pyrophosphohydrolase domain; Region: MazG; cl00345 123214003993 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 123214003994 active site 123214003995 LysE type translocator; Region: LysE; cl00565 123214003996 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs; Region: NDUFA9_like_SDR_a; cd05271 123214003997 putative NAD(P) binding site [chemical binding]; other site 123214003998 active site 123214003999 putative secretion ATPase, PEP-CTERM locus subfamily; Region: pepcterm_ATPase; TIGR03015 123214004000 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 123214004001 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3034 123214004002 L,D-transpeptidase catalytic domain; Region: YkuD; cl15405 123214004003 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 123214004004 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cd00596 123214004005 active site 123214004006 Zn binding site [ion binding]; other site 123214004007 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 123214004008 Survival protein SurE; Region: SurE; cl00448 123214004009 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 123214004010 IHF dimer interface [polypeptide binding]; other site 123214004011 IHF - DNA interface [nucleotide binding]; other site 123214004012 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 123214004013 trimer interface [polypeptide binding]; other site 123214004014 putative metal binding site [ion binding]; other site 123214004015 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 123214004016 active site 123214004017 dihydroorotate dehydrogenase electron transfer subunit; Reviewed; Region: PRK00054 123214004018 FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-dihydroorotate to...; Region: DHOD_e_trans; cd06218 123214004019 FAD binding pocket [chemical binding]; other site 123214004020 FAD binding motif [chemical binding]; other site 123214004021 phosphate binding motif [ion binding]; other site 123214004022 beta-alpha-beta structure motif; other site 123214004023 NAD binding pocket [chemical binding]; other site 123214004024 Iron coordination center [ion binding]; other site 123214004025 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214004026 succinate dehydrogenase or fumarate reductase, flavoprotein subunitGram-negative/mitochondrial subgroup; Region: sdhA_frdA_Gneg; TIGR01812 123214004027 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 123214004028 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 123214004029 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 123214004030 ATP-grasp domain; Region: ATP-grasp_4; cl03087 123214004031 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 123214004032 diaminopimelate decarboxylase; Region: lysA; TIGR01048 123214004033 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 123214004034 active site 123214004035 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 123214004036 substrate binding site [chemical binding]; other site 123214004037 catalytic residues [active] 123214004038 dimer interface [polypeptide binding]; other site 123214004039 septum site-determining protein MinC; Region: minC; TIGR01222 123214004040 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 123214004041 septum site-determining protein MinD; Region: minD_bact; TIGR01968 123214004042 Bacterial cell division requires the formation of a septum at mid-cell. The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a pivotal...; Region: MinD; cd02036 123214004043 Switch I; other site 123214004044 Switch II; other site 123214004045 Septum formation topological specificity factor MinE; Region: MinE; cl00538 123214004046 ATP phosphoribosyltransferase; Region: HisG; cl15266 123214004047 UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase; Region: glmU; TIGR01173 123214004048 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 123214004049 Substrate binding site; other site 123214004050 Mg++ binding site; other site 123214004051 N-acetyl-glucosamine-1-phosphate uridyltransferase (GlmU), C-terminal left-handed beta-helix (LbH) acetyltransferase domain: GlmU is also known as UDP-N-acetylglucosamine pyrophosphorylase. It is a bifunctional bacterial enzyme that catalyzes two...; Region: LbH_GlmU_C; cd03353 123214004052 active site 123214004053 substrate binding site [chemical binding]; other site 123214004054 CoA binding site [chemical binding]; other site 123214004055 SurA N-terminal domain; Region: SurA_N_3; cl07813 123214004056 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 123214004057 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 123214004058 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 123214004059 7-alpha-hydroxysteroid dehydrogenase; Provisional; Region: PRK08416 123214004060 1-cyclohexenylcarbonyl_coenzyme A_reductase (ChcA)_like, classical (c) SDRs; Region: ChcA_like_SDR_c; cd05359 123214004061 putative NAD(P) binding site [chemical binding]; other site 123214004062 active site 123214004063 RNA polymerase sigma factor, FliA/WhiG family; Region: FliA_WhiG; TIGR02479 123214004064 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 123214004065 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 123214004066 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 123214004067 DNA binding residues [nucleotide binding] 123214004068 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 123214004069 FleN is a member of the Fer4_NifH superfamily. It shares the common function as an ATPase, with the ATP-binding domain at the N-terminus. In Pseudomonas aeruginosa, FleN gene is involved in regulating the number of flagella and chemotactic motility by...; Region: FleN-like; cd02038 123214004070 P-loop; other site 123214004071 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 123214004072 flagellar biosynthetic protein FlhF; Region: FlhF; TIGR03499 123214004073 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 123214004074 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 123214004075 shikimate kinase; Reviewed; Region: aroK; PRK00131 123214004076 Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants. Chorismic acid is a important intermediate in the synthesis...; Region: SK; cd00464 123214004077 ADP binding site [chemical binding]; other site 123214004078 magnesium binding site [ion binding]; other site 123214004079 putative shikimate binding site; other site 123214004080 Uncharacterized ACR, YggU family COG1872; Region: DUF167; cl00811 123214004081 Queuosine biosynthesis protein; Region: Queuosine_synth; cl00523 123214004082 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 123214004083 Protein of unknown function (DUF2905); Region: DUF2905; pfam11146 123214004084 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 123214004085 thiamine phosphate binding site [chemical binding]; other site 123214004086 active site 123214004087 pyrophosphate binding site [ion binding]; other site 123214004088 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3; Region: Oxidored_q4; cl00535 123214004089 NADH dehydrogenase subunit B; Validated; Region: PRK06411 123214004090 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl15792 123214004091 bifunctional NADH:ubiquinone oxidoreductase subunit C/D; Provisional; Region: PRK11742 123214004092 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; cl15771 123214004093 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; cl00417 123214004094 NADH dehydrogenase; Region: NADHdh; cl00469 123214004095 Formate hydrogenlyase subunit 6/NADH:ubiquinone oxidoreductase 23 kD subunit (chain I) [Energy production and conversion]; Region: NuoI; COG1143 123214004096 4Fe-4S binding domain; Region: Fer4; cl02805 123214004097 NADH:ubiquinone oxidoreductase subunit 6 (chain J) [Energy production and conversion]; Region: NuoJ; COG0839 123214004098 NADH dehydrogenase subunit J; Provisional; Region: PRK06433; cl14634 123214004099 NADH dehydrogenase subunit J; Provisional; Region: PRK06433; cl14634 123214004100 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 123214004101 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 123214004102 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 123214004103 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 123214004104 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 123214004105 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 123214004106 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 123214004107 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 123214004108 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 123214004109 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 123214004110 catalytic site [active] 123214004111 G-X2-G-X-G-K; other site 123214004112 RNA polymerase Rpb6; Region: RNA_pol_Rpb6; cl14651 123214004113 adaptive-response sensory kinase; Validated; Region: PRK09303 123214004114 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 123214004115 dimer interface [polypeptide binding]; other site 123214004116 phosphorylation site [posttranslational modification] 123214004117 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 123214004118 ATP binding site [chemical binding]; other site 123214004119 Mg2+ binding site [ion binding]; other site 123214004120 G-X-G motif; other site 123214004121 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 123214004122 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 123214004123 active site 123214004124 phosphorylation site [posttranslational modification] 123214004125 intermolecular recognition site; other site 123214004126 dimerization interface [polypeptide binding]; other site 123214004127 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 123214004128 Walker A motif; other site 123214004129 ATP binding site [chemical binding]; other site 123214004130 Walker B motif; other site 123214004131 arginine finger; other site 123214004132 Helix-turn-helix domains; Region: HTH; cl00088 123214004133 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 123214004134 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 123214004135 LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop; Region: LysRS_N; cd04322 123214004136 dimer interface [polypeptide binding]; other site 123214004137 putative anticodon binding site; other site 123214004138 Lys_tRNA synthetase (LysRS) class II core domain. Class II LysRS is a dimer which attaches a lysine to the 3' OH group of ribose of the appropriate tRNA. Its assignment to class II aaRS is based upon its structure and the presence of three...; Region: LysRS_core; cd00775 123214004139 motif 1; other site 123214004140 active site 123214004141 motif 2; other site 123214004142 motif 3; other site 123214004143 ADP-ribosylglycohydrolase; Region: ADP_ribosyl_GH; cl00614 123214004144 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of...; Region: Sm_like; cl00259 123214004145 Sm1 motif; other site 123214004146 D1 - D2 interaction site; other site 123214004147 D3 - B interaction site; other site 123214004148 Hfq - Hfq interaction site; other site 123214004149 RNA binding pocket [nucleotide binding]; other site 123214004150 Sm2 motif; other site 123214004151 Cytochrome c peroxidase [Inorganic ion transport and metabolism]; Region: MauG; COG1858 123214004152 Uncharacterized P-loop hydrolase UPF0079; Region: UPF0079; cl00520 123214004153 Predicted RNA-binding protein (contains KH domain) [General function prediction only]; Region: COG1837 123214004154 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that...; Region: KH-I; cl00098 123214004155 Ribosomal protein S16; Region: Ribosomal_S16; cl00368 123214004156 signal recognition particle protein; Provisional; Region: PRK10867 123214004157 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 123214004158 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 123214004159 P loop; other site 123214004160 GTP binding site [chemical binding]; other site 123214004161 Signal peptide binding domain; Region: SRP_SPB; pfam02978 123214004162 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 123214004163 Outer membrane protein/protective antigen OMA87 [Cell envelope biogenesis, outer membrane]; Region: COG4775 123214004164 Surface antigen; Region: Bac_surface_Ag; cl03097 123214004165 SapC; Region: SapC; pfam07277 123214004166 haemagglutination activity domain; Region: Haemagg_act; cl05436 123214004167 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 123214004168 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 123214004169 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 123214004170 spermidine synthase; Provisional; Region: PRK00811 123214004171 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 123214004172 S-adenosylmethionine binding site [chemical binding]; other site 123214004173 Predicted methyltransferases [General function prediction only]; Region: COG1568 123214004174 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 123214004175 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 123214004176 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 123214004177 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 123214004178 Aconitase B swivel domain. Aconitate hydratase B is involved in energy metabolism as part of the TCA cycle. It catalyses the formation of cis-aconitate from citrate. This is the aconitase swivel domain, which undergoes swivelling conformational change in...; Region: AcnB_Swivel; cd01576 123214004179 substrate binding site [chemical binding]; other site 123214004180 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 123214004181 substrate binding site [chemical binding]; other site 123214004182 ligand binding site [chemical binding]; other site 123214004183 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 123214004184 Carbonic anhydrase alpha, prokaryotic-like subfamily. