-- dump date 20140619_145549 -- class Genbank::misc_feature -- table misc_feature_note -- id note 349215000001 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 349215000002 substrate binding site [chemical binding]; other site 349215000003 active site 349215000004 ferrochelatase; Reviewed; Region: hemH; PRK00035 349215000005 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 349215000006 C-terminal domain interface [polypeptide binding]; other site 349215000007 active site 349215000008 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 349215000009 active site 349215000010 N-terminal domain interface [polypeptide binding]; other site 349215000011 Uncharacterized protein family (UPF0093); Region: UPF0093; pfam03653 349215000012 transcription termination factor Rho; Provisional; Region: rho; PRK09376 349215000013 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 349215000014 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 349215000015 RNA binding site [nucleotide binding]; other site 349215000016 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 349215000017 multimer interface [polypeptide binding]; other site 349215000018 Walker A motif; other site 349215000019 ATP binding site [chemical binding]; other site 349215000020 Walker B motif; other site 349215000021 Pectic acid lyase; Region: Pec_lyase; pfam09492 349215000022 DnaJ central domain; Region: DnaJ_CXXCXGXG; pfam00684 349215000023 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 349215000024 Zn binding sites [ion binding]; other site 349215000025 DnaJ central domain; Region: DnaJ_CXXCXGXG; pfam00684 349215000026 Dienelactone hydrolase family; Region: DLH; pfam01738 349215000027 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 349215000028 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 349215000029 trmE is a tRNA modification GTPase; Region: trmE; cd04164 349215000030 G1 box; other site 349215000031 GTP/Mg2+ binding site [chemical binding]; other site 349215000032 Switch I region; other site 349215000033 G2 box; other site 349215000034 Switch II region; other site 349215000035 G3 box; other site 349215000036 G4 box; other site 349215000037 G5 box; other site 349215000038 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 349215000039 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 349215000040 tRNA (uracil-5-)-methyltransferase Gid; Reviewed; Region: PRK05335 349215000041 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 349215000042 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 349215000043 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 349215000044 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 349215000045 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 349215000046 P-loop; other site 349215000047 Magnesium ion binding site [ion binding]; other site 349215000048 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 349215000049 Magnesium ion binding site [ion binding]; other site 349215000050 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 349215000051 ParB-like nuclease domain; Region: ParB; smart00470 349215000052 Na+/H+ antiporter, bacterial form; Region: a_cpa1; TIGR00831 349215000053 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 349215000054 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 349215000055 uncharacterized peroxidase-related enzyme; Region: peroxid_rel; TIGR01926 349215000056 Carboxymuconolactone decarboxylase family; Region: CMD; cl00460 349215000057 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 349215000058 Zn binding site [ion binding]; other site 349215000059 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 349215000060 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 349215000061 HIGH motif; other site 349215000062 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 349215000063 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 349215000064 active site 349215000065 KMSKS motif; other site 349215000066 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 349215000067 tRNA binding surface [nucleotide binding]; other site 349215000068 Lipopolysaccharide-assembly; Region: LptE; cl01125 349215000069 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK06585 349215000070 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 349215000071 Domain of unknown function (DUF3576); Region: DUF3576; pfam12100 349215000072 Gram-negative porin; Region: Porin_4; pfam13609 349215000073 Outer membrane protein (porin) [Cell envelope biogenesis, outer membrane]; Region: OmpC; COG3203 349215000074 Gram-negative porin; Region: Porin_4; pfam13609 349215000075 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 349215000076 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 349215000077 catalytic residue [active] 349215000078 Transcriptional regulatory protein, C terminal; Region: Trans_reg_C; pfam00486 349215000079 DNA binding site [nucleotide binding] 349215000080 Smr domain; Region: Smr; pfam01713 349215000081 Peptidase family M23; Region: Peptidase_M23; pfam01551 349215000082 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 349215000083 RimK-like ATPgrasp N-terminal domain; Region: RLAN; pfam14401 349215000084 Glutathione synthase/Ribosomal protein S6 modification enzyme (glutaminyl transferase) [Coenzyme metabolism / Translation, ribosomal structure and biogenesis]; Region: RimK; COG0189 349215000085 ATP-grasp domain; Region: ATP-grasp_4; cl17255 349215000086 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 349215000087 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 349215000088 Coenzyme A binding pocket [chemical binding]; other site 349215000089 integral membrane protein, TerC family; Region: R_switched_Alx; TIGR03718 349215000090 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 349215000091 Coenzyme A binding pocket [chemical binding]; other site 349215000092 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 349215000093 nucleotide binding site/active site [active] 349215000094 HIT family signature motif; other site 349215000095 catalytic residue [active] 349215000096 MASE1; Region: MASE1; pfam05231 349215000097 CHASE domain; Region: CHASE; pfam03924 349215000098 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 349215000099 dimer interface [polypeptide binding]; other site 349215000100 phosphorylation site [posttranslational modification] 349215000101 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 349215000102 ATP binding site [chemical binding]; other site 349215000103 Mg2+ binding site [ion binding]; other site 349215000104 G-X-G motif; other site 349215000105 Response regulator receiver domain; Region: Response_reg; pfam00072 349215000106 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 349215000107 active site 349215000108 phosphorylation site [posttranslational modification] 349215000109 intermolecular recognition site; other site 349215000110 dimerization interface [polypeptide binding]; other site 349215000111 Hpt domain; Region: Hpt; pfam01627 349215000112 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 349215000113 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 349215000114 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 349215000115 Walker A motif; other site 349215000116 ATP binding site [chemical binding]; other site 349215000117 Walker B motif; other site 349215000118 arginine finger; other site 349215000119 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 349215000120 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 349215000121 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 349215000122 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 349215000123 metal binding site [ion binding]; metal-binding site 349215000124 active site 349215000125 I-site; other site 349215000126 FG-GAP repeat; Region: FG-GAP_2; pfam14312 349215000127 FOG: WD40 repeat [General function prediction only]; Region: COG2319 349215000128 FG-GAP repeat; Region: FG-GAP_2; pfam14312 349215000129 FG-GAP repeat; Region: FG-GAP_2; pfam14312 349215000130 FG-GAP repeat; Region: FG-GAP_2; pfam14312 349215000131 FG-GAP repeat; Region: FG-GAP_2; pfam14312 349215000132 FG-GAP repeat; Region: FG-GAP_2; pfam14312 349215000133 ATP-dependent DNA helicase PcrA; Region: pcrA; TIGR01073 349215000134 Part of AAA domain; Region: AAA_19; pfam13245 349215000135 Family description; Region: UvrD_C_2; pfam13538 349215000136 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs; Region: NDUFA9_like_SDR_a; cd05271 349215000137 Predicted nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG0702 349215000138 putative NAD(P) binding site [chemical binding]; other site 349215000139 active site 349215000140 SurA N-terminal domain; Region: SurA_N; pfam09312 349215000141 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 349215000142 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 349215000143 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 349215000144 S-adenosylmethionine binding site [chemical binding]; other site 349215000145 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 349215000146 cytidylate kinase, putative; Region: cyt_kin_arch; TIGR02173 349215000147 CMP-binding site; other site 349215000148 The sites determining sugar specificity; other site 349215000149 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 349215000150 NAD(P) binding site [chemical binding]; other site 349215000151 active site 349215000152 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 349215000153 dimerization interface [polypeptide binding]; other site 349215000154 putative DNA binding site [nucleotide binding]; other site 349215000155 putative Zn2+ binding site [ion binding]; other site 349215000156 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 349215000157 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 349215000158 putative active site [active] 349215000159 This family is most closely related to the GT1 family of glycosyltransferases. WavL in Vibrio cholerae has been shown to be involved in the biosynthesis of the lipopolysaccharide core; Region: GT1_WavL_like; cd03819 349215000160 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 349215000161 putative ADP-binding pocket [chemical binding]; other site 349215000162 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 349215000163 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 349215000164 TAP-like protein; Region: Abhydrolase_4; pfam08386 349215000165 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 349215000166 HIUase (5-hydroxyisourate hydrolase) catalyzes the second step in a three-step ureide pathway in which 5-hydroxyisourate (HIU), a product of the uricase (urate oxidase) reaction, is hydrolyzed to 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU); Region: TLP_HIUase; cd05822 349215000167 homotetramer interface [polypeptide binding]; other site 349215000168 active site 349215000169 Domain of unknown function (DUF305); Region: DUF305; cl17794 349215000170 Predicted soluble lytic transglycosylase fused to an ABC-type amino acid-binding protein [Cell envelope biogenesis, outer membrane]; Region: COG4623 349215000171 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 349215000172 substrate binding pocket [chemical binding]; other site 349215000173 membrane-bound complex binding site; other site 349215000174 hinge residues; other site 349215000175 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 349215000176 N-acetyl-D-glucosamine binding site [chemical binding]; other site 349215000177 catalytic residue [active] 349215000178 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 349215000179 active site clefts [active] 349215000180 zinc binding site [ion binding]; other site 349215000181 dimer interface [polypeptide binding]; other site 349215000182 Ammonia permease [Inorganic ion transport and metabolism]; Region: AmtB; COG0004 349215000183 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 349215000184 uncharacterized flavoprotein, PP_4765 family; Region: flavo_PP4765; TIGR03862 349215000185 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_like_2; cd13149 349215000186 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 349215000187 Domain of unknown function (DUF4114); Region: DUF4114; pfam13448 349215000188 type I secretion C-terminal target domain (VC_A0849 subclass); Region: T1SS_VCA0849; TIGR03661 349215000189 Left-handed beta-roll, including virulence factors and various other proteins; Region: LbR-like; cl17507 349215000190 trimer interface [polypeptide binding]; other site 349215000191 type I secretion C-terminal target domain (VC_A0849 subclass); Region: T1SS_VCA0849; TIGR03661 349215000192 16S RNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]; Region: RsmC; COG2813 349215000193 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 349215000194 S-adenosylmethionine binding site [chemical binding]; other site 349215000195 Haloacid dehalogenase-like hydrolase; Region: HAD_2; pfam13419 349215000196 HAD-hyrolase-like; Region: Hydrolase_like; pfam13242 349215000197 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 349215000198 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 349215000199 Walker A motif; other site 349215000200 ATP binding site [chemical binding]; other site 349215000201 Walker B motif; other site 349215000202 arginine finger; other site 349215000203 Phosphoserine phosphatase [Amino acid transport and metabolism]; Region: SerB; COG0560 349215000204 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 349215000205 motif II; other site 349215000206 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; cd01494 349215000207 