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon...; Region: alpha_CA_prokaryotic_like; cd03124 123214004185 active site 123214004186 zinc binding site [ion binding]; other site 123214004187 ResB-like family; Region: ResB; pfam05140 123214004188 ResB-like family; Region: ResB; pfam05140 123214004189 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 123214004190 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 123214004191 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; cl09905 123214004192 Cytochrome c; Region: Cytochrom_C; cl11414 123214004193 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; cl09905 123214004194 decaheme c-type cytochrome, DmsE family; Region: decahem_SO; TIGR03508 123214004195 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; cl09905 123214004196 Uncharacterized conserved protein [Function unknown]; Region: COG3391 123214004197 NHL repeat; Region: NHL; pfam01436 123214004198 NHL repeat; Region: NHL; pfam01436 123214004199 NHL repeat; Region: NHL; pfam01436 123214004200 NHL repeat; Region: NHL; pfam01436 123214004201 Sporulation related domain; Region: SPOR; cl10051 123214004202 P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimD; COG3188 123214004203 TonB-linked outer membrane protein, SusC/RagA family; Region: OMP_RagA_SusC; TIGR04056 123214004204 SurA N-terminal domain; Region: SurA_N_3; cl07813 123214004205 nitrogen fixation protein NifM; Region: nifM_nitrog; TIGR02933 123214004206 PPIC-type PPIASE domain; Region: Rotamase; cl08278 123214004207 Uncharacterized conserved protein [Function unknown]; Region: COG3391 123214004208 NHL repeat; Region: NHL; pfam01436 123214004209 NHL repeat; Region: NHL; pfam01436 123214004210 NHL repeat; Region: NHL; pfam01436 123214004211 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; cl09905 123214004212 Uncharacterized conserved protein [Function unknown]; Region: COG3391 123214004213 NHL repeat; Region: NHL; pfam01436 123214004214 NHL repeat; Region: NHL; pfam01436 123214004215 NHL repeat; Region: NHL; pfam01436 123214004216 NHL repeat; Region: NHL; pfam01436 123214004217 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; cl09905 123214004218 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; cl09905 123214004219 decaheme c-type cytochrome, DmsE family; Region: decahem_SO; TIGR03508 123214004220 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; cl09905 123214004221 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; cl09905 123214004222 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; cl09905 123214004223 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; cl09905 123214004224 NapC/NirT cytochrome c family, N-terminal region; Region: Cytochrom_NNT; pfam03264 123214004225 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; cl09905 123214004226 decaheme c-type cytochrome, DmsE family; Region: decahem_SO; TIGR03508 123214004227 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; cl09905 123214004228 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; cl09905 123214004229 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; cl09905 123214004230 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; cl09905 123214004231 decaheme c-type cytochrome, DmsE family; Region: decahem_SO; TIGR03508 123214004232 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; cl09905 123214004233 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; cl09905 123214004234 decaheme c-type cytochrome, DmsE family; Region: decahem_SO; TIGR03508 123214004235 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; cl09905 123214004236 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; cl09905 123214004237 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214004238 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_3; pfam13738 123214004239 ATP-dependent Clp protease adaptor protein ClpS; Region: ClpS; cl00933 123214004240 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 123214004241 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 123214004242 active site 123214004243 (T/H)XGH motif; other site 123214004244 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 123214004245 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 123214004246 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 123214004247 protein binding site [polypeptide binding]; other site 123214004248 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 123214004249 protein binding site [polypeptide binding]; other site 123214004250 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 123214004251 Predicted sugar phosphatases of the HAD superfamily [Carbohydrate transport and metabolism]; Region: NagD; COG0647 123214004252 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 123214004253 UbiA prenyltransferase family; Region: UbiA; cl00337 123214004254 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 123214004255 hypothetical protein; Reviewed; Region: PRK00024 123214004256 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 123214004257 MPN+ (JAMM) motif; other site 123214004258 Zinc-binding site [ion binding]; other site 123214004259 peptidyl-prolyl cis-trans isomerase B (rotamase B); Provisional; Region: PRK10791 123214004260 cyclophilin_EcCYP_like: cyclophilin-type A-like peptidylprolyl cis- trans isomerase (PPIase) domain similar to the cytosolic E. coli cyclophilin A and Streptomyces antibioticus SanCyp18. Compared to the archetypal cyclophilin Human cyclophilin A, these...; Region: cyclophilin_EcCYP_like; cd01920 123214004261 substrate binding site [chemical binding]; other site 123214004262 N-methylhydantoinase B/acetone carboxylase, alpha subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuB; COG0146 123214004263 N-methylhydantoinase A/acetone carboxylase, beta subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuA; COG0145 123214004264 Hydantoinase/oxoprolinase N-terminal region; Region: Hydant_A_N; pfam05378 123214004265 Hydantoinase/oxoprolinase; Region: Hydantoinase_A; cl00668 123214004266 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 123214004267 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 123214004268 active site 123214004269 HIGH motif; other site 123214004270 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 123214004271 KMSKS motif; other site 123214004272 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 123214004273 tRNA binding surface [nucleotide binding]; other site 123214004274 anticodon binding site; other site 123214004275 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 123214004276 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 123214004277 S-adenosylmethionine binding site [chemical binding]; other site 123214004278 Predicted alternative 3-dehydroquinate synthase [Amino acid transport and metabolism]; Region: COG1465 123214004279 3-dehydroquinate synthase (EC 4.6.1.3); Region: DHQS; cl00640 123214004280 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 123214004281 mce related protein; Region: MCE; pfam02470 123214004282 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 123214004283 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 123214004284 ligand binding site [chemical binding]; other site 123214004285 flexible hinge region; other site 123214004286 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 123214004287 putative switch regulator; other site 123214004288 non-specific DNA interactions [nucleotide binding]; other site 123214004289 DNA binding site [nucleotide binding] 123214004290 sequence specific DNA binding site [nucleotide binding]; other site 123214004291 putative cAMP binding site [chemical binding]; other site 123214004292 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 123214004293 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 123214004294 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 123214004295 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 123214004296 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 123214004297 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 123214004298 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214004299 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 123214004300 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 123214004301 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 123214004302 FtsX-like permease family; Region: FtsX; cl15850 123214004303 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 123214004304 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 123214004305 FtsX-like permease family; Region: FtsX; cl15850 123214004306 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 123214004307 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 123214004308 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 123214004309 dimer interface [polypeptide binding]; other site 123214004310 putative CheW interface [polypeptide binding]; other site 123214004311 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 123214004312 Amidase; Region: Amidase; cl11426 123214004313 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 123214004314 phosphoribosylglycinamide formyltransferase 2; Validated; Region: purT; PRK09288 123214004315 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214004316 ATP-grasp domain; Region: ATP-grasp_4; cl03087 123214004317 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 123214004318 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 123214004319 active site 123214004320 phosphorylation site [posttranslational modification] 123214004321 intermolecular recognition site; other site 123214004322 dimerization interface [polypeptide binding]; other site 123214004323 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 123214004324 Walker A motif; other site 123214004325 ATP binding site [chemical binding]; other site 123214004326 Walker B motif; other site 123214004327 arginine finger; other site 123214004328 Helix-turn-helix domains; Region: HTH; cl00088 123214004329 Response regulator containing a CheY-like receiver domain and an HD-GYP domain [Transcription / Signal transduction mechanisms]; Region: COG3437 123214004330 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 123214004331 active site 123214004332 phosphorylation site [posttranslational modification] 123214004333 intermolecular recognition site; other site 123214004334 dimerization interface [polypeptide binding]; other site 123214004335 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 123214004336 Zn2+ binding site [ion binding]; other site 123214004337 Mg2+ binding site [ion binding]; other site 123214004338 Response regulator receiver domain; Region: Response_reg; pfam00072 123214004339 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 123214004340 active site 123214004341 phosphorylation site [posttranslational modification] 123214004342 intermolecular recognition site; other site 123214004343 dimerization interface [polypeptide binding]; other site 123214004344 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: VicK; COG5002 123214004345 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 123214004346 dimerization interface [polypeptide binding]; other site 123214004347 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 123214004348 dimer interface [polypeptide binding]; other site 123214004349 phosphorylation site [posttranslational modification] 123214004350 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 123214004351 ATP binding site [chemical binding]; other site 123214004352 Mg2+ binding site [ion binding]; other site 123214004353 G-X-G motif; other site 123214004354 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional; Region: purH; PRK00881 123214004355 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 123214004356 purine monophosphate binding site [chemical binding]; other site 123214004357 dimer interface [polypeptide binding]; other site 123214004358 putative catalytic residues [active] 123214004359 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 123214004360 AICARFT/IMPCHase bienzyme; Region: AICARFT_IMPCHas; cl03362 123214004361 RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; Region: Rel-Spo_like; cl11966 123214004362 metal binding triad [ion binding]; metal-binding site 123214004363 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 123214004364 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 123214004365 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 123214004366 Ligand Binding Site [chemical binding]; other site 123214004367 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 123214004368 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 123214004369 Type II secretion system (T2SS), protein F; Region: T2SF; cl00906 123214004370 pilus retraction protein PilT; Region: pilT_fam; TIGR01420 123214004371 Pilus retraction ATPase PilT. PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism...; Region: PilT; cd01131 123214004372 Walker A motif; other site 123214004373 ATP binding site [chemical binding]; other site 123214004374 Walker B motif; other site 123214004375 type IV-A pilus assembly ATPase PilB; Region: type_IV_pilB; TIGR02538 123214004376 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 123214004377 PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which...; Region: PulE-GspE; cd01129 123214004378 Walker A motif; other site 123214004379 ATP binding site [chemical binding]; other site 123214004380 Walker B motif; other site 123214004381 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 123214004382 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 123214004383 ATP-grasp domain; Region: ATP-grasp_4; cl03087 123214004384 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 123214004385 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 123214004386 AP endonuclease family 2; Region: AP2Ec; smart00518 123214004387 AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites; the alignment also contains hexulose-6-phosphate isomerases, enzymes that catalyze the epimerization of...; Region: AP2Ec; cd00019 123214004388 AP (apurinic/apyrimidinic) site pocket; other site 123214004389 DNA interaction; other site 123214004390 Metal-binding active site; metal-binding site 123214004391 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 123214004392 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 123214004393 substrate binding pocket [chemical binding]; other site 123214004394 chain length determination region; other site 123214004395 substrate-Mg2+ binding site; other site 123214004396 catalytic residues [active] 123214004397 aspartate-rich region 1; other site 123214004398 active site lid residues [active] 123214004399 aspartate-rich region 2; other site 123214004400 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 123214004401 tetramerization interface [polypeptide binding]; other site 123214004402 active site 123214004403 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 123214004404 N-acetyl-D-glucosamine binding site [chemical binding]; other site 123214004405 catalytic residue [active] 123214004406 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 123214004407 putative peptidoglycan binding site; other site 123214004408 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 123214004409 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 123214004410 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 123214004411 Plant protein of unknown function (DUF946); Region: DUF946; pfam06101 123214004412 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 123214004413 feedback inhibition sensing region; other site 123214004414 homohexameric interface [polypeptide binding]; other site 123214004415 nucleotide binding site [chemical binding]; other site 123214004416 N-acetyl-L-glutamate binding site [chemical binding]; other site 123214004417 DNA helicase, putative; Region: TIGR00376 123214004418 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 123214004419 Family description; Region: UvrD_C_2; cl15862 123214004420 Globin domain present in Globin-Coupled-Sensors (GCS). These domains detect changes in intracellular concentrations of oxygen, carbon monoxyde, or nitrous oxide, which result in aerotaxis and/or gene regulation. One subgroup, the HemATs, are aerotactic...; Region: sensor_globin; cd01068 123214004421 heme-binding site [chemical binding]; other site 123214004422 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 123214004423 SecA preprotein cross-linking domain; Region: SecA_PP_bind; cl03078 123214004424 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 123214004425 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 123214004426 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 123214004427 metabolite-proton symporter; Region: 2A0106; TIGR00883 123214004428 putative substrate translocation pore; other site 123214004429 Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the glyoxylate...; Region: citrate_synt_like_1; cd06118 123214004430 dimer interface [polypeptide binding]; other site 123214004431 Citrate synthase; Region: Citrate_synt; pfam00285 123214004432 active site 123214004433 coenzyme A binding site [chemical binding]; other site 123214004434 citrylCoA binding site [chemical binding]; other site 123214004435 oxalacetate/citrate binding site [chemical binding]; other site 123214004436 catalytic triad [active] 123214004437 copper-(or silver)-translocating P-type ATPase; Region: ATPase-IB1_Cu; TIGR01511 123214004438 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 123214004439 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 123214004440 Predicted periplasmic solute-binding protein [General function prediction only]; Region: COG1427 123214004441 NMT1-like family; Region: NMT1_2; cl15260 123214004442 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; cl11421 123214004443 bifunctional tRNA (mnm(5)s(2)U34)-methyltransferase/FAD-dependent cmnm(5)s(2)U34 oxidoreductase; Reviewed; Region: mnmC; PRK01747 123214004444 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; cl15754 123214004445 DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA. DNA-directed DNA polymerases are multifunctional with both synthetic; Region: POLBc; cl10023 123214004446 active site 123214004447 metal-binding site 123214004448 LexA repressor; Validated; Region: PRK00215 123214004449 Helix-turn-helix domains; Region: HTH; cl00088 123214004450 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 123214004451 Catalytic site [active] 123214004452 DNA polymerase III subunit beta; Validated; Region: PRK05643 123214004453 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 123214004454 putative DNA binding surface [nucleotide binding]; other site 123214004455 dimer interface [polypeptide binding]; other site 123214004456 beta-clamp/clamp loader binding surface; other site 123214004457 beta-clamp/translesion DNA polymerase binding surface; other site 123214004458 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 123214004459 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 123214004460 ATP binding site [chemical binding]; other site 123214004461 Mg2+ binding site [ion binding]; other site 123214004462 G-X-G motif; other site 123214004463 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 123214004464 anchoring element; other site 123214004465 dimer interface [polypeptide binding]; other site 123214004466 ATP binding site [chemical binding]; other site 123214004467 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 123214004468 active site 123214004469 putative metal-binding site [ion binding]; other site 123214004470 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 123214004471 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 123214004472 Cytochrome c; Region: Cytochrom_C; cl11414 123214004473 PAS fold; Region: PAS_3; pfam08447 123214004474 PAS domain S-box; Region: sensory_box; TIGR00229 123214004475 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cl02459 123214004476 GAF domain; Region: GAF_2; pfam13185 123214004477 GAF domain; Region: GAF; cl15785 123214004478 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214004479 metal binding site [ion binding]; metal-binding site 123214004480 active site 123214004481 I-site; other site 123214004482 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 123214004483 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 123214004484 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 123214004485 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 123214004486 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 123214004487 anthranilate synthase component I; Provisional; Region: PRK13570 123214004488 chorismate binding enzyme; Region: Chorismate_bind; cl10555 123214004489 Surface presentation of antigens (SPOA); Region: SpoA; cl00819 123214004490 GAF domain; Region: GAF; cl15785 123214004491 sensory histidine kinase AtoS; Provisional; Region: PRK11360 123214004492 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 123214004493 dimer interface [polypeptide binding]; other site 123214004494 phosphorylation site [posttranslational modification] 123214004495 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 123214004496 ATP binding site [chemical binding]; other site 123214004497 Mg2+ binding site [ion binding]; other site 123214004498 G-X-G motif; other site 123214004499 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 123214004500 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 123214004501 active site 123214004502 phosphorylation site [posttranslational modification] 123214004503 intermolecular recognition site; other site 123214004504 dimerization interface [polypeptide binding]; other site 123214004505 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 123214004506 Walker A motif; other site 123214004507 ATP binding site [chemical binding]; other site 123214004508 Walker B motif; other site 123214004509 arginine finger; other site 123214004510 recombination and DNA strand exchange inhibitor protein; Reviewed; Region: PRK00409 123214004511 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 123214004512 Walker A/P-loop; other site 123214004513 ATP binding site [chemical binding]; other site 123214004514 Q-loop/lid; other site 123214004515 ABC transporter signature motif; other site 123214004516 Walker B; other site 123214004517 D-loop; other site 123214004518 H-loop/switch region; other site 123214004519 Smr domain; Region: Smr; cl02619 123214004520 A type 1 glutamine amidotransferase (GATase1)-like domain found in PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_like; cd03134 123214004521 intracellular protease, PfpI family; Region: PfpI; TIGR01382 123214004522 proposed catalytic triad [active] 123214004523 conserved cys residue [active] 123214004524 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 123214004525 FGGY family of carbohydrate kinases, N-terminal domain; Region: FGGY_N; cl09121 123214004526 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 123214004527 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 123214004528 Protein export membrane protein; Region: SecD_SecF; cl14618 123214004529 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 123214004530 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 123214004531 Protein export membrane protein; Region: SecD_SecF; cl14618 123214004532 glucose-6-phosphate isomerase; Provisional; Region: PRK00973 123214004533 Phosphoglucose isomerase (PGI) contains two SIS (Sugar ISomerase) domains. This classification is based on the alignment of the first SIS domain. PGI is a multifunctional enzyme which as an intracellular dimer catalyzes the reversible isomerization of...; Region: SIS_PGI_1; cd05015 123214004534 active site 123214004535 dimer interface [polypeptide binding]; other site 123214004536 Phosphoglucose isomerase (PGI) contains two SIS (Sugar ISomerase) domains. This classification is based on the alignment of the second SIS domain. PGI is a multifunctional enzyme which as an intracellular dimer catalyzes the reversible isomerization of...; Region: SIS_PGI_2; cd05016 123214004537 dimer interface [polypeptide binding]; other site 123214004538 active site 123214004539 seryl-tRNA synthetase; Provisional; Region: PRK05431 123214004540 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 123214004541 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 123214004542 dimer interface [polypeptide binding]; other site 123214004543 active site 123214004544 motif 1; other site 123214004545 motif 2; other site 123214004546 motif 3; other site 123214004547 TPR repeat; Region: TPR_11; pfam13414 123214004548 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 123214004549 TPR motif; other site 123214004550 binding surface 123214004551 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 123214004552 binding surface 123214004553 TPR motif; other site 123214004554 TPR repeat; Region: TPR_11; pfam13414 123214004555 Family of unknown function (DUF490); Region: DUF490; pfam04357 123214004556 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 123214004557 para-aminobenzoate synthase component II; Provisional; Region: PRK08857 123214004558 glutamine binding [chemical binding]; other site 123214004559 catalytic triad [active] 123214004560 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; cl00148 123214004561 CAP-like domain; other site 123214004562 active site 123214004563 replicative DNA helicase; Validated; Region: PRK07773 123214004564 Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein; Region: Hint; cd00081 123214004565 protein-splicing catalytic site; other site 123214004566 thioester formation/cholesterol transfer; other site 123214004567 Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein; Region: Hint; cl15780 123214004568 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 123214004569 primary dimer interface [polypeptide binding]; other site 123214004570 DNA gyrase subunit A; Validated; Region: PRK05560 123214004571 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 123214004572 Domain of unknown function (DUF4416); Region: DUF4416; pfam14385 123214004573 bifunctional molybdenum cofactor biosynthesis protein MoaC/MogA; Provisional; Region: moaC; PRK03604 123214004574 MoaC family, prokaryotic and eukaryotic. Members of this family are involved in molybdenum cofactor (Moco) biosynthesis, an essential cofactor of a diverse group of redox enzymes. MoaC, a small hexameric protein, converts, together with MoaA, a guanosine...; Region: MoaC_PE; cd01420 123214004575 trimer interface [polypeptide binding]; other site 123214004576 dimer interface [polypeptide binding]; other site 123214004577 putative active site [active] 123214004578 MogA_MoaB family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF) an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea; Region: MogA_MoaB; cd00886 123214004579 MPT binding site; other site 123214004580 trimer interface [polypeptide binding]; other site 123214004581 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 123214004582 active site 123214004583 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 123214004584 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 123214004585 Coenzyme A binding pocket [chemical binding]; other site 123214004586 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional; Region: PRK09311 123214004587 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; cl00336 123214004588 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 123214004589 dimerization interface [polypeptide binding]; other site 123214004590 active site 123214004591 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 123214004592 phosphate ABC transporter, permease protein PstC; Region: phosphate_pstC; TIGR02138 123214004593 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 123214004594 dimer interface [polypeptide binding]; other site 123214004595 conserved gate region; other site 123214004596 putative PBP binding loops; other site 123214004597 ABC-ATPase subunit interface; other site 123214004598 phosphate ABC transporter, permease protein PstA; Region: 3a0107s02c; TIGR00974 123214004599 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 123214004600 dimer interface [polypeptide binding]; other site 123214004601 conserved gate region; other site 123214004602 putative PBP binding loops; other site 123214004603 ABC-ATPase subunit interface; other site 123214004604 phosphate transporter ATP-binding protein; Provisional; Region: pstB; PRK10744 123214004605 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 123214004606 Walker A/P-loop; other site 123214004607 ATP binding site [chemical binding]; other site 123214004608 Q-loop/lid; other site 123214004609 ABC transporter signature motif; other site 123214004610 Walker B; other site 123214004611 D-loop; other site 123214004612 H-loop/switch region; other site 123214004613 phosphate transport system regulatory protein PhoU; Region: phoU_full; TIGR02135 123214004614 PhoU domain; Region: PhoU; pfam01895 123214004615 PhoU domain; Region: PhoU; pfam01895 123214004616 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 123214004617 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 123214004618 dimer interface [polypeptide binding]; other site 123214004619 phosphorylation site [posttranslational modification] 123214004620 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 123214004621 ATP binding site [chemical binding]; other site 123214004622 Mg2+ binding site [ion binding]; other site 123214004623 G-X-G motif; other site 123214004624 mannosyl-3-phosphoglycerate phosphatase; Reviewed; Region: PRK00192 123214004625 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 123214004626 active site 123214004627 motif I; other site 123214004628 motif II; other site 123214004629 Putative glycerate kinase [Carbohydrate transport and metabolism]; Region: GckA; COG2379 123214004630 Domain of unknown function (DUF4147); Region: DUF4147; pfam13660 123214004631 MOFRL family; Region: MOFRL; pfam05161 123214004632 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 123214004633 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 123214004634 active site 123214004635 putative glucosyl-3-phosphoglycerate synthase; Provisional; Region: PRK13915 123214004636 cysteine synthase B; Region: cysM; TIGR01138 123214004637 CBS_like: This subgroup includes Cystathionine beta-synthase (CBS) and Cysteine synthase. CBS is a unique heme-containing enzyme that catalyzes a pyridoxal 5'-phosphate (PLP)-dependent condensation of serine and homocysteine to give cystathionine; Region: CBS_like; cd01561 123214004638 dimer interface [polypeptide binding]; other site 123214004639 pyridoxal 5'-phosphate binding site [chemical binding]; other site 123214004640 catalytic residue [active] 123214004641 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 123214004642 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 123214004643 Uncharacterized ALDH (y4uC) with similarity to Tortula ruralis aldehyde dehydrogenase ALDH21A1; Region: ALDH_y4uC; cd07149 123214004644 NAD(P) binding site [chemical binding]; other site 123214004645 catalytic residues [active] 123214004646 Nitrogen regulatory protein P-II; Region: P-II; cl00412 123214004647 Nitrogen regulatory protein P-II; Region: P-II; smart00938 123214004648 glutamine synthetase, type I; Region: GlnA; TIGR00653 123214004649 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 123214004650 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 123214004651 PilZ domain; Region: PilZ; cl01260 123214004652 Protein of unknown function (DUF445); Region: DUF445; pfam04286 123214004653 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 123214004654 binding surface 123214004655 TPR motif; other site 123214004656 Anaphase-promoting complex, cyclosome, subunit 3; Region: Apc3; pfam12895 123214004657 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 123214004658 TPR motif; other site 123214004659 binding surface 123214004660 TPR repeat; Region: TPR_11; pfam13414 123214004661 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 123214004662 TPR motif; other site 123214004663 binding surface 123214004664 TPR repeat; Region: TPR_11; pfam13414 123214004665 Tetratricopeptide repeat; Region: TPR_12; pfam13424 123214004666 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 123214004667 binding surface 123214004668 TPR motif; other site 123214004669 Tetratricopeptide repeat; Region: TPR_16; pfam13432 123214004670 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 123214004671 binding surface 123214004672 TPR motif; other site 123214004673 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 123214004674 binding surface 123214004675 TPR repeat; Region: TPR_11; pfam13414 123214004676 TPR motif; other site 123214004677 TPR repeat; Region: TPR_11; pfam13414 123214004678 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 123214004679 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs); Region: APH_ChoK_like; cd05120 123214004680 active site 123214004681 substrate binding site [chemical binding]; other site 123214004682 ATP binding site [chemical binding]; other site 123214004683 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 123214004684 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 123214004685 CoA-binding site [chemical binding]; other site 123214004686 ATP-binding [chemical binding]; other site 123214004687 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 123214004688 Permeases of the major facilitator superfamily [General function prediction only]; Region: COG2270 123214004689 Permeases of the major facilitator superfamily [General function prediction only]; Region: COG2270 123214004690 PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like. This group is comprised of eukaryotic and bacterial proteins similar to Escherichia coli RsuA. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA...; Region: PseudoU_synth_RsuA; cd02553 123214004691 pseudouridine synthase; Region: TIGR00093 123214004692 active site 123214004693 uracil binding [chemical binding]; other site 123214004694 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 123214004695 IHF - DNA interface [nucleotide binding]; other site 123214004696 IHF dimer interface [polypeptide binding]; other site 123214004697 4Fe-4S single cluster domain; Region: Fer4_15; pfam13459 123214004698 chromosome segregation protein; Provisional; Region: PRK01156 123214004699 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 123214004700 Walker A/P-loop; other site 123214004701 ATP binding site [chemical binding]; other site 123214004702 The catalytic domains of Rad50 are similar to the ATP-binding cassette of ABC transporters, but are not associated with membrane-spanning domains. The conserved ATP-binding motifs common to Rad50 and the ABC transporter family include the Walker A and...; Region: ABC_Rad50; cd03240 123214004703 ABC transporter signature motif; other site 123214004704 Walker B; other site 123214004705 D-loop; other site 123214004706 H-loop/switch region; other site 123214004707 Domain of unknown function DUF77; Region: DUF77; cl00307 123214004708 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 123214004709 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 123214004710 S-adenosylmethionine binding site [chemical binding]; other site 123214004711 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 123214004712 The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; Region: ABC_NikE_OppD_transporters; cd03257 123214004713 Walker A/P-loop; other site 123214004714 ATP binding site [chemical binding]; other site 123214004715 Q-loop/lid; other site 123214004716 ABC transporter signature motif; other site 123214004717 Walker B; other site 123214004718 D-loop; other site 123214004719 H-loop/switch region; other site 123214004720 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 123214004721 Domain of unknown function DUF21; Region: DUF21; pfam01595 123214004722 gliding motility-associated protein GldE; Region: GldE; TIGR03520 123214004723 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 123214004724 Transporter associated domain; Region: CorC_HlyC; cl08393 123214004725 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 123214004726 Domain of unknown function DUF21; Region: DUF21; pfam01595 123214004727 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 123214004728 Transporter associated domain; Region: CorC_HlyC; cl08393 123214004729 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 123214004730 Major Facilitator Superfamily; Region: MFS_1; pfam07690 123214004731 putative substrate translocation pore; other site 123214004732 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; cl15754 123214004733 N-glycosylase/DNA lyase; Provisional; Region: PRK01229 123214004734 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 123214004735 minor groove reading motif; other site 123214004736 helix-hairpin-helix signature motif; other site 123214004737 substrate binding pocket [chemical binding]; other site 123214004738 active site 123214004739 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 123214004740 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 123214004741 HNH endonuclease; Region: HNH_3; pfam13392 123214004742 Helix-turn-helix domains; Region: HTH; cl00088 123214004743 Ribbon-helix-helix protein, copG family; Region: RHH_1; cl15783 123214004744 magnesium Mg(2+) and cobalt Co(2+) transport protein (corA); Region: corA; TIGR00383 123214004745 magnesium/nickel/cobalt transporter CorA; Provisional; Region: PRK11085; cl00459 123214004746 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK07739 123214004747 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; cl15855 123214004748 flagellar hook-associated protein 3; Region: flagell_flgL; TIGR02550 123214004749 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 123214004750 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 123214004751 Flagellar protein FliS; Region: FliS; cl00654 123214004752 Flagellar capping protein [Cell motility and secretion]; Region: FliD; COG1345 123214004753 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 123214004754 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 123214004755 FlaG protein; Region: FlaG; cl00591 123214004756 flagellin; Provisional; Region: PRK12804 123214004757 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 123214004758 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 123214004759 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2604 123214004760 CMP-NeuAc_Synthase activates N-acetylneuraminic acid by adding CMP moiety; Region: CMP-NeuAc_Synthase; cd02513 123214004761 ligand binding site; other site 123214004762 tetramer interface; other site 123214004763 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain associated with the NTP (Nucleotidyl transferase) domain downstream. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently...; Region: CBS_pair_NTP_transferase_assoc; cd04607 123214004764 NTP_trnasferase_like_2 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_2; cd06426 123214004765 Substrate binding site; other site 123214004766 metal-binding site 123214004767 UDP-N-acetyl-D-glucosamine 2-epimerase, UDP-hydrolysing; Region: NeuC_NnaA; TIGR03568 123214004768 Bacterial members of the UDP-N-Acetylglucosamine (GlcNAc) 2-Epimerase family are known to catalyze the reversible interconversion of UDP-GlcNAc and UDP-N-acetylmannosamine (UDP-ManNAc). The enzyme serves to produce an activated form of ManNAc residues; Region: GT1_UDP-GlcNAc_2-Epimerase; cd03786 123214004769 active site 123214004770 homodimer interface [polypeptide binding]; other site 123214004771 PIN domains of VapC and Smg6 ribonucleases, ribosome assembly factor NOB1, Archaeoglobus fulgidus AF0591 protein and homologs; Region: PIN_VapC-Smg6-like; cd09855 123214004772 putative active site [active] 123214004773 N-acetylneuraminate synthase; Region: NeuB_NnaB; TIGR03569 123214004774 NeuB family; Region: NeuB; cl00496 123214004775 SAF domain; Region: SAF; cl00555 123214004776 sugar O-acyltransferase, sialic acid O-acetyltransferase NeuD family; Region: NeuD_NnaD; TIGR03570 123214004777 Putative Acyltransferase (AT), Left-handed parallel beta-Helix (LbH) domain; This group is composed of mostly uncharacterized proteins containing an N-terminal helical subdomain followed by a LbH domain. The alignment contains 6 turns, each containing...; Region: LbH_AT_putative; cd03360 123214004778 putative trimer interface [polypeptide binding]; other site 123214004779 putative CoA binding site [chemical binding]; other site 123214004780 aminotransferase, LLPSF_NHT_00031 family; Region: NHT_00031; TIGR04181 123214004781 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary...; Region: AHBA_syn; cd00616 123214004782 inhibitor-cofactor binding pocket; inhibition site 123214004783 pyridoxal 5'-phosphate binding site [chemical binding]; other site 123214004784 catalytic residue [active] 123214004785 Arna decarboxylase_like, extended (e) SDRs; Region: Arna_like_SDR_e; cd05257 123214004786 NAD dependent epimerase/dehydratase, LLPSF_EDH_00030 family; Region: EDH_00030; TIGR04180 123214004787 NAD binding site [chemical binding]; other site 123214004788 substrate binding site [chemical binding]; other site 123214004789 active site 123214004790 Predicted permeases [General function prediction only]; Region: COG0730; cl00498 123214004791 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 123214004792 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl15769 123214004793 PyridoxaL 5'-Phosphate Dependent Enzymes class IV (PLPDE_IV). This D-amino acid superfamily, one of five classes of PLPDE, consists of branched-chain amino acid aminotransferases (BCAT), D-amino acid transferases (DAAT), and 4-amino-4-deoxychorismate...; Region: PLPDE_IV; cd00449 123214004794 homodimer interface [polypeptide binding]; other site 123214004795 substrate-cofactor binding pocket; other site 123214004796 pyridoxal 5'-phosphate binding site [chemical binding]; other site 123214004797 catalytic residue [active] 123214004798 aspartate kinase; Reviewed; Region: PRK06635 123214004799 AAK_AKii-LysC-BS: Amino Acid Kinase Superfamily (AAK), AKii; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis 168, and the lysine plus threonine-sensitive...; Region: AAK_AKii-LysC-BS; cd04261 123214004800 putative nucleotide binding site [chemical binding]; other site 123214004801 putative catalytic residues [active] 123214004802 putative Mg ion binding site [ion binding]; other site 123214004803 putative aspartate binding site [chemical binding]; other site 123214004804 ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related proteins; Region: ACT_AKii-LysC-BS-like_1; cd04913 123214004805 putative allosteric regulatory site; other site 123214004806 ACT domains of the lysine-sensitive, aspartokinase (AK) isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related domains; Region: ACT_AKii-LysC-BS-like_2; cd04936 123214004807 putative allosteric regulatory residue; other site 123214004808 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 123214004809 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 123214004810 ATP-grasp domain; Region: ATP-grasp_4; cl03087 123214004811 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 123214004812 enolase; Provisional; Region: eno; PRK00077 123214004813 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 123214004814 dimer interface [polypeptide binding]; other site 123214004815 metal binding site [ion binding]; metal-binding site 123214004816 substrate binding pocket [chemical binding]; other site 123214004817 Septum formation initiator; Region: DivIC; cl11433 123214004818 phosphoglycolate phosphatase; Provisional; Region: PRK13222 123214004819 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 123214004820 motif II; other site 123214004821 Ornithine acetyltransferase (OAT) family; also referred to as ArgJ. OAT catalyzes the first and fifth steps in arginine biosynthesis, coupling acetylation of glutamate with deacetylation of N-acetylornithine, which allows recycling of the acetyl group in...; Region: OAT; cd02152 123214004822 heterotetramer interface [polypeptide binding]; other site 123214004823 active site pocket [active] 123214004824 cleavage site 123214004825 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 123214004826 catalytic loop [active] 123214004827 iron binding site [ion binding]; other site 123214004828 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; cl11210 123214004829 NADH dehydrogenase subunit G; Validated; Region: PRK09129 123214004830 4Fe-4S binding domain; Region: Fer4; cl02805 123214004831 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 123214004832 molybdopterin cofactor binding site; other site 123214004833 Uncharacterized ACR, COG1399; Region: DUF177; cl00616 123214004834 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 123214004835 trimer interface [polypeptide binding]; other site 123214004836 active site 123214004837 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 123214004838 YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no...; Region: YjgF_YER057c_UK114_family; cd00448 123214004839 homotrimer interaction site [polypeptide binding]; other site 123214004840 putative active site [active] 123214004841 HisA. Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase catalyzes the fourth step in histidine biosynthesis, an isomerisation of the aminoaldose moiety of ProFAR to the aminoketose of PRFAR (N-(5'-phospho-D-1...; Region: HisA; cd04732 123214004842 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase; Region: TIGR00007 123214004843 catalytic residues [active] 123214004844 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 123214004845 Thymidylate synthase complementing protein; Region: Thy1; cl03630 123214004846 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 123214004847 Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]; Region: COG3434 123214004848 Macro domain, Appr-1'-pase_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose...; Region: Macro_Appr_pase_like; cd02908 123214004849 putative ADP-ribose binding site [chemical binding]; other site 123214004850 putative active site [active] 123214004851 Restriction endonuclease; Region: Mrr_cat; cl00516 123214004852 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 123214004853 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 123214004854 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 123214004855 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214004856 metal binding site [ion binding]; metal-binding site 123214004857 active site 123214004858 I-site; other site 123214004859 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 123214004860 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK12879 123214004861 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl00284 123214004862 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 123214004863 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 123214004864 GTP binding site; other site 123214004865 Outer membrane efflux protein; Region: OEP; pfam02321 123214004866 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 123214004867 metal binding site 2 [ion binding]; metal-binding site 123214004868 putative DNA binding helix; other site 123214004869 metal binding site 1 [ion binding]; metal-binding site 123214004870 dimer interface [polypeptide binding]; other site 123214004871 structural Zn2+ binding site [ion binding]; other site 123214004872 Flavin Reductases; Region: FlaRed; cl00801 123214004873 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 123214004874 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 123214004875 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 123214004876 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 123214004877 Outer membrane protein/protective antigen OMA87 [Cell envelope biogenesis, outer membrane]; Region: COG4775 123214004878 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 123214004879 Surface antigen; Region: Bac_surface_Ag; cl03097 123214004880 4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family [Cell envelope biogenesis, outer membrane]; Region: ArnT; COG1807 123214004881 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl15769 123214004882 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 123214004883 dimer interface [polypeptide binding]; other site 123214004884 substrate binding site [chemical binding]; other site 123214004885 ATP binding site [chemical binding]; other site 123214004886 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 123214004887 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 123214004888 active site 123214004889 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 123214004890 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 123214004891 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 123214004892 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214004893 pheromone autoinducer 2 transporter; Reviewed; Region: tqsA; cl00465 123214004894 S-adenosylmethionine