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 349215000208 catalytic residue [active] 349215000209 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK13581 349215000210 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_4; cd12173 349215000211 ligand binding site [chemical binding]; other site 349215000212 NAD binding site [chemical binding]; other site 349215000213 dimerization interface [polypeptide binding]; other site 349215000214 catalytic site [active] 349215000215 C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH); Region: ACT_3PGDH-xct; cd04902 349215000216 putative L-serine binding site [chemical binding]; other site 349215000217 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 349215000218 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 349215000219 active site 349215000220 phosphorylation site [posttranslational modification] 349215000221 intermolecular recognition site; other site 349215000222 dimerization interface [polypeptide binding]; other site 349215000223 TspO/MBR family; Region: TspO_MBR; pfam03073 349215000224 succinic semialdehyde dehydrogenase; Region: PLN02278 349215000225 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 349215000226 tetramerization interface [polypeptide binding]; other site 349215000227 NAD(P) binding site [chemical binding]; other site 349215000228 catalytic residues [active] 349215000229 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 349215000230 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 349215000231 metal ion-dependent adhesion site (MIDAS); other site 349215000232 T1SS-143 repeat domain; Region: T1SS_rpt_143; TIGR03660 349215000233 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 349215000234 metal ion-dependent adhesion site (MIDAS); other site 349215000235 type I secretion C-terminal target domain (VC_A0849 subclass); Region: T1SS_VCA0849; TIGR03661 349215000236 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 349215000237 A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various...; Region: Peptidase_C39_likeD; cd02421 349215000238 type I secretion system ATPase, LssB family; Region: type_I_sec_LssB; TIGR03375 349215000239 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 349215000240 ATP-binding cassette domain of bacteriocin exporters, subfamily C; Region: ABCC_bacteriocin_exporters; cd03245 349215000241 Walker A/P-loop; other site 349215000242 ATP binding site [chemical binding]; other site 349215000243 Q-loop/lid; other site 349215000244 ABC transporter signature motif; other site 349215000245 Walker B; other site 349215000246 D-loop; other site 349215000247 H-loop/switch region; other site 349215000248 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 349215000249 HlyD family secretion protein; Region: HlyD_3; pfam13437 349215000250 Protein of unknown function (DUF3478); Region: DUF3478; pfam11964 349215000251 Protein of unknown function (DUF3478); Region: DUF3478; pfam11964 349215000252 Protein of unknown function (DUF3478); Region: DUF3478; pfam11964 349215000253 Protein of unknown function (DUF3478); Region: DUF3478; pfam11964 349215000254 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 349215000255 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 349215000256 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 349215000257 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 349215000258 active site 349215000259 dimer interface [polypeptide binding]; other site 349215000260 motif 1; other site 349215000261 motif 2; other site 349215000262 motif 3; other site 349215000263 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 349215000264 anticodon binding site; other site 349215000265 Translation initiation factor 3 (IF-3) [Translation, ribosomal structure and biogenesis]; Region: InfC; COG0290 349215000266 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 349215000267 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 349215000268 Chaperone of endosialidase; Region: Peptidase_S74; pfam13884 349215000269 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 349215000270 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 349215000271 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 349215000272 Walker A/P-loop; other site 349215000273 ATP binding site [chemical binding]; other site 349215000274 Q-loop/lid; other site 349215000275 ABC transporter signature motif; other site 349215000276 Walker B; other site 349215000277 D-loop; other site 349215000278 H-loop/switch region; other site 349215000279 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 349215000280 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 349215000281 catalytic residues [active] 349215000282 double-strand break repair helicase AddA, alphaproteobacterial type; Region: addA_alphas; TIGR02784 349215000283 Family description; Region: UvrD_C_2; pfam13538 349215000284 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 349215000285 double-strand break repair protein AddB, alphaproteobacterial type; Region: addB_alphas; TIGR02786 349215000286 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 349215000287 Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis/translation initiation factor 2B, gamma/epsilon subunits (eIF-2Bgamma/eIF-2Bepsilon) [Cell envelope biogenesis, outer membrane / Translation, ribosomal structure...; Region: GCD1; COG1208 349215000288 NTP_transferase_like_1 is a member of the nucleotidyl transferase family; Region: NTP_transferase_like_1; cd06422 349215000289 Substrate binding site; other site 349215000290 metal-binding site 349215000291 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 349215000292 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 349215000293 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 349215000294 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 349215000295 Predicted acetyltransferase [General function prediction only]; Region: COG2388 349215000296 PAS fold; Region: PAS_7; pfam12860 349215000297 PAS domain; Region: PAS; smart00091 349215000298 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 349215000299 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 349215000300 dimer interface [polypeptide binding]; other site 349215000301 phosphorylation site [posttranslational modification] 349215000302 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 349215000303 ATP binding site [chemical binding]; other site 349215000304 Mg2+ binding site [ion binding]; other site 349215000305 G-X-G motif; other site 349215000306 FG-GAP repeat; Region: FG-GAP_2; pfam14312 349215000307 PQQ-like domain; Region: PQQ_2; pfam13360 349215000308 FG-GAP repeat; Region: FG-GAP_2; pfam14312 349215000309 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 349215000310 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1_2; pfam13540 349215000311 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1_2; pfam13540 349215000312 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 349215000313 S-adenosyl-L-homocysteine hydrolase; Provisional; Region: PRK05476 349215000314 S-Adenosylhomocysteine Hydrolase, NAD-binding and catalytic domains; Region: SAHH; cd00401 349215000315 homotetramer interface [polypeptide binding]; other site 349215000316 ligand binding site [chemical binding]; other site 349215000317 catalytic site [active] 349215000318 NAD binding site [chemical binding]; other site 349215000319 glmZ(sRNA)-inactivating NTPase; Provisional; Region: PRK05416 349215000320 shikimate kinase; Reviewed; Region: aroK; PRK00131 349215000321 Sensor N-terminal transmembrane domain; Region: Sensor_TM1; pfam13755 349215000322 Stimulus-sensing domain; Region: Stimulus_sens_1; pfam13756 349215000323 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 349215000324 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 349215000325 dimerization interface [polypeptide binding]; other site 349215000326 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 349215000327 dimer interface [polypeptide binding]; other site 349215000328 phosphorylation site [posttranslational modification] 349215000329 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 349215000330 ATP binding site [chemical binding]; other site 349215000331 Mg2+ binding site [ion binding]; other site 349215000332 G-X-G motif; other site 349215000333 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 349215000334 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 349215000335 active site 349215000336 phosphorylation site [posttranslational modification] 349215000337 intermolecular recognition site; other site 349215000338 dimerization interface [polypeptide binding]; other site 349215000339 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 349215000340 DNA binding site [nucleotide binding] 349215000341 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 349215000342 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 349215000343 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 349215000344 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 349215000345 YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been...; Region: YdcF-like; cd06259 349215000346 putative active site [active] 349215000347 Orotidine 5'-phosphate decarboxylase (ODCase) is a dimeric enzyme that decarboxylates orotidine 5'-monophosphate (OMP) to form uridine 5'-phosphate (UMP), an essential step in the pyrimidine biosynthetic pathway. In mammals, UMP synthase...; Region: OMP_decarboxylase_like; cd04725 349215000348 active site 349215000349 dimer interface [polypeptide binding]; other site 349215000350 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 349215000351 IHF dimer interface [polypeptide binding]; other site 349215000352 IHF - DNA interface [nucleotide binding]; other site 349215000353 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 349215000354 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture...; Region: S1_RPS1_repeat_ec1_hs1; cd05687 349215000355 RNA binding site [nucleotide binding]; other site 349215000356 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture...; Region: S1_RPS1_repeat_ec2_hs2; cd04465 349215000357 RNA binding site [nucleotide binding]; other site 349215000358 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec3; cd05688 349215000359 RNA binding site [nucleotide binding]; other site 349215000360 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec4; cd05689 349215000361 RNA binding site [nucleotide binding]; other site 349215000362 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 349215000363 RNA binding site [nucleotide binding]; other site 349215000364 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec6; cd05691 349215000365 RNA binding site [nucleotide binding]; other site 349215000366 cytidylate kinase; Provisional; Region: cmk; PRK00023 349215000367 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 349215000368 CMP-binding site; other site 349215000369 The sites determining sugar specificity; other site 349215000370 FG-GAP repeat; Region: FG-GAP_2; pfam14312 349215000371 FG-GAP repeat; Region: FG-GAP_2; pfam14312 349215000372 PQQ-like domain; Region: PQQ_2; pfam13360 349215000373 FG-GAP repeat; Region: FG-GAP_2; pfam14312 349215000374 FG-GAP repeat; Region: FG-GAP_2; pfam14312 349215000375 FG-GAP repeat; Region: FG-GAP_2; pfam14312 349215000376 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 349215000377 structural tetrad; other site 349215000378 PQQ-like domain; Region: PQQ_2; pfam13360 349215000379 FG-GAP repeat; Region: FG-GAP_2; pfam14312 349215000380 FG-GAP repeat; Region: FG-GAP_2; pfam14312 349215000381 FG-GAP repeat; Region: FG-GAP_2; pfam14312 349215000382 FG-GAP repeat; Region: FG-GAP_2; pfam14312 349215000383 FG-GAP repeat; Region: FG-GAP_2; pfam14312 349215000384 FG-GAP repeat; Region: FG-GAP_2; pfam14312 349215000385 FG-GAP repeat; Region: FG-GAP_2; pfam14312 349215000386 FG-GAP repeat; Region: FG-GAP_2; pfam14312 349215000387 FG-GAP repeat; Region: FG-GAP_2; pfam14312 349215000388 FG-GAP repeat; Region: FG-GAP_2; pfam14312 349215000389 FG-GAP repeat; Region: FG-GAP_2; pfam14312 349215000390 PQQ-like domain; Region: PQQ_2; pfam13360 349215000391 FG-GAP repeat; Region: FG-GAP_2; pfam14312 349215000392 FG-GAP repeat; Region: FG-GAP_2; pfam14312 349215000393 FG-GAP repeat; Region: FG-GAP_2; pfam14312 349215000394 FG-GAP repeat; Region: FG-GAP_2; pfam14312 349215000395 FG-GAP repeat; Region: FG-GAP_2; pfam14312 349215000396 FG-GAP repeat; Region: FG-GAP_2; pfam14312 349215000397 PQQ-like domain; Region: PQQ_2; pfam13360 349215000398 FG-GAP repeat; Region: FG-GAP_2; pfam14312 349215000399 FG-GAP repeat; Region: FG-GAP_2; pfam14312 349215000400 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 349215000401 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 349215000402 hinge; other site 349215000403 active site 349215000404 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 349215000405 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 349215000406 metal binding site [ion binding]; metal-binding site 349215000407 active site 349215000408 I-site; other site 349215000409 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 349215000410 dihydroorotase; Validated; Region: PRK09060 349215000411 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 349215000412 Dihydroorotase (DHOase), subgroup IIb; DHOases catalyze the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in pyrimidine biosynthesis. This group contains the archeal members of the DHOase family; Region: DHOase_IIb; cd01318 349215000413 active site 349215000414 Response regulator receiver domain; Region: Response_reg; pfam00072 349215000415 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 349215000416 active site 349215000417 phosphorylation site [posttranslational modification] 349215000418 intermolecular recognition site; other site 349215000419 dimerization interface [polypeptide binding]; other site 349215000420 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 349215000421 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 349215000422 active site 349215000423 HIGH motif; other site 349215000424 nucleotide binding site [chemical binding]; other site 349215000425 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 349215000426 KMSKS motif; other site 349215000427 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 349215000428 tRNA binding surface [nucleotide binding]; other site 349215000429 anticodon binding site; other site 349215000430 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 349215000431 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 349215000432 Walker A/P-loop; other site 349215000433 ATP binding site [chemical binding]; other site 349215000434 Q-loop/lid; other site 349215000435 ABC transporter signature motif; other site 349215000436 Walker B; other site 349215000437 D-loop; other site 349215000438 H-loop/switch region; other site 349215000439 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 349215000440 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 349215000441 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 349215000442 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 349215000443 RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal...; Region: RaiA; cd00552 349215000444 30S subunit binding site; other site 349215000445 Response regulator receiver domain; Region: Response_reg; pfam00072 349215000446 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 349215000447 active site 349215000448 phosphorylation site [posttranslational modification] 349215000449 intermolecular recognition site; other site 349215000450 dimerization interface [polypeptide binding]; other site 349215000451 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 349215000452 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 349215000453 catalytic site [active] 349215000454 putative active site [active] 349215000455 putative substrate binding site [chemical binding]; other site 349215000456 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 349215000457 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 349215000458 putative active site [active] 349215000459 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 349215000460 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 349215000461 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 349215000462 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5375 349215000463 OstA-like protein; Region: OstA; cl00844 349215000464 OstA-like protein; Region: OstA; cl00844 349215000465 Zinc-finger domain; Region: zf-CHCC; cl01821 349215000466 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 349215000467 Alpha-crystallin domain (ACD) found in Escherichia coli inclusion body-associated proteins IbpA and IbpB, and similar proteins. IbpA and IbpB are 16 kDa small heat shock proteins (sHsps). sHsps are molecular chaperones that suppress protein aggregation...; Region: ACD_IbpA-B_like; cd06470 349215000468 putative dimer interface [polypeptide binding]; other site 349215000469 Protein of unknown function (DUF1150); Region: DUF1150; pfam06620 349215000470 PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_fru; cd00211 349215000471 active site 349215000472 phosphorylation site [posttranslational modification] 349215000473 recombination protein RecR; Reviewed; Region: recR; PRK00076 349215000474 RecR protein; Region: RecR; pfam02132 349215000475 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 349215000476 putative active site [active] 349215000477 putative metal-binding site [ion binding]; other site 349215000478 tetramer interface [polypeptide binding]; other site 349215000479 Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport...; Region: FNR_like; cl06868 349215000480 FAD binding pocket [chemical binding]; other site 349215000481 conserved FAD binding motif [chemical binding]; other site 349215000482 phosphate binding motif [ion binding]; other site 349215000483 beta-alpha-beta structure motif; other site 349215000484 NAD binding pocket [chemical binding]; other site 349215000485 Outer membrane lipoprotein-sorting protein [Cell envelope biogenesis, outer membrane]; Region: LolA; COG2834 349215000486 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 349215000487 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 349215000488 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 349215000489 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 349215000490 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 349215000491 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 349215000492 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 349215000493 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: COG1585 349215000494 Cytochrome c2 [Energy production and conversion]; Region: COG3474 349215000495 DNA polymerase III subunit chi; Validated; Region: PRK05728 349215000496 multifunctional aminopeptidase A; Provisional; Region: PRK00913 349215000497 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 349215000498 interface (dimer of trimers) [polypeptide binding]; other site 349215000499 Substrate-binding/catalytic site; other site 349215000500 Zn-binding sites [ion binding]; other site 349215000501 elongation factor P; Validated; Region: PRK00529 349215000502 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 349215000503 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 349215000504 RNA binding site [nucleotide binding]; other site 349215000505 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 349215000506 RNA binding site [nucleotide binding]; other site 349215000507 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4394 349215000508 Uncharacterized protein conserved in bacteria (DUF2331); Region: DUF2331; pfam10093 349215000509 multifunctional aminopeptidase A; Provisional; Region: PRK00913 349215000510 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 349215000511 interface (dimer of trimers) [polypeptide binding]; other site 349215000512 Substrate-binding/catalytic site; other site 349215000513 Zn-binding sites [ion binding]; other site 349215000514 Predicted permeases [General function prediction only]; Region: COG0795 349215000515 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 349215000516 Predicted permeases [General function prediction only]; Region: COG0795 349215000517 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 349215000518 VacJ like lipoprotein; Region: VacJ; cl01073 349215000519 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; pfam05494 349215000520 conjugal transfer/type IV secretion protein DotA/TraY; Region: DotA_TraY; TIGR04346 349215000521 conjugal transfer/type IV secretion protein DotA/TraY; Region: DotA_TraY; TIGR04346 349215000522 conjugal transfer/type IV secretion protein DotA/TraY; Region: DotA_TraY; TIGR04346 349215000523 conjugal transfer/type IV secretion protein DotA/TraY; Region: DotA_TraY; TIGR04346 349215000524 RIP metalloprotease RseP; Region: TIGR00054 349215000525 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 349215000526 active site 349215000527 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 349215000528 protein binding site [polypeptide binding]; other site 349215000529 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 349215000530 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 349215000531 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 349215000532 ABC transporter; Region: ABC_tran_2; pfam12848 349215000533 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 349215000534 Uncharacterized protein involved in stress response [General function prediction only]; Region: COG4110 349215000535 Uncharacterized proteins involved in stress response, similar to tellurium resistance terD; Region: TerD_like; cd06974 349215000536 putative metal binding site [ion binding]; other site 349215000537 Uncharacterized proteins involved in stress response, homologs of TerZ and putative cAMP-binding protein CABP1 [Signal transduction mechanisms]; Region: TerZ; COG2310 349215000538 Uncharacterized proteins involved in stress response, similar to tellurium resistance terD; Region: TerD_like; cd06974 349215000539 putative metal binding site [ion binding]; other site 349215000540 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 349215000541 ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a...; Region: ExoVII_LU_OBF; cd04489 349215000542 generic binding surface II; other site 349215000543 generic binding surface I; other site 349215000544 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 349215000545 pyridoxal 5'-phosphate binding site [chemical binding]; other site 349215000546 homodimer interface [polypeptide binding]; other site 349215000547 catalytic residue [active] 349215000548 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed; Region: PRK11904 349215000549 Proline dehydrogenase; Region: Pro_dh; pfam01619 349215000550 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 349215000551 Glutamate binding site [chemical binding]; other site 349215000552 NAD binding site [chemical binding]; other site 349215000553 catalytic residues [active] 349215000554 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 349215000555 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 349215000556 ligand binding site [chemical binding]; other site 349215000557 flexible hinge region; other site 349215000558 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 349215000559 Uncharacterized conserved protein [Function unknown]; Region: COG1633 349215000560 Uncharacterized family of ferritin-like proteins found in archaea and bacteria; Region: Ferritin_like_AB; cd01045 349215000561 diiron binding motif [ion binding]; other site 349215000562 Uncharacterized conserved protein [Function unknown]; Region: COG1633 349215000563 CCC1-related protein family; Region: CCC1_like_1; cd02437 349215000564 Type IV pilin N-term methylation site GFxxxE; Region: N_methyl_2; pfam13544 349215000565 type II secretion system protein G; Region: typeII_sec_gspG; TIGR01710 349215000566 Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulG; COG2165 349215000567 von Willebrand factor type A domain; Region: VWA_2; pfam13519 349215000568 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 349215000569 nucleoside/Zn binding site; other site 349215000570 dimer interface [polypeptide binding]; other site 349215000571 catalytic motif [active] 349215000572 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 349215000573 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 349215000574 RNA binding surface [nucleotide binding]; other site 349215000575 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 349215000576 active site 349215000577 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 349215000578 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 349215000579 motif II; other site 349215000580 Bacitracin resistance protein BacA; Region: BacA; pfam02673 349215000581 Uncharacterized conserved protein [Function unknown]; Region: COG2353 349215000582 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 349215000583 YceI-like domain; Region: YceI; pfam04264 349215000584 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 349215000585 active site 349215000586 catalytic residues [active] 349215000587 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 349215000588 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cl00107 349215000589 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 349215000590 active site 349215000591 catalytic residues [active] 349215000592 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 349215000593 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 349215000594 Glutathione S-transferase, N-terminal domain; Region: GST_N_3; pfam13417 349215000595 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 349215000596 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 349215000597 N-terminal domain interface [polypeptide binding]; other site 349215000598 dimer interface [polypeptide binding]; other site 349215000599 substrate binding pocket (H-site) [chemical binding]; other site 349215000600 atypical (a) SDRs, subgroup 4; Region: SDR_a4; cd05266 349215000601 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 349215000602 putative NAD(P) binding site [chemical binding]; other site 349215000603 PAS domain S-box; Region: sensory_box; TIGR00229 349215000604 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 349215000605 putative active site [active] 349215000606 heme pocket [chemical binding]; other site 349215000607 PAS fold; Region: PAS_3; pfam08447 349215000608 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 349215000609 putative active site [active] 349215000610 heme pocket [chemical binding]; other site 349215000611 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 349215000612 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 349215000613 dimer interface [polypeptide binding]; other site 349215000614 phosphorylation site [posttranslational modification] 349215000615 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 349215000616 ATP binding site [chemical binding]; other site 349215000617 Mg2+ binding site [ion binding]; other site 349215000618 G-X-G motif; other site 349215000619 