decarboxylase; Region: AdoMet_dc; cl00687 123214004895 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]; Region: MetH; cl14105 123214004896 5-methyltetrahydrofolate--homocysteine methyltransferase; Region: metH; TIGR02082 123214004897 MeTr subgroup of pterin binding enzymes. This family includes cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). Cobalamin-dependent...; Region: MeTr; cd00740 123214004898 substrate binding pocket [chemical binding]; other site 123214004899 B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase; Region: B12-binding_like; cl00293 123214004900 B12 binding site [chemical binding]; other site 123214004901 Vitamin B12 dependent methionine synthase, activation domain; Region: Met_synt_B12; pfam02965 123214004902 Protein of unknown function (DUF523); Region: DUF523; cl00733 123214004903 Ferrochelatase; Region: Ferrochelatase; pfam00762 123214004904 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 123214004905 C-terminal domain interface [polypeptide binding]; other site 123214004906 active site 123214004907 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 123214004908 active site 123214004909 N-terminal domain interface [polypeptide binding]; other site 123214004910 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 123214004911 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 123214004912 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 123214004913 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; cl00148 123214004914 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 123214004915 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 123214004916 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 123214004917 DNA binding residues [nucleotide binding] 123214004918 DNA primase, catalytic core; Region: dnaG; TIGR01391 123214004919 CHC2 zinc finger; Region: zf-CHC2; cl15369 123214004920 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 123214004921 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 123214004922 active site 123214004923 metal binding site [ion binding]; metal-binding site 123214004924 interdomain interaction site; other site 123214004925 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 123214004926 dihydropteroate synthase; Region: DHPS; TIGR01496 123214004927 substrate binding pocket [chemical binding]; other site 123214004928 dimer interface [polypeptide binding]; other site 123214004929 inhibitor binding site; inhibition site 123214004930 TIGR00159 family protein; Region: TIGR00159 123214004931 DisA bacterial checkpoint controller nucleotide-binding; Region: DisA_N; pfam02457 123214004932 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 123214004933 TGS _ThrRS_N: ThrRS (threonyl-tRNA Synthetase) is a class II tRNA synthetase that couples threonine to its cognate tRNA. In addition to its catalytic and anticodon-binding domains, ThrRS has an N-terminal TGS domain, named after the ThrRS, GTPase, and...; Region: TGS_ThrRS_N; cd01667 123214004934 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 123214004935 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 123214004936 active site 123214004937 dimer interface [polypeptide binding]; other site 123214004938 motif 1; other site 123214004939 motif 2; other site 123214004940 motif 3; other site 123214004941 ThrRS Threonyl-anticodon binding domain. ThrRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is...; Region: ThrRS_anticodon; cd00860 123214004942 anticodon binding site; other site 123214004943 phosphate regulon transcriptional regulatory protein PhoB; Region: PhoB; TIGR02154 123214004944 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 123214004945 active site 123214004946 phosphorylation site [posttranslational modification] 123214004947 intermolecular recognition site; other site 123214004948 dimerization interface [polypeptide binding]; other site 123214004949 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 123214004950 DNA binding site [nucleotide binding] 123214004951 Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19; Region: ALDH_F18-19_ProA-GPR; cd07079 123214004952 gamma-glutamyl phosphate reductase; Region: proA; TIGR00407 123214004953 putative catalytic cysteine [active] 123214004954 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 123214004955 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 123214004956 ligand binding site [chemical binding]; other site 123214004957 flexible hinge region; other site 123214004958 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 123214004959 putative switch regulator; other site 123214004960 non-specific DNA interactions [nucleotide binding]; other site 123214004961 DNA binding site [nucleotide binding] 123214004962 sequence specific DNA binding site [nucleotide binding]; other site 123214004963 putative cAMP binding site [chemical binding]; other site 123214004964 Ketopantoate hydroxymethyltransferase (KPHMT) is the first enzyme in the pantothenate biosynthesis pathway. Ketopantoate hydroxymethyltransferase (KPHMT) catalyzes the first committed step in the biosynthesis of pantothenate (vitamin B5), which is a...; Region: KPHMT-like; cd06557 123214004965 oligomerization interface [polypeptide binding]; other site 123214004966 active site 123214004967 metal binding site [ion binding]; metal-binding site 123214004968 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 123214004969 Malic enzyme [Energy production and conversion]; Region: SfcA; COG0281 123214004970 Malic enzyme, N-terminal domain; Region: malic; pfam00390 123214004971 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 123214004972 putative NAD(P) binding site [chemical binding]; other site 123214004973 S-adenosylmethionine decarboxylase; Region: AdoMet_dc; cl00687 123214004974 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional; Region: PRK05222 123214004975 CIMS - Cobalamine-independent methonine synthase, or MetE, N-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme...; Region: CIMS_N_terminal_like; cd03312 123214004976 THF binding site; other site 123214004977 CIMS - Cobalamine-independent methonine synthase, or MetE, C-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme...; Region: CIMS_C_terminal_like; cd03311 123214004978 substrate binding site [chemical binding]; other site 123214004979 THF binding site; other site 123214004980 zinc-binding site [ion binding]; other site 123214004981 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 123214004982 metal binding site 2 [ion binding]; metal-binding site 123214004983 putative DNA binding helix; other site 123214004984 metal binding site 1 [ion binding]; metal-binding site 123214004985 dimer interface [polypeptide binding]; other site 123214004986 structural Zn2+ binding site [ion binding]; other site 123214004987 Outer membrane cobalamin receptor protein [Coenzyme metabolism]; Region: BtuB; COG4206 123214004988 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 123214004989 N-terminal plug; other site 123214004990 ligand-binding site [chemical binding]; other site 123214004991 Protein of unknown function, DUF481; Region: DUF481; cl01213 123214004992 Putative F0F1-ATPase subunit (ATPase_gene1); Region: ATPase_gene1; cl09754 123214004993 ATP synthase, Delta/Epsilon chain, beta-sandwich domain; Region: ATP-synt_DE_N; cl10033 123214004994 alternate F1F0 ATPase, F1 subunit epsilon; Region: alt_F1F0_F1_eps; TIGR03166 123214004995 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 123214004996 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 123214004997 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 123214004998 alpha subunit interaction interface [polypeptide binding]; other site 123214004999 Walker A motif; other site 123214005000 ATP binding site [chemical binding]; other site 123214005001 Walker B motif; other site 123214005002 inhibitor binding site; inhibition site 123214005003 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 123214005004 F0F1 ATP synthase subunit gamma; Provisional; Region: PRK13422 123214005005 ATP synthase; Region: ATP-synt; cl00365 123214005006 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 123214005007 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 123214005008 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 123214005009 Walker A motif; other site 123214005010 ATP binding site [chemical binding]; other site 123214005011 Walker B motif; other site 123214005012 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 123214005013 Plant ATP synthase F0; Region: YMF19; cl07975 123214005014 ATP synthase B/B' CF(0); Region: ATP-synt_B; pfam00430 123214005015 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 123214005016 Plant ATP synthase F0; Region: YMF19; cl07975 123214005017 ATP synthase subunit C; Region: ATP-synt_C; cl00466 123214005018 ATP synthase A chain; Region: ATP-synt_A; cl00413 123214005019 N-ATPase, AtpR subunit; Region: AtpR; cl11871 123214005020 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 123214005021 transketolase; Reviewed; Region: PRK05899 123214005022 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 123214005023 TPP-binding site [chemical binding]; other site 123214005024 dimer interface [polypeptide binding]; other site 123214005025 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 123214005026 PYR/PP interface [polypeptide binding]; other site 123214005027 dimer interface [polypeptide binding]; other site 123214005028 TPP binding site [chemical binding]; other site 123214005029 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 123214005030 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 123214005031 PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of...; Region: PseudoU_synth; cl00130 123214005032 tRNA pseudouridine synthase D (TruD); Region: TruD; pfam01142 123214005033 active site 123214005034 Protein of unknown function (DUF507); Region: DUF507; cl01112 123214005035 ADP-glucose phosphorylase; Region: PLN02643 123214005036 Galactose-1-phosphate uridyl transferase (GalT): This enzyme plays a key role in galactose metabolism by catalysing the transfer of a uridine 5'-phosphoryl group from UDP-galactose 1-phosphate. The structure of E.coli GalT reveals that the enzyme...; Region: GalT; cd00608 123214005037 dimer interface [polypeptide binding]; other site 123214005038 active site 123214005039 dUTPase; Region: dUTPase_2; pfam08761 123214005040 Serine dehydrogenase proteinase; Region: SDH_sah; pfam01972 123214005041 Caseinolytic protease (ClpP) is an ATP-dependent protease; Region: Clp_protease_like; cl15763 123214005042 active site 123214005043 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK10792 123214005044 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 123214005045 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 123214005046 homodimer interface [polypeptide binding]; other site 123214005047 NADP binding site [chemical binding]; other site 123214005048 substrate binding site [chemical binding]; other site 123214005049 ATP citrate (pro-S)-lyase; Region: PLN02522 123214005050 CoA-ligase; Region: Ligase_CoA; cl02894 123214005051 Citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CCL cleaves citryl-CoA (CiCoA) to acetyl-CoA (AcCoA) and oxaloacetate (OAA); Region: CCL_ACL-C; cd06100 123214005052 active site 123214005053 oxalacetate binding site [chemical binding]; other site 123214005054 citrylCoA binding site [chemical binding]; other site 123214005055 coenzyme A binding site [chemical binding]; other site 123214005056 catalytic triad [active] 123214005057 ATP citrate (pro-S)-lyase; Region: PLN02235 123214005058 ATP-grasp domain; Region: ATP-grasp_4; cl03087 123214005059 Monomeric isocitrate dehydrogenase; Region: IDH; cl15383 123214005060 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 123214005061 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 123214005062 substrate binding site [chemical binding]; other site 123214005063 ligand binding site [chemical binding]; other site 123214005064 Protein of unknown function (DUF2892); Region: DUF2892; pfam11127 123214005065 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 123214005066 YceG-like family; Region: YceG; pfam02618 123214005067 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 123214005068 dimerization interface [polypeptide binding]; other site 123214005069 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 123214005070 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 123214005071 EPSP synthase domain. 3-phosphoshikimate 1-carboxyvinyltransferase (5-enolpyruvylshikimate-3-phosphate synthase) (EC 2.5.1.19) catalyses the reaction between shikimate-3-phosphate (S3P) and phosphoenolpyruvate (PEP) to form...; Region: EPSP_synthase; cd01556 123214005072 3-phosphoshikimate 1-carboxyvinyltransferase; Region: aroA; TIGR01356 123214005073 hinge; other site 123214005074 active site 123214005075 putative secretion ATPase, PEP-CTERM locus subfamily; Region: pepcterm_ATPase; TIGR03015 123214005076 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 123214005077 Walker A motif; other site 123214005078 ATP binding site [chemical binding]; other site 123214005079 Walker B motif; other site 123214005080 arginine finger; other site 123214005081 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1934 123214005082 OstA-like protein; Region: OstA; cl00844 123214005083 Lipopolysaccharide-assembly, LptC-related; Region: LptC; pfam06835 123214005084 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 123214005085 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 123214005086 tRNA; other site 123214005087 putative tRNA binding site [nucleotide binding]; other site 123214005088 putative NADP binding site [chemical binding]; other site 123214005089 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 123214005090 Sodium:neurotransmitter symporter family; Region: SNF; cl11976 123214005091 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 123214005092 active site 123214005093 multimer interface [polypeptide binding]; other site 123214005094 Domain of unknown function (DUF4149); Region: DUF4149; pfam13664 123214005095 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 123214005096 dimerization interface [polypeptide binding]; other site 123214005097 Roadblock/LC7 domain; Region: Robl_LC7; cl00886 123214005098 Domain of unknown function (DUF4388); Region: DUF4388; pfam14332 123214005099 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cd00882 123214005100 Conserved hypothetical ATP binding protein; Region: ATP_bind_1; pfam03029 123214005101 G1 box; other site 123214005102 GTP/Mg2+ binding site [chemical binding]; other site 123214005103 G2 box; other site 123214005104 Switch I region; other site 123214005105 G3 box; other site 123214005106 Switch II region; other site 123214005107 G4 box; other site 123214005108 G5 box; other site 123214005109 N-ethylammeline chlorohydrolase; Provisional; Region: PRK06038 123214005110 TRZ/ATZ family contains enzymes from the atrazine degradation pathway and related hydrolases. Atrazine, a chlorinated herbizide, can be catabolized by a variety of different bacteria. The first three steps of the atrazine dehalogenation pathway are...; Region: ATZ_TRZ_like; cd01298 123214005111 active site 123214005112 putative substrate binding pocket [chemical binding]; other site 123214005113 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 123214005114 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 123214005115 FtsX-like permease family; Region: FtsX; cl15850 123214005116 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 123214005117 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 123214005118 Walker A/P-loop; other site 123214005119 ATP binding site [chemical binding]; other site 123214005120 Q-loop/lid; other site 123214005121 ABC transporter signature motif; other site 123214005122 Walker B; other site 123214005123 D-loop; other site 123214005124 H-loop/switch region; other site 123214005125 Clp protease ATP binding subunit; Region: clpC; CHL00095 123214005126 Clp amino terminal domain; Region: Clp_N; pfam02861 123214005127 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 123214005128 Walker A motif; other site 123214005129 ATP binding site [chemical binding]; other site 123214005130 Walker B motif; other site 123214005131 arginine finger; other site 123214005132 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 123214005133 Walker A motif; other site 123214005134 ATP binding site [chemical binding]; other site 123214005135 Walker B motif; other site 123214005136 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 123214005137 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 123214005138 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 123214005139 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 123214005140 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 123214005141 Surface antigen; Region: Bac_surface_Ag; cl03097 123214005142 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 123214005143 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 123214005144 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 123214005145 UDP-3-O-acyl-glucosamine N-acyltransferase (LpxD): The enzyme catalyzes the transfer of 3-hydroxymyristic acid or 3-hydroxy-arachidic acid, depending on the organism, from the acyl carrier protein (ACP) to UDP-3-O-acyl-glucosamine to produce UDP-2; Region: LbH_LpxD; cd03352 123214005146 trimer interface [polypeptide binding]; other site 123214005147 active site 123214005148 UDP-GlcNAc binding site [chemical binding]; other site 123214005149 lipid binding site [chemical binding]; lipid-binding site 123214005150 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 123214005151 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 123214005152 catalytic residues [active] 123214005153 Succinate dehydrogenase/fumarate reductase, Fe-S protein subunit [Energy production and conversion]; Region: FrdB; COG0479 123214005154 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 123214005155 Domain of unknown function DUF20; Region: UPF0118; pfam01594 123214005156 pheromone autoinducer 2 transporter; Reviewed; Region: tqsA; cl00465 123214005157 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 123214005158 UDP-glucuronate decarboxylase (UGD) and related proteins, extended (e) SDRs; Region: UGD_SDR_e; cd05230 123214005159 NAD binding site [chemical binding]; other site 123214005160 putative substrate binding site 2 [chemical binding]; other site 123214005161 putative substrate binding site 1 [chemical binding]; other site 123214005162 active site 123214005163 NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]; Region: Ndh; COG1252 123214005164 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 123214005165 DhnA-type fructose-1,6-bisphosphate aldolase and related enzymes [Carbohydrate transport and metabolism]; Region: FbaB; COG1830 123214005166 Class I fructose-1,6-bisphosphate (FBP) aldolases of the archaeal type (DhnA homologs); Region: DhnA; cd00958 123214005167 putative active site; other site 123214005168 catalytic residue [active] 123214005169 Protein of unknown function (DUF1049); Region: DUF1049; cl01539 123214005170 FHIT (fragile histidine family): FHIT proteins, related to the HIT family carry a motif HxHxH/Qxx (x, is a hydrophobic amino acid), On the basis of sequence, substrate specificity, structure, evolution and mechanism, HIT proteins are classified into...; Region: FHIT; cd01275 123214005171 nucleotide binding site/active site [active] 123214005172 HIT family signature motif; other site 123214005173 catalytic residue [active] 123214005174 Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]; Region: PriA; COG1198 123214005175 Protease HslV and the ATPase/chaperone HslU are part of an ATP-dependent proteolytic system that is the prokaryotic homolog of the proteasome. HslV is a dimer of hexamers (a dodecamer) that forms a central proteolytic chamber with active sites on the...; Region: protease_HslV; cd01913 123214005176 active site 123214005177 HslU subunit interaction site [polypeptide binding]; other site 123214005178 NlpC/P60 family; Region: NLPC_P60; cl11438 123214005179 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 123214005180 S-adenosylmethionine binding site [chemical binding]; other site 123214005181 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 123214005182 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 123214005183 active site 123214005184 (T/H)XGH motif; other site 123214005185 Lipopolysaccharide-assembly; Region: LptE; cl01125 123214005186 DNA polymerase III, delta subunit [DNA replication, recombination, and repair]; Region: HolA; COG1466 123214005187 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 123214005188 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 123214005189 Walker A motif; other site 123214005190 ATP binding site [chemical binding]; other site 123214005191 Walker B motif; other site 123214005192 arginine finger; other site 123214005193 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 123214005194 Quinolinate synthetase A protein; Region: NadA; cl00420 123214005195 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cl00125 123214005196 active site residue [active] 123214005197 FAD binding domain; Region: FAD_binding_4; pfam01565 123214005198 glycolate oxidase, subunit GlcD; Region: glcD; TIGR00387 123214005199 CRISPR/Cas system-associated RAMP superfamily protein Cas6; Region: Cas6-I-III; cd09652 123214005200 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 123214005201 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214005202 metal binding site [ion binding]; metal-binding site 123214005203 active site 123214005204 I-site; other site 123214005205 M28 Zn-Peptidases; Region: M28_like_1; cd05640 123214005206 metal binding site [ion binding]; metal-binding site 123214005207 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl15774 123214005208 octamerization interface [polypeptide binding]; other site 123214005209 diferric-oxygen binding site [ion binding]; other site 123214005210 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 123214005211 S-adenosylmethionine binding site [chemical binding]; other site 123214005212 ATP-dependent nuclease, subunit B [DNA replication, recombination, and repair]; Region: AddB; COG3857 123214005213 Inactivated superfamily I helicase [DNA replication, recombination, and repair]; Region: COG3893 123214005214 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 123214005215 phage tail tape measure protein, TP901 family, core region; Region: tape_meas_TP901; TIGR01760 123214005216 Phage-related protein [Function unknown]; Region: COG5412 123214005217 Phage virion morphogenesis family; Region: Phage_tail_S; cl02089 123214005218 Phage portal protein, SPP1 Gp6-like; Region: Phage_prot_Gp6; pfam05133 123214005219 Prominin; Region: Prominin; pfam05478 123214005220 Phage Mu protein F like protein; Region: Phage_Mu_F; cl10072 123214005221 Uncharacterized conserved protein (DUF2190); Region: DUF2190; cl02289 123214005222 RecT family; Region: RecT; cl04285 123214005223 YopX protein; Region: YopX; cl09859 123214005224 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 123214005225 IHF - DNA interface [nucleotide binding]; other site 123214005226 IHF dimer interface [polypeptide binding]; other site 123214005227 DNA replication protein [DNA replication, recombination, and repair]; Region: DnaC; COG1484 123214005228 AAA domain; Region: AAA_22; pfam13401 123214005229 Helix-turn-helix domains; Region: HTH; cl00088 123214005230 Integrase core domain; Region: rve; cl01316 123214005231 Mu transposase, C-terminal; Region: Mu-transpos_C; pfam09299 123214005232 ParB-like nuclease domain; Region: ParBc; cl02129 123214005233 Helix-turn-helix domains; Region: HTH; cl00088 123214005234 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 123214005235 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 123214005236 non-specific DNA binding site [nucleotide binding]; other site 123214005237 salt bridge; other site 123214005238 sequence-specific DNA binding site [nucleotide binding]; other site 123214005239 Chalcone-flavanone isomerase; Region: Chalcone; cl03589 123214005240 Baseplate J-like protein; Region: Baseplate_J; cl01294 123214005241 Superfamily of nucleases including Short Patch Repair (Vsr) Endonucleases, archaeal Holliday junction resolvases, MutH methy-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and...; Region: Restriction_endonuclease_like; cl00277 123214005242 putative active site [active] 123214005243 flagellar capping protein; Provisional; Region: PRK12765 123214005244 Terminase-like family; Region: Terminase_6; pfam03237 123214005245 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5410 123214005246 Phage-related terminase [General function prediction only]; Region: COG5362; cl02216 123214005247 Protein of unknown function (DUF2586); Region: DUF2586; pfam10758 123214005248 Protein of unknown function (DUF2597); Region: DUF2597; pfam10772 123214005249 Phage tail protein (Tail_P2_I); Region: Tail_P2_I; cl01817 123214005250 Phage tail-collar fibre protein; Region: DUF3751; pfam12571 123214005251 Protein of unknown function (DUF3380); Region: DUF3380; pfam11860 123214005252 Phosphoheptose isomerase is a member of the SIS (Sugar ISomerase) superfamily. Phosphoheptose isomerase catalyzes the isomerization of sedoheptulose 7-phosphate into D-glycero-D-mannoheptose 7-phosphate. This is the first step of the biosynthesis of...; Region: SIS_GmhA; cd05006 123214005253 dimer interface [polypeptide binding]; other site 123214005254 active site 123214005255 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 123214005256 psp operon transcriptional activator PspF; Region: phageshock_pspF; TIGR02974 123214005257 Walker A motif; other site 123214005258 ATP binding site [chemical binding]; other site 123214005259 Walker B motif; other site 123214005260 arginine finger; other site 123214005261 Helix-turn-helix domains; Region: HTH; cl00088 123214005262 TPR repeat; Region: TPR_11; pfam13414 123214005263 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 123214005264 binding surface 123214005265 TPR motif; other site 123214005266 Major Facilitator Superfamily; Region: MFS_1; pfam07690 123214005267 HerA helicase [Replication, recombination, and repair]; Region: COG0433 123214005268 Domain of unknown function DUF87; Region: DUF87; pfam01935 123214005269 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 123214005270 active site 123214005271 Protein of unknown function (DUF3365); Region: DUF3365; pfam11845 123214005272 Protein of unknown function (DUF1271); Region: DUF1271; cl01443 123214005273 Ferredoxin [Energy production and conversion]; Region: Fer; COG1141 123214005274 Coproporphyrinogen III oxidase and related Fe-S oxidoreductases [Coenzyme metabolism]; Region: HemN; COG0635 123214005275 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 123214005276 FeS/SAM binding site; other site 123214005277 HemN C-terminal domain; Region: HemN_C; pfam06969 123214005278 decaheme c-type cytochrome, DmsE family; Region: decahem_SO; TIGR03508 123214005279 Doubled CXXCH motif (Paired_CXXCH_1); Region: Paired_CXXCH_1; cl09905 123214005280 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 123214005281 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 123214005282 nucleotide binding pocket [chemical binding]; other site 123214005283 K-X-D-G motif; other site 123214005284 catalytic site [active] 123214005285 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 123214005286 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 123214005287 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 123214005288 Dimer interface [polypeptide binding]; other site 123214005289 BRCT sequence motif; other site 123214005290 2-deoxyribose-5-phosphate aldolase (DERA) of the DeoC family; Region: DeoC; cd00959 123214005291 intersubunit interface [polypeptide binding]; other site 123214005292 active site 123214005293 catalytic residue [active] 123214005294 Ribosomal protein L11 methylase [Translation, ribosomal structure and biogenesis]; Region: PrmA; COG2264 123214005295 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 123214005296 S-adenosylmethionine binding site [chemical binding]; other site 123214005297 Helix-Turn-Helix DNA binding domain of the HspR transcription regulator; Region: HTH_HspR; cd04766 123214005298 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 123214005299 DNA binding residues [nucleotide binding] 123214005300 chaperone protein DnaJ; Provisional; Region: PRK14291 123214005301 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 123214005302 HSP70 interaction site [polypeptide binding]; other site 123214005303 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 123214005304 substrate binding site [polypeptide binding]; other site 123214005305 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 123214005306 Zn binding sites [ion binding]; other site 123214005307 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 123214005308 dimer interface [polypeptide binding]; other site 123214005309 Histidinol dehydrogenase, HisD, E.C 1.1.1.23. Histidinol dehydrogenase catalyzes the last two steps in the L-histidine biosynthesis pathway, which is conserved in bacteria, archaea, fungi, and plants. These last two steps are (i) the NAD-dependent...; Region: Histidinol_dh; cd06572 123214005310 histidinol dehydrogenase; Region: hisD; TIGR00069 123214005311 NAD binding site [chemical binding]; other site 123214005312 dimerization interface [polypeptide binding]; other site 123214005313 product binding site; other site 123214005314 substrate binding site [chemical binding]; other site 123214005315 zinc binding site [ion binding]; other site 123214005316 catalytic residues [active] 123214005317 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 123214005318 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 123214005319 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 123214005320 Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes. In E. coli, the synthesis of Moco involves genes from several loci: moa; Region: MobB; cd03116 123214005321 Walker A motif; other site 123214005322 Acylphosphatase; Region: Acylphosphatase; cl00551 123214005323 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 123214005324 putative peptidoglycan binding site; other site 123214005325 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 123214005326 putative peptidoglycan binding site; other site 123214005327 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 123214005328 putative peptidoglycan binding site; other site 123214005329 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 123214005330 putative peptidoglycan binding site; other site 123214005331 Peptidase family M23; Region: Peptidase_M23; pfam01551 123214005332 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 123214005333 aminotransferase; Validated; Region: PRK08175 123214005334 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 123214005335 pyridoxal 5'-phosphate binding site [chemical binding]; other site 123214005336 homodimer interface [polypeptide binding]; other site 123214005337 catalytic residue [active] 123214005338 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 123214005339 The ABC transporters belonging to the YhbG family are similar to members of the Mj1267_LivG