Peroxiredoxin (PRX)-like 1 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a conserved cysteine that aligns to the first cysteine in the CXXC motif of TRX. This does not correspond to the peroxidatic...; Region: PRX_like1; cd02969 349215000620 putative catalytic residue [active] 349215000621 Disulphide bond corrector protein DsbC; Region: DsbC; cl15830 349215000622 Thiol:disulfide interchange protein [Posttranslational modification, protein turnover, chaperones / Energy production and conversion]; Region: COG4232 349215000623 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 349215000624 DsbD gamma family; DsbD gamma is the C-terminal periplasmic domain of the bacterial protein DsbD. It contains a CXXC motif in a TRX fold and shuttles the reducing potential from the membrane domain (DsbD beta) to the N-terminal periplasmic domain (DsbD...; Region: DsbDgamma; cd02953 349215000625 DsbD alpha interface [polypeptide binding]; other site 349215000626 catalytic residues [active] 349215000627 acetoacetyl-CoA synthetase; Provisional; Region: PRK03584 349215000628 Acetoacetyl-CoA synthetase (acetoacetate-CoA ligase, AACS); Region: AACS; cd05943 349215000629 acyl-activating enzyme (AAE) consensus motif; other site 349215000630 putative AMP binding site [chemical binding]; other site 349215000631 putative active site [active] 349215000632 putative CoA binding site [chemical binding]; other site 349215000633 aspartate aminotransferase; Provisional; Region: PRK06108 349215000634 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 349215000635 pyridoxal 5'-phosphate binding site [chemical binding]; other site 349215000636 homodimer interface [polypeptide binding]; other site 349215000637 catalytic residue [active] 349215000638 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 349215000639 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 349215000640 Peptidase family M23; Region: Peptidase_M23; pfam01551 349215000641 Domain of unknown function (DUF4263); Region: DUF4263; pfam14082 349215000642 bifunctional glyoxylate/hydroxypyruvate reductase A; Provisional; Region: ghrA; PRK15469 349215000643 Putative glycerate dehydrogenase and related proteins of the D-specific 2-hydroxy dehydrogenase family; Region: GDH_like_2; cd12164 349215000644 putative ligand binding site [chemical binding]; other site 349215000645 NAD binding site [chemical binding]; other site 349215000646 dimerization interface [polypeptide binding]; other site 349215000647 catalytic site [active] 349215000648 SURF1 superfamily. Surf1/Shy1 has been implicated in the posttranslational steps of the biogenesis of the mitochondrially-encoded Cox1 subunit of cytochrome c oxidase (complex IV). Cytochrome c oxidase (complex IV), the terminal electron-transferring...; Region: SURF1; cd06662 349215000649 Protein of unknown function (DUF983); Region: DUF983; cl02211 349215000650 Cytochrome c oxidase subunit III. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of...; Region: Cyt_c_Oxidase_III; cd01665 349215000651 Subunit III/VIIa interface [polypeptide binding]; other site 349215000652 Phospholipid binding site [chemical binding]; other site 349215000653 Subunit I/III interface [polypeptide binding]; other site 349215000654 Subunit III/VIb interface [polypeptide binding]; other site 349215000655 Subunit III/VIa interface; other site 349215000656 Subunit III/Vb interface [polypeptide binding]; other site 349215000657 cytochrome C oxidase assembly protein; Provisional; Region: PRK05089 349215000658 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 349215000659 UbiA prenyltransferase family; Region: UbiA; pfam01040 349215000660 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 349215000661 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 349215000662 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 349215000663 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 349215000664 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 349215000665 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 349215000666 protease TldD; Provisional; Region: tldD; PRK10735 349215000667 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; COG0312 349215000668 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 349215000669 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 349215000670 protein binding site [polypeptide binding]; other site 349215000671 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 349215000672 Catalytic dyad [active] 349215000673 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 349215000674 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 349215000675 protein binding site [polypeptide binding]; other site 349215000676 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 349215000677 Catalytic dyad [active] 349215000678 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 349215000679 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 349215000680 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 349215000681 protein binding site [polypeptide binding]; other site 349215000682 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 349215000683 Catalytic dyad [active] 349215000684 C-terminal peptidase (prc); Region: prc; TIGR00225 349215000685 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 349215000686 protein binding site [polypeptide binding]; other site 349215000687 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 349215000688 Catalytic dyad [active] 349215000689 Heme/copper-type cytochrome/quinol oxidases, subunit 1 [Energy production and conversion]; Region: CyoB; COG0843 349215000690 Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of...; Region: Cyt_c_Oxidase_I; cd01663 349215000691 Subunit I/III interface [polypeptide binding]; other site 349215000692 D-pathway; other site 349215000693 Subunit I/VIIc interface [polypeptide binding]; other site 349215000694 Subunit I/IV interface [polypeptide binding]; other site 349215000695 Subunit I/II interface [polypeptide binding]; other site 349215000696 Low-spin heme (heme a) binding site [chemical binding]; other site 349215000697 Subunit I/VIIa interface [polypeptide binding]; other site 349215000698 Subunit I/VIa interface [polypeptide binding]; other site 349215000699 Dimer interface; other site 349215000700 Putative water exit pathway; other site 349215000701 Binuclear center (heme a3/CuB) [ion binding]; other site 349215000702 K-pathway; other site 349215000703 Subunit I/Vb interface [polypeptide binding]; other site 349215000704 Putative proton exit pathway; other site 349215000705 Subunit I/VIb interface; other site 349215000706 Subunit I/VIc interface [polypeptide binding]; other site 349215000707 Electron transfer pathway; other site 349215000708 Subunit I/VIIIb interface [polypeptide binding]; other site 349215000709 Subunit I/VIIb interface [polypeptide binding]; other site 349215000710 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 349215000711 cytochrome c oxidase subunit II; Provisional; Region: COX2; MTH00140 349215000712 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 349215000713 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 349215000714 catalytic residues [active] 349215000715 Proprotein convertase P-domain; Region: P_proprotein; pfam01483 349215000716 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 349215000717 RNA methyltransferase, RsmE family; Region: TIGR00046 349215000718 4-hydroxybenzoate polyprenyltransferase; Reviewed; Region: ubiA; PRK12878 349215000719 UbiA prenyltransferase family; Region: UbiA; pfam01040 349215000720 Bacterial NAD-glutamate dehydrogenase; Region: Bac_GDH; pfam05088 349215000721 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Region: ELFV_dehydrog; smart00839 349215000722 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 349215000723 3-hydroxybutyrate dehydrogenase; Region: PHB_DH; TIGR01963 349215000724 NAD(P) binding site [chemical binding]; other site 349215000725 active site 349215000726 4-hydroxyphenylpyruvate dioxygenase and related hemolysins [Amino acid transport and metabolism / General function prediction only]; Region: COG3185 349215000727 N-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate Synthase (HmaS); Region: HPPD_N_like; cd08342 349215000728 dimer interface [polypeptide binding]; other site 349215000729 C-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HppD) and hydroxymandelate Synthase (HmaS); Region: HPPD_C_like; cd07250 349215000730 active site 349215000731 Fe binding site [ion binding]; other site 349215000732 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]; Region: MhpD; COG0179 349215000733 Fumarylacetoacetate (FAA) hydrolase family; Region: FAA_hydrolase; pfam01557 349215000734 maleylacetoacetate isomerase; Region: maiA; TIGR01262 349215000735 GST_N family, Class Zeta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens; Region: GST_N_Zeta; cd03042 349215000736 C-terminal domain interface [polypeptide binding]; other site 349215000737 GSH binding site (G-site) [chemical binding]; other site 349215000738 putative dimer interface [polypeptide binding]; other site 349215000739 C-terminal, alpha helical domain of Class Zeta Glutathione S-transferases; Region: GST_C_Zeta; cd03191 349215000740 dimer interface [polypeptide binding]; other site 349215000741 N-terminal domain interface [polypeptide binding]; other site 349215000742 maleylacetoacetate (MAA) substrate binding site (H site) [chemical binding]; other site 349215000743 Prokaryotic phenylalanine-4-hydroxylase (pro_PheOH); a member of the biopterin-dependent aromatic amino acid hydroxylase family of non-heme, iron(II)-dependent enzymes that also includes the eukaryotic proteins, phenylalanine-4-hydroxylase (eu_PheOH); Region: pro_PheOH; cd03348 349215000744 cofactor binding site; other site 349215000745 metal binding site [ion binding]; metal-binding site 349215000746 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4529 349215000747 FAD-NAD(P)-binding; Region: NAD_binding_9; pfam13454 349215000748 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 349215000749 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 349215000750 DNA-binding site [nucleotide binding]; DNA binding site 349215000751 RNA-binding motif; other site 349215000752 Autoinducer binding domain; Region: Autoind_bind; pfam03472 349215000753 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 349215000754 DNA binding residues [nucleotide binding] 349215000755 dimerization interface [polypeptide binding]; other site 349215000756 Domain of unknown function (DUF4105); Region: DUF4105; pfam13387 349215000757 Isochorismatase family; Region: Isochorismatase; pfam00857 349215000758 YcaC related amidohydrolases; E.coli YcaC is an homooctameric hydrolase with unknown specificity. Despite its weak sequence similarity, it is structurally related to other amidohydrolases and shares conserved active site residues with them; Region: YcaC_related; cd01012 349215000759 catalytic triad [active] 349215000760 dimer interface [polypeptide binding]; other site 349215000761 conserved cis-peptide bond; other site 349215000762 Pirin-related protein [General function prediction only]; Region: COG1741 349215000763 Pirin; Region: Pirin; pfam02678 349215000764 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 349215000765 Predicted transcriptional regulators [Transcription]; Region: COG1733 349215000766 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 349215000767 dimerization interface [polypeptide binding]; other site 349215000768 putative DNA binding site [nucleotide binding]; other site 349215000769 putative Zn2+ binding site [ion binding]; other site 349215000770 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 349215000771 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 349215000772 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 349215000773 biliverdin IX beta reductase (BVR-B, aka flavin reductase)-like proteins; atypical (a) SDRs; Region: BVR-B_like_SDR_a; cd05244 349215000774 NADH(P)-binding; Region: NAD_binding_10; pfam13460 349215000775 NAD binding site [chemical binding]; other site 349215000776 substrate binding site [chemical binding]; other site 349215000777 putative active site [active] 349215000778 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 349215000779 classical (c) SDRs; Region: SDR_c; cd05233 349215000780 NAD(P) binding site [chemical binding]; other site 349215000781 active site 349215000782 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 349215000783 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 349215000784 Pirin-related protein [General function prediction only]; Region: COG1741 349215000785 Pirin; Region: Pirin; pfam02678 349215000786 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 349215000787 azoreductase; Reviewed; Region: PRK00170 349215000788 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 349215000789 Protein of unknown function (DUF2424); Region: DUF2424; pfam10340 349215000790 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 349215000791 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 349215000792 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 349215000793 active site 349215000794 hypothetical protein; Validated; Region: PRK07198 349215000795 GTP cyclohydrolase N terminal; Region: GTP_CH_N; pfam12471 349215000796 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 349215000797 dimerization interface [polypeptide binding]; other site 349215000798 active site 349215000799 Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2; Region: ALDH_F6_MMSDH; cd07085 349215000800 methylmalonic acid semialdehyde dehydrogenase; Region: MMSDH; TIGR01722 349215000801 tetrameric interface [polypeptide binding]; other site 349215000802 NAD binding site [chemical binding]; other site 349215000803 catalytic residues [active] 349215000804 DNA-binding transcriptional regulator CpxR; Provisional; Region: PRK10955 349215000805 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 349215000806 active site 349215000807 phosphorylation site [posttranslational modification] 349215000808 intermolecular recognition site; other site 349215000809 dimerization interface [polypeptide binding]; other site 349215000810 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 349215000811 DNA binding site [nucleotide binding] 349215000812 Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; Region: FDH_GDH_like; cl17240 349215000813 UDP-N-acetyl-D-mannosaminuronate dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: WecC; COG0677 349215000814 NAD binding site [chemical binding]; other site 349215000815 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 349215000816 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; Region: UDPG_MGDP_dh_C; pfam03720 349215000817 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 349215000818 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 349215000819 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 349215000820 putative trimer interface [polypeptide binding]; other site 349215000821 Bacterial transferase hexapeptide (six repeats); Region: Hexapep; pfam00132 349215000822 WcxM-like, Left-handed parallel beta-Helix (LbH) N-terminal domain: This group is composed of Xanthomonas campestris WcxM and proteins with similarity to the WcxM N-terminal domain. WcxM is thought to be bifunctional, catalyzing both the isomerization...; Region: LbH_WxcM_N_like; cd03358 349215000823 putative CoA binding site [chemical binding]; other site 349215000824 putative trimer interface [polypeptide binding]; other site 349215000825 putative active site [active] 349215000826 putative substrate binding site [chemical binding]; other site 349215000827 putative CoA binding site [chemical binding]; other site 349215000828 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 349215000829 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 349215000830 inhibitor-cofactor binding pocket; inhibition site 349215000831 pyridoxal 5'-phosphate binding site [chemical binding]; other site 349215000832 catalytic residue [active] 349215000833 This family is most closely related to the GT1 family of glycosyltransferases. wbuB in E. coli is involved in the biosynthesis of the O26 O-antigen. It has been proposed to function as an N-acetyl-L-fucosamine (L-FucNAc) transferase; Region: GT1_wbuB_like; cd03794 349215000834 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 349215000835 DNA polymerase III subunits gamma and tau; Validated; Region: PRK09111 349215000836 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 349215000837 Walker A motif; other site 349215000838 ATP binding site [chemical binding]; other site 349215000839 Walker B motif; other site 349215000840 arginine finger; other site 349215000841 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 349215000842 DNA polymerase III gamma and tau subunits C terminal; Region: DUF3646; pfam12362 349215000843 hypothetical protein; Validated; Region: PRK00153 349215000844 Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: ExoIII-like_AP-endo; cd09086 349215000845 putative catalytic site [active] 349215000846 putative phosphate binding site [ion binding]; other site 349215000847 active site 349215000848 metal binding site A [ion binding]; metal-binding site 349215000849 DNA binding site [nucleotide binding] 349215000850 putative AP binding site [nucleotide binding]; other site 349215000851 putative metal binding site B [ion binding]; other site 349215000852 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 349215000853 putative substrate translocation pore; other site 349215000854 Major Facilitator Superfamily; Region: MFS_1; pfam07690 349215000855 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 349215000856 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 349215000857 ribosomal protein S12 methylthiotransferase; Provisional; Region: rimO; PRK14862 349215000858 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 349215000859 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 349215000860 FeS/SAM binding site; other site 349215000861 EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to...; Region: EFh; cl17302 349215000862 Ca2+ binding site [ion binding]; other site 349215000863 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 349215000864 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 349215000865 G1 box; other site 349215000866 putative GEF interaction site [polypeptide binding]; other site 349215000867 GTP/Mg2+ binding site [chemical binding]; other site 349215000868 Switch I region; other site 349215000869 G2 box; other site 349215000870 G3 box; other site 349215000871 Switch II region; other site 349215000872 G4 box; other site 349215000873 G5 box; other site 349215000874 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 349215000875 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 349215000876 Chorismate mutase type II; Region: CM_2; smart00830 349215000877 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity. They also contain a...; Region: Nudix_Hydrolase_1; cd03674 349215000878 nudix motif; other site 349215000879 Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]; Region: Rpe; COG0036 349215000880 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 349215000881 substrate binding site [chemical binding]; other site 349215000882 hexamer interface [polypeptide binding]; other site 349215000883 metal binding site [ion binding]; metal-binding site 349215000884 Heparinase II/III-like protein; Region: Hepar_II_III; cl15421 349215000885 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 349215000886 active site 349215000887 metal binding site [ion binding]; metal-binding site 349215000888 DNA repair protein RadA; Provisional; Region: PRK11823 349215000889 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 349215000890 Walker A motif/ATP binding site; other site 349215000891 ATP binding site [chemical binding]; other site 349215000892 Walker B motif; other site 349215000893 Colicin V production protein; Region: Colicin_V; pfam02674 349215000894 Bacterial protein of unknown function (DUF883); Region: DUF883; cl01888 349215000895 putative oxoacyl-(acyl carrier protein) reductase; Provisional; Region: PRK08945 349215000896 classical (c) SDRs; Region: SDR_c; cd05233 349215000897 NAD(P) binding site [chemical binding]; other site 349215000898 active site 349215000899 GTP-binding protein Der; Reviewed; Region: PRK00093 349215000900 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 349215000901 G1 box; other site 349215000902 GTP/Mg2+ binding site [chemical binding]; other site 349215000903 Switch I region; other site 349215000904 G2 box; other site 349215000905 Switch II region; other site 349215000906 G3 box; other site 349215000907 G4 box; other site 349215000908 G5 box; other site 349215000909 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 349215000910 G1 box; other site 349215000911 GTP/Mg2+ binding site [chemical binding]; other site 349215000912 Switch I region; other site 349215000913 G2 box; other site 349215000914 G3 box; other site 349215000915 Switch II region; other site 349215000916 G4 box; other site 349215000917 G5 box; other site 349215000918 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 349215000919 Trp docking motif [polypeptide binding]; other site 349215000920 active site 349215000921 PQQ-like domain; Region: PQQ_2; pfam13360 349215000922 PQQ-like domain; Region: PQQ_2; pfam13360 349215000923 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4649 349215000924 Uncharacterized protein conserved in bacteria (DUF2133); Region: DUF2133; pfam09976 349215000925 isocitrate dehydrogenase; Validated; Region: PRK08299 349215000926 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 349215000927 AMIN domain; Region: AMIN; pfam11741 349215000928 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 349215000929 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 349215000930 active site 349215000931 metal binding site [ion binding]; metal-binding site 349215000932 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 349215000933 RNA binding site [nucleotide binding]; other site 349215000934 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 349215000935 Ribonuclease E/G family; Region: RNase_E_G; pfam10150 349215000936 Cytochrome oxidase assembly protein; Region: COX15-CtaA; cl15852 349215000937 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 349215000938 Mitochondrial biogenesis AIM24; Region: AIM24; pfam01987 349215000939 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 349215000940 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 349215000941 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 349215000942 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 349215000943 catalytic loop [active] 349215000944 iron binding site [ion binding]; other site 349215000945 Usg-like family; Region: Usg; cl11567 349215000946 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 349215000947 oligomerisation interface [polypeptide binding]; other site 349215000948 mobile loop; other site 349215000949 roof hairpin; other site 349215000950 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 349215000951 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 349215000952 ring oligomerisation interface [polypeptide binding]; other site 349215000953 ATP/Mg binding site [chemical binding]; other site 349215000954 stacking interactions; other site 349215000955 hinge regions; other site 349215000956 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 349215000957 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 349215000958 DNA binding site [nucleotide binding] 349215000959 catalytic residue [active] 349215000960 H2TH interface [polypeptide binding]; other site 349215000961 putative catalytic residues [active] 349215000962 turnover-facilitating residue; other site 349215000963 intercalation triad [nucleotide binding]; other site 349215000964 8OG recognition residue [nucleotide binding]; other site 349215000965 putative reading head residues; other site 349215000966 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 349215000967 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 349215000968 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 349215000969 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 349215000970 DnaA N-terminal domain; Region: DnaA_N; pfam11638 349215000971 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 349215000972 Walker A motif; other site 349215000973 ATP binding site [chemical binding]; other site 349215000974 Walker B motif; other site 349215000975 arginine finger; other site 349215000976 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 349215000977 DnaA box-binding interface [nucleotide binding]; other site 349215000978 DNA polymerase III subunit beta; Validated; Region: PRK05643 349215000979 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 349215000980 putative DNA binding surface [nucleotide binding]; other site 349215000981 dimer interface [polypeptide binding]; other site 349215000982 beta-clamp/clamp loader binding surface; other site 349215000983 beta-clamp/translesion DNA polymerase binding surface; other site 349215000984 recombination protein F; Reviewed; Region: recF; PRK00064 349215000985 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 349215000986 Walker A/P-loop; other site 349215000987 ATP binding site [chemical binding]; other site 349215000988 Q-loop/lid; other site 349215000989 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 349215000990 ABC transporter signature motif; other site 349215000991 Walker B; other site 349215000992 D-loop; other site 349215000993 H-loop/switch region; other site 349215000994 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 349215000995 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 349215000996 Mg2+ binding site [ion binding]; other site 349215000997 G-X-G motif; other site 349215000998 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 349215000999 anchoring element; other site 349215001000 dimer interface [polypeptide binding]; other site 349215001001 ATP binding site [chemical binding]; other site 349215001002 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 349215001003 active site 349215001004 putative metal-binding site [ion binding]; other site 349215001005 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 349215001006 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 349215001007 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 349215001008 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 349215001009 active site 349215001010 HIGH motif; other site 349215001011 nucleotide binding site [chemical binding]; other site 349215001012 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 349215001013 KMSK motif region; other site 349215001014 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 349215001015 tRNA binding surface [nucleotide binding]; other site 349215001016 anticodon binding site; other site 349215001017 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 349215001018 AAA-like domain; Region: AAA_10; pfam12846 349215001019 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 349215001020 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 349215001021 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 349215001022 AefR-like transcriptional repressor, C-terminal region; Region: TetR_C_7; pfam14246 349215001023 Bacterial protein of unknown function (DUF853); Region: DUF853; pfam05872 349215001024 SlyX; Region: SlyX; pfam04102 349215001025 transcription elongation factor GreB; Reviewed; Region: greB; PRK01885 349215001026 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 349215001027 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 349215001028 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 349215001029 Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]; Region: COG1765 349215001030 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 349215001031 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 349215001032 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 349215001033 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 349215001034 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 349215001035 protein binding site [polypeptide binding]; other site 349215001036 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 349215001037 protein binding site [polypeptide binding]; other site 349215001038 Uncharacterized protein conserved in bacteria (DUF2065); Region: DUF2065; pfam09838 349215001039 HflC protein; Region: hflC; TIGR01932 349215001040 Band_7_HflC: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfC (High frequency of lysogenization C). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflC; cd03405 349215001041 HflK protein; Region: hflK; TIGR01933 349215001042 Band_7_HflK: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfK (High frequency of lysogenization K). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflK; cd03404 349215001043 Domain of unknown function DUF59; Region: DUF59; pfam01883 349215001044 MinD superfamily P-loop ATPase containing an inserted ferredoxin domain [Energy production and conversion]; Region: COG1149 349215001045 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 349215001046 Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5; Region: DHFR; cd00209 349215001047 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 349215001048 folate binding site [chemical binding]; other site 349215001049 NADP+ binding site [chemical binding]; other site 349215001050 thymidylate synthase; Reviewed; Region: thyA; PRK01827 349215001051 Thymidylate synthase and pyrimidine hydroxymethylase: Thymidylate synthase (TS) and deoxycytidylate hydroxymethylase (dCMP-HMase) are homologs that catalyze analogous alkylation of C5 of pyrimidine nucleotides. Both enzymes are involved in the...; Region: TS_Pyrimidine_HMase; cd00351 349215001052 dimerization interface [polypeptide binding]; other site 349215001053 active site 349215001054 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 349215001055 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 349215001056 dimerization interface [polypeptide binding]; other site 349215001057 DPS ferroxidase diiron center [ion binding]; other site 349215001058 ion pore; other site 349215001059 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 349215001060 O-Antigen ligase; Region: Wzy_C; pfam04932 349215001061 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 349215001062 TPR motif; other site 349215001063 binding surface 349215001064 Stringent starvation protein B; Region: SspB; cl01120 349215001065 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 349215001066 macrolide transporter subunit MacA; Provisional; Region: PRK11578 349215001067 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 349215001068 HlyD family secretion protein; Region: HlyD_3; pfam13437 349215001069 macrolide transporter ATP-binding /permease protein; Provisional; Region: PRK10535 349215001070 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 349215001071 Walker A/P-loop; other site 349215001072 ATP binding site [chemical binding]; other site 349215001073 Q-loop/lid; other site 349215001074 ABC transporter signature motif; other site 349215001075 Walker B; other site 349215001076 D-loop; other site 349215001077 H-loop/switch region; other site 349215001078 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 349215001079 FtsX-like permease family; Region: FtsX; pfam02687 349215001080 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 349215001081 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 349215001082 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_15; cd07264 349215001083 Predicted unusual protein kinase [General function prediction only]; Region: AarF; COG0661 349215001084 ABC1 family; Region: ABC1; pfam03109 349215001085 rpsU-divergently transcribed protein; Region: diverge_rpsU; TIGR02396 349215001086 COQ9; Region: COQ9; pfam08511 349215001087 Macrophage killing protein with similarity to conjugation protein; Region: IcmL; pfam11393 349215001088 N-formylglutamate amidohydrolase; Region: FGase; cl01522 349215001089 Uncharacterized protein conserved in bacteria (DUF2312); Region: DUF2312; pfam10073 349215001090 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 349215001091 O-Antigen ligase; Region: Wzy_C; pfam04932 349215001092 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 349215001093 TPR motif; other site 349215001094 binding surface 349215001095 acetyl-CoA synthetase; Provisional; Region: PRK00174 349215001096 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 349215001097 active site 349215001098 CoA binding site [chemical binding]; other site 349215001099 acyl-activating enzyme (AAE) consensus motif; other site 349215001100 AMP binding site [chemical binding]; other site 349215001101 acetate binding site [chemical binding]; other site 349215001102 O-acetylserine/cysteine export protein; Provisional; Region: PRK11453 349215001103 EamA-like transporter family; Region: EamA; pfam00892 349215001104 EamA-like transporter family; Region: EamA; pfam00892 349215001105 EVE domain; Region: EVE; pfam01878 349215001106 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 349215001107 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 349215001108 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 349215001109 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 349215001110 Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12. HMBS catalyzes the conversion of...; Region: HMBS; cl17708 349215001111 domain interfaces; other site 349215001112 active site 349215001113 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 349215001114 Uroporphyrinogen-III synthase [Coenzyme metabolism]; Region: HemD; COG1587 349215001115 active site 349215001116 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4223 349215001117 Uncharacterized membrane-bound protein [Function unknown]; Region: COG3898 349215001118 Membrane associated serine protease [Amino acid transport and metabolism]; Region: COG0705 349215001119 beta alanine--pyruvate transaminase; Provisional; Region: PRK09221 349215001120 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 349215001121 inhibitor-cofactor binding pocket; inhibition site 349215001122 pyridoxal 5'-phosphate binding site [chemical binding]; other site 349215001123 catalytic residue [active] 349215001124 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 349215001125 This family is most closely related to the GT1 family of glycosyltransferases. wbuB in E. coli is involved in the biosynthesis of the O26 O-antigen. It has been proposed to function as an N-acetyl-L-fucosamine (L-FucNAc) transferase; Region: GT1_wbuB_like; cd03794 349215001126 Glycosyltransferase Family 4; Region: Glyco_transf_4; pfam13439 349215001127 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 349215001128 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 349215001129 active site 349215001130 WfgS and WfeV are involved in O-antigen biosynthesis; Region: GT_2_WfgS_like; cd06433 349215001131 metal-binding site 349215001132 polysaccharide export protein EpsE; Region: EpsE; TIGR03028 349215001133 SLBB domain; Region: SLBB; pfam10531 349215001134 SLBB domain; Region: SLBB; pfam10531 349215001135 Capsule biosynthesis GfcC; Region: Caps_synth_GfcC; pfam06251 349215001136 Protein of unknown function (DUF1489); Region: DUF1489; pfam07370 349215001137 Protein of unknown function, DUF486; Region: DUF486; cl01236 349215001138 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Ada; COG2169 349215001139 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 349215001140 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 349215001141 The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases...; Region: ATase; cd06445 349215001142 DNA binding site [nucleotide binding] 349215001143 active site 349215001144 short chain dehydrogenase; Validated; Region: PRK08264 349215001145 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 349215001146 NAD(P) binding site [chemical binding]; other site 349215001147 active site 349215001148 PAS domain; Region: PAS_9; pfam13426 349215001149 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 349215001150 PAS domain; Region: PAS_9; pfam13426 349215001151 putative active site [active] 349215001152 heme pocket [chemical binding]; other site 349215001153 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 349215001154 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 349215001155 dimer interface [polypeptide binding]; other site 349215001156 putative CheW interface [polypeptide binding]; other site 349215001157 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 349215001158 intermolecular recognition site; other site 349215001159 active site 349215001160 dimerization interface [polypeptide binding]; other site 349215001161 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 349215001162 putative binding surface; other site 349215001163 active site 349215001164 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 349215001165 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 349215001166 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 349215001167 ATP binding site [chemical binding]; other site 349215001168 Mg2+ binding site [ion binding]; other site 349215001169 G-X-G motif; other site 349215001170 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 349215001171 Response regulator receiver domain; Region: Response_reg; pfam00072 349215001172 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 349215001173 active site 349215001174 phosphorylation site [posttranslational modification] 349215001175 intermolecular recognition site; other site 349215001176 dimerization interface [polypeptide binding]; other site 349215001177 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 349215001178 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 349215001179 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 349215001180 active site 349215001181 phosphorylation site [posttranslational modification] 349215001182 intermolecular recognition site; other site 349215001183 dimerization interface [polypeptide binding]; other site 349215001184 CheB methylesterase; Region: CheB_methylest; pfam01339 349215001185 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 349215001186 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 349215001187 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 349215001188 S-adenosylmethionine binding site [chemical binding]; other site 349215001189 Homospermidine synthase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG5310 349215001190 Saccharopine dehydrogenase; Region: Saccharop_dh; pfam03435 349215001191 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 349215001192 UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]; Region: GalE; COG1087 349215001193 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 349215001194 NAD(P) binding site [chemical binding]; other site 349215001195 active site 349215001196 This family is most closely related to the GT1 family of glycosyltransferases. cap1E in Streptococcus pneumoniae is required for the synthesis of type 1 capsular polysaccharides; Region: GT1_cap1E_like; cd03808 349215001197 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 349215001198 putative ADP-binding pocket [chemical binding]; other site 349215001199 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 349215001200 putative substrate translocation pore; other site 349215001201 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 349215001202 Tetratricopeptide repeat; Region: TPR_16; pfam13432 349215001203 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 349215001204 TPR motif; other site 349215001205 binding surface 349215001206 TPR repeat; Region: TPR_11; pfam13414 349215001207 TPR repeat; Region: TPR_11; pfam13414 349215001208 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 349215001209 binding surface 349215001210 TPR motif; other site 349215001211 TPR repeat; Region: TPR_11; pfam13414 349215001212 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 349215001213 binding surface 349215001214 TPR motif; other site 349215001215 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 349215001216 TPR repeat; Region: TPR_11; pfam13414 349215001217 binding surface 349215001218 TPR motif; other site 349215001219 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 349215001220 binding surface 349215001221 Tetratricopeptide repeat; Region: TPR_16; pfam13432 349215001222 TPR motif; other site 349215001223 Sulfotransferase family; Region: Sulfotransfer_3; pfam13469 349215001224 Domain of unknown function (DUF4402); Region: DUF4402; pfam14352 349215001225 