family, which is involved in the transport of branched-chain amino acids. The genes yhbG and yhbN are located in a single operon and may function together in...; Region: ABC_YhbG; cd03218 123214005340 Walker A/P-loop; other site 123214005341 ATP binding site [chemical binding]; other site 123214005342 Q-loop/lid; other site 123214005343 ABC transporter signature motif; other site 123214005344 Walker B; other site 123214005345 D-loop; other site 123214005346 H-loop/switch region; other site 123214005347 6-carboxyhexanoate--CoA ligase; Region: BioW; cl00625 123214005348 Pimeloyl-CoA synthetase [Coenzyme metabolism]; Region: BioW; COG1424 123214005349 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 123214005350 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 123214005351 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 123214005352 S-adenosylmethionine binding site [chemical binding]; other site 123214005353 Protein of unknown function (DUF433); Region: DUF433; cl01030 123214005354 PIN domain of ribonucleases (toxins), VapC and FitB, of prokaryotic toxin/antitoxin operons, Pyrococcus horikoshii protein PH0500, and other similar bacterial and archaeal homologs; Region: PIN_VapC-FitB; cd09881 123214005355 oligomeric interface; other site 123214005356 putative active site [active] 123214005357 homodimer interface [polypeptide binding]; other site 123214005358 Uncharacterized protein family (UPF0175); Region: UPF0175; cl01085 123214005359 Domain of unknown function (DUF3368); Region: DUF3368; pfam11848 123214005360 PIN (PilT N terminus) domain: Superfamily; Region: PIN_SF; cl14812 123214005361 putative active site [active] 123214005362 Antidote-toxin recognition MazE; Region: Antitoxin-MazE; cl00877 123214005363 PIN domain of ribonucleases (toxins), VapC and FitB, of prokaryotic toxin/antitoxin operons, Pyrococcus horikoshii protein PH0500, and other similar bacterial and archaeal homologs; Region: PIN_VapC-FitB; cd09881 123214005364 oligomeric interface; other site 123214005365 putative active site [active] 123214005366 homodimer interface [polypeptide binding]; other site 123214005367 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 123214005368 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214005369 metal binding site [ion binding]; metal-binding site 123214005370 active site 123214005371 I-site; other site 123214005372 Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II); Region: Aldolase_II; cl00214 123214005373 intersubunit interface [polypeptide binding]; other site 123214005374 active site 123214005375 Zn2+ binding site [ion binding]; other site 123214005376 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1791 123214005377 Cupin domain; Region: Cupin_2; cl09118 123214005378 Enoyl-[acyl-carrier-protein]; Region: FabI; COG0623 123214005379 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 123214005380 NAD binding site [chemical binding]; other site 123214005381 homotetramer interface [polypeptide binding]; other site 123214005382 homodimer interface [polypeptide binding]; other site 123214005383 substrate binding site [chemical binding]; other site 123214005384 active site 123214005385 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 123214005386 thiS-thiF/thiG interaction site; other site 123214005387 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 123214005388 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 123214005389 dimer interface [polypeptide binding]; other site 123214005390 motif 1; other site 123214005391 active site 123214005392 motif 2; other site 123214005393 motif 3; other site 123214005394 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 123214005395 anticodon binding site; other site 123214005396 Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the...; Region: Hemerythrin; cl15774 123214005397 octamerization interface [polypeptide binding]; other site 123214005398 diferric-oxygen binding site [ion binding]; other site 123214005399 tRNA-guanine transglycosylases, various specificities; Region: tgt_general; TIGR00449 123214005400 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; cl00409 123214005401 Uncharacterized conserved protein [Function unknown]; Region: COG1432 123214005402 LabA_like proteins; Region: LabA_like/DUF88; cl10034 123214005403 putative metal binding site [ion binding]; other site 123214005404 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 123214005405 Histone deacetylase domain; Region: Hist_deacetyl; cl02986 123214005406 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 123214005407 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 123214005408 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 123214005409 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 123214005410 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 123214005411 metal binding site [ion binding]; metal-binding site 123214005412 active site 123214005413 I-site; other site 123214005414 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 123214005415 TonB-dependent Receptor Plug Domain; Region: Plug; cl08461 123214005416 Domain of unknown function DUF302; Region: DUF302; cl01364 123214005417 Thermus thermophilus SoxB and related proteins, N-terminal metallophosphatase domain; Region: MPP_SoxB_N; cd07411 123214005418 active site 123214005419 metal binding site [ion binding]; metal-binding site 123214005420 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases [Nucleotide transport and metabolism]; Region: UshA; COG0737 123214005421 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 123214005422 Cytochrome c [Energy production and conversion]; Region: COG3258 123214005423 Cytochrome c [Energy production and conversion]; Region: COG3258 123214005424 Sulphur oxidation protein SoxZ; Region: SoxZ; pfam08770 123214005425 Superoxide reductase-like (SORL) domain; present in a family of mononuclear non-heme iron proteins that includes superoxide reductase and desulfoferrodoxin. Superoxide reductase-like proteins scavenge superoxide anion radicals as a defense mechanism...; Region: SORL; cl00014 123214005426 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 123214005427 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 123214005428 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 123214005429 active site 123214005430 phosphorylation site [posttranslational modification] 123214005431 intermolecular recognition site; other site 123214005432 dimerization interface [polypeptide binding]; other site 123214005433 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 123214005434 Walker A motif; other site 123214005435 ATP binding site [chemical binding]; other site 123214005436 Walker B motif; other site 123214005437 arginine finger; other site 123214005438 Helix-turn-helix domains; Region: HTH; cl00088 123214005439 DsrE/DsrF-like family; Region: DrsE; cl00672 123214005440 NMT1-like family; Region: NMT1_2; cl15260 123214005441 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; pfam12974 123214005442 TPR repeat; Region: TPR_11; pfam13414 123214005443 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 123214005444 N-acetyl-D-glucosamine binding site [chemical binding]; other site 123214005445 catalytic residue [active] 123214005446 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 123214005447 Lumazine binding domain; Region: Lum_binding; pfam00677 123214005448 Lumazine binding domain; Region: Lum_binding; pfam00677 123214005449 Ion channel; Region: Ion_trans_2; cl11596 123214005450 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 123214005451 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214005452 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl15357 123214005453 ATP-dependent DNA ligase; Provisional; Region: PRK01109 123214005454 Adenylation domain of archaeal and bacterial LigB-like DNA ligases; Region: Adenylation_DNA_ligase_Arch_LigB; cd07901 123214005455 active site 123214005456 DNA binding site [nucleotide binding] 123214005457 The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase I is a DNA-binding module that is part of the catalytic core unit; Region: OBF_DNA_ligase_I; cd07969 123214005458 DNA binding site [nucleotide binding] 123214005459 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 123214005460 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214005461 multifunctional aminopeptidase A; Provisional; Region: PRK00913 123214005462 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 123214005463 interface (dimer of trimers) [polypeptide binding]; other site 123214005464 Substrate-binding/catalytic site; other site 123214005465 Zn-binding sites [ion binding]; other site 123214005466 Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the...; Region: cond_enzymes; cl09938 123214005467 Predicted naringenin-chalcone synthase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: BcsA; COG3424 123214005468 active site 123214005469 Superoxide reductase-like (SORL) domain; present in a family of mononuclear non-heme iron proteins that includes superoxide reductase and desulfoferrodoxin. Superoxide reductase-like proteins scavenge superoxide anion radicals as a defense mechanism...; Region: SORL; cl00014 123214005470 non-heme iron binding site [ion binding]; other site 123214005471 riboflavin biosynthesis protein RibD; Region: eubact_ribD; TIGR00326 123214005472 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 123214005473 catalytic motif [active] 123214005474 Zn binding site [ion binding]; other site 123214005475 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 123214005476 Nucleotidyltransferase (NT) domain of family X DNA Polymerases; Region: NT_POLXc; cd00141 123214005477 hypothetical protein; Provisional; Region: PRK08609 123214005478 active site 123214005479 primer binding site [nucleotide binding]; other site 123214005480 NTP binding site [chemical binding]; other site 123214005481 metal binding triad [ion binding]; metal-binding site 123214005482 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 123214005483 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 123214005484 HIGH motif; other site 123214005485 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 123214005486 active site 123214005487 KMSKS motif; other site 123214005488 Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr; Region: PTPc; cl00053 123214005489 active site 123214005490 catalytic residues [active] 123214005491 Domain of unknown function (DUF305); Region: DUF305; cl15795 123214005492 CRISPR/Cas system-associated RAMP superfamily protein Cas6; Region: Cas6-I-III; cl11443 123214005493 CRISPR/Cas system-associated RAMP superfamily protein Cas6; Region: Cas6-I-III; cl11443 123214005494 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 123214005495 sulfate ABC transporter, ATP-binding protein; Region: 3a0106s01; TIGR00968 123214005496 Walker A/P-loop; other site 123214005497 ATP binding site [chemical binding]; other site 123214005498 Q-loop/lid; other site 123214005499 ABC transporter signature motif; other site 123214005500 Walker B; other site 123214005501 D-loop; other site 123214005502 H-loop/switch region; other site 123214005503 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 123214005504 dimer interface [polypeptide binding]; other site 123214005505 conserved gate region; other site 123214005506 putative PBP binding loops; other site 123214005507 ABC-ATPase subunit interface; other site 123214005508 TOBE domain; Region: TOBE_2; cl01440 123214005509 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 123214005510 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 123214005511 Helix-turn-helix domains; Region: HTH; cl00088 123214005512 DNA-binding transcriptional regulator ModE; Provisional; Region: PRK10676 123214005513 TOBE domain; Region: TOBE_2; cl01440 123214005514 TOBE domain; Region: TOBE_2; cl01440 123214005515 Myo-inositol-1-phosphate synthase; Region: NAD_binding_5; cl00554 123214005516 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 123214005517 active site 123214005518 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 123214005519 chromosome segregation protein SMC, primarily archaeal type; Region: SMC_prok_A; TIGR02169 123214005520 Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large; Region: ABC_SMC_barmotin; cd03278 123214005521 Walker A/P-loop; other site 123214005522 ATP binding site [chemical binding]; other site 123214005523 Q-loop/lid; other site 123214005524 SMC proteins Flexible Hinge Domain; Region: SMC_hinge; cl05797 123214005525 Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large; Region: ABC_SMC_barmotin; cd03278 123214005526 ABC transporter signature motif; other site 123214005527 Walker B; other site 123214005528 D-loop; other site 123214005529 H-loop/switch region; other site 123214005530 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK06187 123214005531 AMP-binding enzyme; Region: AMP-binding; cl15778 123214005532 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 123214005533 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 123214005534 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 123214005535 histidinol-phosphate aminotransferase; Region: hisC; TIGR01141 123214005536 pyridoxal 5'-phosphate binding site [chemical binding]; other site 123214005537 homodimer interface [polypeptide binding]; other site 123214005538 catalytic residue [active] 123214005539 Protein of unknown function (DUF1461); Region: DUF1461; cl01862 123214005540 Highly conserved protein containing a thioredoxin domain [Posttranslational modification, protein turnover, chaperones]; Region: COG1331 123214005541 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 123214005542 AGE domain; N-acyl-D-glucosamine 2-epimerase domain; Responsible for intermediate epimerization during biosynthesis of N-acetylneuraminic acid. Catalytic mechanism is believed to be via nucleotide elimination and readdition and is ATP modulated. AGE is...; Region: AGE; cl00183 123214005543 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 123214005544 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 123214005545 Cytidylyltransferase; Region: CTP_transf_2; pfam01467 123214005546 active site 123214005547 nucleotide binding site [chemical binding]; other site 123214005548 HIGH motif; other site 123214005549 KMSKS motif; other site 123214005550 Helix-turn-helix domains; Region: HTH; cl00088 123214005551 Type II secretory pathway, prepilin signal peptidase PulO and related peptidases [Cell motility and secretion / Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: PulO; COG1989 123214005552 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 123214005553 Type IV leader peptidase family; Region: Peptidase_A24; cl02077 123214005554 N-ATPase, AtpR subunit; Region: AtpR; cl11871 123214005555 Domain of unknown function (DUF4324); Region: DUF4324; pfam14212 123214005556 Domain of unknown function (DUF4323); Region: DUF4323; pfam14211 123214005557 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 123214005558 dimer interface [polypeptide binding]; other site 123214005559 substrate binding site [chemical binding]; other site 123214005560 metal binding sites [ion binding]; metal-binding site 123214005561 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 123214005562 active site 123214005563 HIGH motif; other site 123214005564 nucleotide binding site [chemical binding]; other site 123214005565 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 123214005566 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 123214005567 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 123214005568 active site 123214005569 KMSKS motif; other site 123214005570 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 