Fn3-like domain (DUF1034); Region: DUF1034; pfam06280 349215001226 P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimD; COG3188 349215001227 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 349215001228 Carboxypeptidase regulatory-like domain; Region: CarboxypepD_reg; pfam13620 349215001229 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 349215001230 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 349215001231 active site 349215001232 phosphorylation site [posttranslational modification] 349215001233 intermolecular recognition site; other site 349215001234 dimerization interface [polypeptide binding]; other site 349215001235 Sterol desaturase [Lipid metabolism]; Region: ERG3; COG3000 349215001236 Fatty acid hydroxylase superfamily; Region: FA_hydroxylase; pfam04116 349215001237 GDP-D-mannose dehydratase [Cell envelope biogenesis, outer membrane]; Region: Gmd; COG1089 349215001238 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 349215001239 NADP-binding site; other site 349215001240 homotetramer interface [polypeptide binding]; other site 349215001241 substrate binding site [chemical binding]; other site 349215001242 homodimer interface [polypeptide binding]; other site 349215001243 active site 349215001244 GDP-4-keto-6-deoxymannose-3, 5-epimerase-4-reductase; Region: PLN02725 349215001245 GDP-fucose synthetase, extended (e) SDRs; Region: GDP_FS_SDR_e; cd05239 349215001246 NADP binding site [chemical binding]; other site 349215001247 active site 349215001248 putative substrate binding site [chemical binding]; other site 349215001249 Mannose-1-phosphate guanylyltransferase [Cell envelope biogenesis, outer membrane]; Region: {ManC}; COG0836 349215001250 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 349215001251 Substrate binding site; other site 349215001252 Arginase family; Region: Arginase; cd09989 349215001253 active site 349215001254 Mn binding site [ion binding]; other site 349215001255 oligomer interface [polypeptide binding]; other site 349215001256 probable methyltransferase domain, EasF family; Region: methyl_EasF; TIGR03439 349215001257 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 349215001258 non-specific DNA binding site [nucleotide binding]; other site 349215001259 salt bridge; other site 349215001260 sequence-specific DNA binding site [nucleotide binding]; other site 349215001261 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 349215001262 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 349215001263 active site 349215001264 Zn binding site [ion binding]; other site 349215001265 Zn-dependent oligopeptidases [Amino acid transport and metabolism]; Region: Dcp; COG0339 349215001266 Peptidase family M3 dipeptidyl carboxypeptidase (DCP); Region: M3A_DCP; cd06456 349215001267 active site 349215001268 Zn binding site [ion binding]; other site 349215001269 bifunctional tRNA (mnm(5)s(2)U34)-methyltransferase/FAD-dependent cmnm(5)s(2)U34 oxidoreductase; Reviewed; Region: mnmC; PRK01747 349215001270 Uncharacterized conserved protein [Function unknown]; Region: COG4121 349215001271 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 349215001272 This subfamily contains Escherichia coli WecA, Bacillus subtilis TagO and related proteins. WecA is an UDP-N-acetylglucosamine (GlcNAc):undecaprenyl-phosphate (Und-P) GlcNAc-1-phosphate transferase that catalyzes the formation of a phosphodiester bond...; Region: GT_WecA_like; cd06853 349215001273 Mg++ binding site [ion binding]; other site 349215001274 putative catalytic motif [active] 349215001275 substrate binding site [chemical binding]; other site 349215001276 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 349215001277 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 349215001278 Predicted sulfurtransferase [General function prediction only]; Region: COG1054 349215001279 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 349215001280 active site residue [active] 349215001281 DNA-binding transcriptional regulator OxyR; Provisional; Region: PRK11151 349215001282 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 349215001283 The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily; Region: PBP2_OxyR; cd08411 349215001284 dimerization interface [polypeptide binding]; other site 349215001285 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 349215001286 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 349215001287 dimer interface [polypeptide binding]; other site 349215001288 decamer (pentamer of dimers) interface [polypeptide binding]; other site 349215001289 catalytic triad [active] 349215001290 peroxidatic and resolving cysteines [active] 349215001291 alkylhydroperoxidase, AhpD family; Region: ahpD; TIGR00777 349215001292 alkylhydroperoxidase AhpD family core domain; Region: ahpD_dom; TIGR00778 349215001293 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 349215001294 Mechanosensitive ion channel; Region: MS_channel; pfam00924 349215001295 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 349215001296 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 349215001297 alpha-L-glutamate ligases, RimK family; Region: rimK_fam; TIGR00768 349215001298 ATP-grasp domain; Region: ATP-grasp_4; cl17255 349215001299 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 349215001300 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 349215001301 putative ligand binding site [chemical binding]; other site 349215001302 Predicted methyltransferases [General function prediction only]; Region: COG0313 349215001303 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 349215001304 putative SAM binding site [chemical binding]; other site 349215001305 putative homodimer interface [polypeptide binding]; other site 349215001306 Ethanolamine utilisation protein and carboxysome structural protein domain family; Region: EutN_CcmL; cl01889 349215001307 hypothetical protein; Reviewed; Region: PRK12497 349215001308 BON domain; Region: BON; pfam04972 349215001309 Predicted periplasmic or secreted lipoprotein [General function prediction only]; Region: OsmY; COG2823 349215001310 BON domain; Region: BON; pfam04972 349215001311 Transglutaminase-like superfamily; Region: Transglut_core2; pfam13369 349215001312 Tetratricopeptide repeat; Region: TPR_9; pfam13371 349215001313 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 349215001314 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 349215001315 ligand binding site [chemical binding]; other site 349215001316 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1729 349215001317 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 349215001318 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 349215001319 Ligand Binding Site [chemical binding]; other site 349215001320 FtsH Extracellular; Region: FtsH_ext; pfam06480 349215001321 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 349215001322 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 349215001323 Walker A motif; other site 349215001324 ATP binding site [chemical binding]; other site 349215001325 Walker B motif; other site 349215001326 arginine finger; other site 349215001327 Peptidase family M41; Region: Peptidase_M41; pfam01434 349215001328 phosphoglucosamine mutase; Provisional; Region: glmM; PRK14315 349215001329 GlmM is a bacterial phosphoglucosamine mutase (PNGM) that belongs to the alpha-D-phosphohexomutase superfamily. It is required for the interconversion of glucosamine-6-phosphate and glucosamine-1-phosphate in the biosynthetic pathway of...; Region: GlmM; cd05802 349215001330 active site 349215001331 substrate binding site [chemical binding]; other site 349215001332 metal binding site [ion binding]; metal-binding site 349215001333 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 349215001334 active site 349215001335 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 349215001336 catalytic tetrad [active] 349215001337 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 349215001338 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 349215001339 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 349215001340 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 349215001341 GDP-binding site [chemical binding]; other site 349215001342 ACT binding site; other site 349215001343 IMP binding site; other site 349215001344 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 349215001345 active site 349215001346 ATP binding site [chemical binding]; other site 349215001347 substrate binding site [chemical binding]; other site 349215001348 activation loop (A-loop); other site 349215001349 Flp pilus assembly protein TadG [Intracellular trafficking and secretion]; Region: TadG; COG4961 349215001350 TadE-like protein; Region: TadE; pfam07811 349215001351 Flp pilus assembly protein TadG [Intracellular trafficking and secretion]; Region: TadG; COG4961 349215001352 Putative Flp pilus-assembly TadE/G-like; Region: Tad; pfam13400 349215001353 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 349215001354 von Willebrand factor type A domain; Region: VWA_2; pfam13519 349215001355 metal ion-dependent adhesion site (MIDAS); other site 349215001356 Flp/Fap pilin component; Region: Flp_Fap; cl01585 349215001357 Flp pilus assembly protein, protease CpaA [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: CpaA; COG4960 349215001358 Flp pilus assembly protein CpaB [Intracellular trafficking and secretion]; Region: CpaB; COG3745 349215001359 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 349215001360 Flp pilus assembly protein, secretin CpaC [Intracellular trafficking and secretion]; Region: CpaC; COG4964 349215001361 Pilus formation protein N terminal region; Region: T2SS-T3SS_pil_N; pfam13629 349215001362 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 349215001363 Type IV pili component [Cell motility and secretion]; Region: COG5461 349215001364 Pilus biogenesis CpaD protein (pilus_cpaD); Region: Pilus_CpaD; pfam09476 349215001365 AAA domain; Region: AAA_31; pfam13614 349215001366 This protein family consists of proteins similar to the cpaE protein of the Caulobacter pilus assembly and the orf4 protein of Actinobacillus pilus formation gene cluster. The function of these proteins are unkown. The Caulobacter pilus assembly contains...; Region: CpaE_like; cd03111 349215001367 Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]; Region: CpaF; COG4962 349215001368 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 349215001369 ATP binding site [chemical binding]; other site 349215001370 Walker A motif; other site 349215001371 hexamer interface [polypeptide binding]; other site 349215001372 Walker B motif; other site 349215001373 Flp pilus assembly protein TadB [Intracellular trafficking and secretion]; Region: TadB; COG4965 349215001374 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 349215001375 Flp pilus assembly protein TadC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: TadC; COG2064 349215001376 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 349215001377 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 349215001378 binding surface 349215001379 TPR motif; other site 349215001380 Pilus formation protein N terminal region; Region: T2SS-T3SS_pil_N; pfam13629 349215001381 Response regulator receiver domain; Region: Response_reg; pfam00072 349215001382 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 349215001383 active site 349215001384 phosphorylation site [posttranslational modification] 349215001385 intermolecular recognition site; other site 349215001386 dimerization interface [polypeptide binding]; other site 349215001387 glucokinase; Provisional; Region: glk; PRK00292 349215001388 glucokinase, proteobacterial type; Region: glk; TIGR00749 349215001389 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 349215001390 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can...; Region: GT1_like_2; cd03814 349215001391 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 349215001392 pseudouridine synthase, RluA family; Region: rluA_subfam; TIGR00005 349215001393 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 349215001394 RNA binding surface [nucleotide binding]; other site 349215001395 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 349215001396 active site 349215001397 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 349215001398 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Region: ELFV_dehydrog; pfam00208 349215001399 NAD(P) binding domain of leucine dehydrogenase, phenylalanine dehydrogenase, and valine dehydrogenase; Region: NAD_bind_Leu_Phe_Val_DH; cd01075 349215001400 NAD binding site [chemical binding]; other site 349215001401 Phe binding site; other site 349215001402 Bacterial putative lipoprotein (DUF940); Region: DUF940; pfam06082 349215001403 glycerol-3-phosphate dehydrogenase; Reviewed; Region: glpD; PRK12266 349215001404 glycerol kinase; Provisional; Region: glpK; PRK00047 349215001405 Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases; Region: FGGY_EcGK_like; cd07786 349215001406 N- and C-terminal domain interface [polypeptide binding]; other site 349215001407 active site 349215001408 MgATP binding site [chemical binding]; other site 349215001409 catalytic site [active] 349215001410 metal binding site [ion binding]; metal-binding site 349215001411 glycerol binding site [chemical binding]; other site 349215001412 homotetramer interface [polypeptide binding]; other site 349215001413 homodimer interface [polypeptide binding]; other site 349215001414 FBP binding site [chemical binding]; other site 349215001415 protein IIAGlc interface [polypeptide binding]; other site 