123214005571 tRNA binding surface [nucleotide binding]; other site 123214005572 anticodon binding site; other site 123214005573 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 123214005574 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; cl01155 123214005575 Argininosuccinate synthase [Amino acid transport and metabolism]; Region: ArgG; COG0137 123214005576 Argininosuccinate synthase. The Argininosuccinate synthase is a urea cycle enzyme that catalyzes the penultimate step in arginine biosynthesis: the ATP-dependent ligation of citrulline to aspartate to form argininosuccinate, AMP and pyrophosphate . In...; Region: Argininosuccinate_Synthase; cd01999 123214005577 ANP binding site [chemical binding]; other site 123214005578 Substrate Binding Site II [chemical binding]; other site 123214005579 Substrate Binding Site I [chemical binding]; other site 123214005580 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 123214005581 binding surface 123214005582 TPR motif; other site 123214005583 TPR repeat; Region: TPR_11; pfam13414 123214005584 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 123214005585 binding surface 123214005586 TPR motif; other site 123214005587 Tetratricopeptide repeat; Region: TPR_12; pfam13424 123214005588 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 123214005589 TPR motif; other site 123214005590 TPR repeat; Region: TPR_11; pfam13414 123214005591 binding surface 123214005592 Tetratricopeptide repeat; Region: TPR_12; pfam13424 123214005593 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 123214005594 binding surface 123214005595 TPR motif; other site 123214005596 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 123214005597 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]; Region: Tas; COG0667 123214005598 active site 123214005599 catalytic tetrad [active] 123214005600 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 123214005601 MiaB-like tRNA modifying enzyme; Region: MiaB-like-C; TIGR01579 123214005602 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 123214005603 FeS/SAM binding site; other site 123214005604 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 123214005605 catalytic residues [active] 123214005606 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cd00158 123214005607 active site residue [active] 123214005608 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 123214005609 N-acetyl-D-glucosamine binding site [chemical binding]; other site 123214005610 catalytic residue [active] 123214005611 Domain of unknown function (DUF3393); Region: DUF3393; pfam11873 123214005612 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic 'goose-type' lysozymes (GEWL). LTs catalyze...; Region: LT_GEWL; cd00254 123214005613 N-acetyl-D-glucosamine binding site [chemical binding]; other site 123214005614 catalytic residue [active] 123214005615 LPP20 lipoprotein; Region: LPP20; cl15824 123214005616 TolB amino-terminal domain; Region: TolB_N; cl00639 123214005617 LPP20 lipoprotein; Region: LPP20; cl15824 123214005618 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 123214005619 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 123214005620 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 123214005621 RimM N-terminal domain; Region: RimM; pfam01782 123214005622 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 123214005623 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 123214005624 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1729 123214005625 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 123214005626 Tetratricopeptide repeat; Region: TPR_6; pfam13174 123214005627 Tetratricopeptide repeat; Region: TPR_6; pfam13174 123214005628 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 123214005629 binding surface 123214005630 TPR motif; other site 123214005631 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 123214005632 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 123214005633 active site 123214005634 Riboflavin kinase; Region: Flavokinase; cl03312 123214005635 RecX family; Region: RecX; cl00936 123214005636 pilus retraction protein PilT; Region: pilT_fam; TIGR01420 123214005637 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 123214005638 Walker A motif; other site 123214005639 ATP binding site [chemical binding]; other site 123214005640 Walker B motif; other site 123214005641 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 123214005642 recombinase A; Provisional; Region: recA; PRK09354 123214005643 hexamer interface [polypeptide binding]; other site 123214005644 Walker A motif; other site 123214005645 ATP binding site [chemical binding]; other site 123214005646 Walker B motif; other site 123214005647 Glu-tRNAGln amidotransferase C subunit; Region: Glu-tRNAGln; cl00495 123214005648 Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from...; Region: TOPRIM; cl00718 123214005649 DNA topoisomerase I, bacterial; Region: topA_bact; TIGR01051 123214005650 active site 123214005651 metal binding site [ion binding]; metal-binding site 123214005652 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 123214005653 domain I; other site 123214005654 DNA binding groove [nucleotide binding] 123214005655 phosphate binding site [ion binding]; other site 123214005656 domain II; other site 123214005657 domain III; other site 123214005658 nucleotide binding site [chemical binding]; other site 123214005659 catalytic site [active] 123214005660 domain IV; other site 123214005661 ExsB is a transcription regulator related protein. It is a subfamily of a Adenosine nucleotide binding superfamily of proteins. This protein family is represented by a single member in nearly every completed large (> 1000 genes) prokaryotic genome. In...; Region: ExsB; cd01995 123214005662 Ligand Binding Site [chemical binding]; other site 123214005663 Peptidase family M23; Region: Peptidase_M23; pfam01551 123214005664 peptide chain release factor 2; Validated; Region: prfB; PRK00578 123214005665 RF-1 domain; Region: RF-1; cl02875 123214005666 RF-1 domain; Region: RF-1; cl02875 123214005667 Uncharacterized conserved protein [Function unknown]; Region: COG1565 123214005668 Putative S-adenosyl-L-methionine-dependent methyltransferase; Region: Methyltransf_28; pfam02636 123214005669 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 123214005670 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 123214005671 Glutamine amidotransferases class-II (Gn-AT)_GFAT-type. This domain is found at the N-terminus of glucosamine-6P synthase (GlmS, or GFAT in humans). The glutaminase domain catalyzes amide nitrogen transfer from glutamine to the appropriate substrate. In...; Region: GFAT; cd00714 123214005672 glutaminase active site [active] 123214005673 SIS (Sugar ISomerase) domain repeat 1 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal...; Region: SIS_GlmS_GlmD_1; cd05008 123214005674 dimer interface [polypeptide binding]; other site 123214005675 active site 123214005676 SIS (Sugar ISomerase) domain repeat 2 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal...; Region: SIS_GlmS_GlmD_2; cd05009 123214005677 dimer interface [polypeptide binding]; other site 123214005678 active site 123214005679 sulfate adenylyltransferase; Reviewed; Region: sat; PRK04149 123214005680 ATP-sulfurylase; Region: ATPS; cd00517 123214005681 active site 123214005682 HXXH motif; other site 123214005683 flexible loop; other site 123214005684 Domain of unknown function (DUF820). This family consists of hypothetical proteins that are greatly expanded in cyanobacteria. The proteins are found sporadically in other bacteria. They have been predicted to belong to the PD-(D/E)xK superfamily of...; Region: DUF820; cl01898 123214005685 putative active site [active] 123214005686 RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; Region: Rel-Spo_like; cl11966 123214005687 metal binding triad [ion binding]; metal-binding site 123214005688 CysQ, a 3'-Phosphoadenosine-5'-phosphosulfate (PAPS) 3'-phosphatase, is a bacterial member of the inositol monophosphatase family. It has been proposed that CysQ helps control intracellular levels of PAPS, which is an intermediate in cysteine...; Region: CysQ; cd01638 123214005689 active site 123214005690 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl15357 123214005691 transmembrane helices; other site 123214005692 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl15357 123214005693 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl15357 123214005694 Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS). The end-product PAPS is a biologically 'activated' sulfate form important for the assimilation of...; Region: APSK; cd02027 123214005695 Gluconate kinase [Carbohydrate transport and metabolism]; Region: GntK; COG3265 123214005696 ligand-binding site [chemical binding]; other site 123214005697 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 123214005698 active site 123214005699 NTP binding site [chemical binding]; other site 123214005700 metal binding triad [ion binding]; metal-binding site 123214005701 antibiotic binding site [chemical binding]; other site 123214005702 Nucleotidyltransferase substrate binding protein like; Region: NTase_sub_bind; cl08495 123214005703 G1P_cytidylyltransferase catalyzes the production of CDP-D-Glucose; Region: G1P_cytidylyltransferase; cd02524 123214005704 substrate binding site; other site 123214005705 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214005706 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 123214005707 NAD(P) binding site [chemical binding]; other site 123214005708 active site 123214005709 CDP-glucose 4,6-dehydratase; Region: CDP_4_6_dhtase; TIGR02622 123214005710 CDP-D-glucose 4,6-dehydratase, extended (e) SDRs; Region: CDP_GD_SDR_e; cd05252 123214005711 NAD binding site [chemical binding]; other site 123214005712 homotetramer interface [polypeptide binding]; other site 123214005713 homodimer interface [polypeptide binding]; other site 123214005714 substrate binding site [chemical binding]; other site 123214005715 active site 123214005716 DegT/DnrJ/EryC1/StrS aminotransferase family; Region: DegT_DnrJ_EryC1; pfam01041 123214005717 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary...; Region: AHBA_syn; cd00616 123214005718 inhibitor-cofactor binding pocket; inhibition site 123214005719 pyridoxal 5'-phosphate binding site [chemical binding]; other site 123214005720 catalytic residue [active] 123214005721 CDP-tyvelose 2-epimerase, extended (e) SDRs; Region: CDP_TE_SDR_e; cd05258 123214005722 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 123214005723 NAD binding site [chemical binding]; other site 123214005724 homotetramer interface [polypeptide binding]; other site 123214005725 homodimer interface [polypeptide binding]; other site 123214005726 active site 123214005727 substrate binding site [chemical binding]; other site 123214005728 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 123214005729 active site 123214005730 MatE; Region: MatE; cl10513 123214005731 O-Antigen ligase; Region: Wzy_C; cl04850 123214005732 Sulfotransferase domain; Region: Sulfotransfer_1; pfam00685 123214005733 GDP-D-mannose dehydratase [Cell envelope biogenesis, outer membrane]; Region: Gmd; COG1089 123214005734 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 123214005735 NADP-binding site; other site 123214005736 homotetramer interface [polypeptide binding]; other site 123214005737 substrate binding site [chemical binding]; other site 123214005738 homodimer interface [polypeptide binding]; other site 123214005739 active site 123214005740 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 123214005741 This family is most closely related to the GT1 family of glycosyltransferases. wbaZ in Salmonella enterica has been shown to possess the mannosyl transferase activity. The members of this family are found in certain bacteria and Archaea; Region: GT1_wbaZ_like; cd03804 123214005742 putative ADP-binding pocket [chemical binding]; other site 123214005743 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 123214005744 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 123214005745 Substrate binding site; other site 123214005746 Cupin domain; Region: Cupin_2; cl09118 123214005747 PIN domain of ribonucleases (toxins), VapC, FitB, and PAE0151 of bacterial and archaeal toxin/antitoxin-like operons, and other similar homologs; Region: PIN_VapC-like; cd09861 123214005748 putative active site [active] 123214005749 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 123214005750 UDP-glucose-4-epimerase; Region: galE; TIGR01179 123214005751 NAD binding site [chemical binding]; other site 123214005752 homodimer interface [polypeptide binding]; other site 123214005753 active site 123214005754 substrate binding site [chemical binding]; other site 123214005755 exopolysaccharide biosynthesis polyprenyl glycosylphosphotransferase; Region: EPS_sugtrans; TIGR03025 123214005756 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 123214005757 Bacterial sugar transferase; Region: Bac_transf; cl00939 123214005758 VanZ like family; Region: VanZ; cl01971 123214005759 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 123214005760 Domain of unknown function (DUF820). This family consists of hypothetical proteins that are greatly expanded in cyanobacteria. The proteins are found sporadically in other bacteria. They have been predicted to belong to the PD-(D/E)xK superfamily of...; Region: DUF820; cd06260 123214005761 putative active site [active] 123214005762 Nucleotidyltransferase substrate binding protein like; Region: NTase_sub_bind; cl08495 123214005763 Domain of unknown function (DUF820). This family consists of hypothetical proteins that are greatly expanded in cyanobacteria. The proteins are found sporadically in other bacteria. They have been predicted to belong to the PD-(D/E)xK superfamily of...; Region: DUF820; cd06260 123214005764 putative active site [active] 123214005765 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 123214005766 catalytic center binding site [active] 123214005767 ATP binding site [chemical binding]; other site 123214005768 Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function; Region: LysM; cd00118 123214005769 putative peptidoglycan binding site; other site 123214005770 L,D-transpeptidase catalytic domain; Region: YkuD; cl15405 123214005771 alanine--tRNA ligase; Region: alaS; TIGR00344 123214005772 Low specificity phosphatase (HAD superfamily) [General function prediction only]; Region: COG1778 123214005773 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 123214005774 active site 123214005775 motif I; other site 123214005776 motif II; other site 123214005777 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 123214005778 S-adenosylmethionine binding site [chemical binding]; other site 123214005779 Competence protein; Region: Competence; cl00471 123214005780 Outer membrane protein family (DUF1597); Region: DUF1597; pfam07642 123214005781 Ammonium Transporter Family; Region: Ammonium_transp; cl03012 123214005782 Nitrogen regulatory protein P-II; Region: P-II; cl00412 123214005783 Nitrogen regulatory protein P-II; Region: P-II; smart00938 123214005784 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 123214005785 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 123214005786 ring oligomerisation interface [polypeptide binding]; other site 123214005787 ATP/Mg binding site [chemical binding]; other site 123214005788 stacking interactions; other site 123214005789 hinge regions; other site 123214005790 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 123214005791 roof hairpin; other site 123214005792 oligomerisation interface [polypeptide binding]; other site