349215001416 OmpW family; Region: OmpW; cl17427 349215001417 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 349215001418 RNA binding site [nucleotide binding]; other site 349215001419 Ribonuclease E/G family; Region: RNase_E_G; pfam10150 349215001420 Maf-like protein; Region: Maf; pfam02545 349215001421 Nucleotide binding protein Maf. Maf has been implicated in inhibition of septum formation in eukaryotes, bacteria and archaea, but homologs in B.subtilis and S.cerevisiae are nonessential for cell division. Maf has been predicted to be a nucleotide- or...; Region: Maf; cd00555 349215001422 active site 349215001423 dimer interface [polypeptide binding]; other site 349215001424 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 349215001425 rRNA binding site [nucleotide binding]; other site 349215001426 predicted 30S ribosome binding site; other site 349215001427 Uncharacterized protein family (UPF0262); Region: UPF0262; cl11489 349215001428 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 349215001429 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 349215001430 hinge; other site 349215001431 active site 349215001432 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 349215001433 trimer interface [polypeptide binding]; other site 349215001434 active site 349215001435 Invasion associated locus B (IalB) protein; Region: IalB; pfam06776 349215001436 potassium/proton antiporter; Reviewed; Region: PRK05326 349215001437 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 349215001438 Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: ExoIII-like_AP-endo; cd09086 349215001439 putative catalytic site [active] 349215001440 putative phosphate binding site [ion binding]; other site 349215001441 active site 349215001442 metal binding site A [ion binding]; metal-binding site 349215001443 DNA binding site [nucleotide binding] 349215001444 putative AP binding site [nucleotide binding]; other site 349215001445 putative metal binding site B [ion binding]; other site 349215001446 Iron-sulfur cluster assembly accessory protein; Region: TIGR00049 349215001447 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 349215001448 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 349215001449 Zn2+ binding site [ion binding]; other site 349215001450 Mg2+ binding site [ion binding]; other site 349215001451 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 349215001452 Sporulation related domain; Region: SPOR; pfam05036 349215001453 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 349215001454 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 349215001455 Rec8/ScpA/Scc1-like protein (kleisin family) [Replication, recombination, and repair]; Region: scpA; COG1354 349215001456 Putative transcriptional regulators (Ypuh-like); Region: DUF387; pfam04079 349215001457 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 349215001458 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 349215001459 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 349215001460 Predicted ATPase [General function prediction only]; Region: COG1485 349215001461 Uncharacterized protein conserved in bacteria (DUF2336); Region: DUF2336; pfam10098 349215001462 malate dehydrogenase; Reviewed; Region: PRK06223 349215001463 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 349215001464 NAD(P) binding site [chemical binding]; other site 349215001465 dimer interface [polypeptide binding]; other site 349215001466 tetramer (dimer of dimers) interface [polypeptide binding]; other site 349215001467 substrate binding site [chemical binding]; other site 349215001468 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 349215001469 salt bridge; other site 349215001470 non-specific DNA binding site [nucleotide binding]; other site 349215001471 sequence-specific DNA binding site [nucleotide binding]; other site 349215001472 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 349215001473 catalytic residue [active] 349215001474 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 349215001475 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 349215001476 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 349215001477 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 349215001478 CoA-ligase; Region: Ligase_CoA; pfam00549 349215001479 Uncharacterized protein conserved in bacteria (DUF2059); Region: DUF2059; pfam09832 349215001480 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 349215001481 CoA binding domain; Region: CoA_binding; smart00881 349215001482 CoA-ligase; Region: Ligase_CoA; pfam00549 349215001483 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 349215001484 Thiamine pyrophosphate (TPP) family, E1 of OGDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the 2-oxoglutarate dehydrogenase multienzyme complex (OGDC). OGDC catalyzes the oxidative decarboxylation of...; Region: TPP_E1_OGDC_like; cd02016 349215001485 TPP-binding site [chemical binding]; other site 349215001486 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 349215001487 PYR/PP interface [polypeptide binding]; other site 349215001488 dimer interface [polypeptide binding]; other site 349215001489 TPP binding site [chemical binding]; other site 349215001490 Small Multidrug Resistance protein; Region: Multi_Drug_Res; cl00910 349215001491 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 349215001492 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 349215001493 E3 interaction surface; other site 349215001494 lipoyl attachment site [posttranslational modification]; other site 349215001495 e3 binding domain; Region: E3_binding; pfam02817 349215001496 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 349215001497 Cytidine and deoxycytidylate deaminase zinc-binding region. The family contains cytidine deaminases, nucleoside deaminases, deoxycytidylate deaminases and riboflavin deaminases. Also included are the apoBec family of mRNA editing enzymes. All members...; Region: cytidine_deaminase-like; cl00269 349215001498 Cytidine and deoxycytidylate deaminase zinc-binding region. The family contains cytidine deaminases, nucleoside deaminases, deoxycytidylate deaminases and riboflavin deaminases. Also included are the apoBec family of mRNA editing enzymes. All members...; Region: cytidine_deaminase-like; cl00269 349215001499 active site 349215001500 Zn binding site [ion binding]; other site 349215001501 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 349215001502 catalytic site [active] 349215001503 putative active site [active] 349215001504 putative substrate binding site [chemical binding]; other site 349215001505 CYTH-like (also known as triphosphate tunnel metalloenzyme (TTM)-like) Phosphatases; Region: CYTH-like_Pase; cl11964 349215001506 putative active site; other site 349215001507 signature motif; other site 349215001508 putative triphosphate binding site [ion binding]; other site 349215001509 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 349215001510 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 349215001511 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 349215001512 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 349215001513 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 349215001514 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 349215001515 active site 349215001516 DNA binding site [nucleotide binding] 349215001517 Int/Topo IB signature motif; other site 349215001518 Protein of unknown function, DUF484; Region: DUF484; cl17449 349215001519 Transaldolase-like fructose-6-phosphate aldolases (FSA) found in bacteria and archaea; Region: Transaldolase_FSA; cd00956 349215001520 active site 349215001521 intersubunit interactions; other site 349215001522 catalytic residue [active] 349215001523 primosome assembly protein PriA; Validated; Region: PRK05580 349215001524 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 349215001525 ATP binding site [chemical binding]; other site 349215001526 putative Mg++ binding site [ion binding]; other site 349215001527 helicase superfamily c-terminal domain; Region: HELICc; smart00490 349215001528 TraX protein; Region: TraX; cl05434 349215001529 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 349215001530 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 349215001531 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 349215001532 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 349215001533 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 349215001534 beta subunit interaction interface [polypeptide binding]; other site 349215001535 Walker A motif; other site 349215001536 ATP binding site [chemical binding]; other site 349215001537 Walker B motif; other site 349215001538 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 349215001539 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 349215001540 core domain interface [polypeptide binding]; other site 349215001541 delta subunit interface [polypeptide binding]; other site 349215001542 epsilon subunit interface [polypeptide binding]; other site 349215001543 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 349215001544 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 349215001545 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 349215001546 alpha subunit interaction interface [polypeptide binding]; other site 349215001547 Walker A motif; other site 349215001548 ATP binding site [chemical binding]; other site 349215001549 Walker B motif; other site 349215001550 inhibitor binding site; inhibition site 349215001551 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 349215001552 F0F1-type ATP synthase, epsilon subunit (mitochondrial delta subunit) [Energy production and conversion]; Region: AtpC; COG0355 349215001553 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 349215001554 gamma subunit interface [polypeptide binding]; other site 349215001555 epsilon subunit interface [polypeptide binding]; other site 349215001556 LBP interface [polypeptide binding]; other site 349215001557 Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]; Region: DinG; COG1199 349215001558 CRISPR/Cas system-associated DinG family helicase Csf4; Region: Csf4_U; cl17460 349215001559 Helicase C-terminal domain; Region: Helicase_C_2; pfam13307 349215001560 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 349215001561 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 349215001562 dimer interface [polypeptide binding]; other site 349215001563 putative anticodon binding site; other site 349215001564 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 349215001565 motif 1; other site 349215001566 active site 349215001567 motif 2; other site 349215001568 motif 3; other site 349215001569 YcfA-like protein; Region: YcfA; pfam07927 349215001570 Uncharacterized protein family (UPF0150); Region: UPF0150; pfam03681 349215001571 Nitroreductase-like family which includes NADH oxidase and arsenite oxidiase. NADH oxidase catalyses the oxidation of NAD(P)H and accepts a wide broad range of compounds as electron acceptors, such as nitrocompound. Arsenite oxidase in a...; Region: Arsenite_oxidase; cd02135 349215001572 putative FMN binding site [chemical binding]; other site 349215001573 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 349215001574 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 349215001575 active site 349215001576 phosphorylation site [posttranslational modification] 349215001577 intermolecular recognition site; other site 349215001578 dimerization interface [polypeptide binding]; other site 349215001579 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 349215001580 DNA binding site [nucleotide binding] 349215001581 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 349215001582 Leucyl aminopeptidase (aminopeptidase T) [Amino acid transport and metabolism]; Region: AmpS; COG2309 349215001583 excinuclease ABC subunit B; Provisional; Region: PRK05298 349215001584 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 349215001585 ATP binding site [chemical binding]; other site 349215001586 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 349215001587 nucleotide binding region [chemical binding]; other site 349215001588 ATP-binding site [chemical binding]; other site 349215001589 Ultra-violet resistance protein B; Region: UvrB; pfam12344 349215001590 UvrB/uvrC motif; Region: UVR; pfam02151 349215001591 Protein of unknown function (DUF541); Region: SIMPL; pfam04402 349215001592 N-acetylmuramic acid-6-phosphate etherase; Reviewed; Region: murQ; PRK05441 349215001593 N-acetylmuramic acid 6-phosphate etherase. Members of this family contain the SIS (Sugar ISomerase) domain. The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. The bacterial cell wall sugar N-acetylmuramic acid...; Region: SIS_Etherase; cd05007 349215001594 putative active site [active] 349215001595 peroxiredoxin, Ohr subfamily; Region: organ_hyd_perox; TIGR03561 349215001596 GTP-binding protein LepA; Provisional; Region: PRK05433 349215001597 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 349215001598 G1 box; other site 349215001599 putative GEF interaction site [polypeptide binding]; other site 349215001600 GTP/Mg2+ binding site [chemical binding]; other site 349215001601 Switch I region; other site 349215001602 G2 box; other site 349215001603 G3 box; other site 349215001604 Switch II region; other site 349215001605 G4 box; other site 349215001606 G5 box; other site 349215001607 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 349215001608 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 349215001609 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 349215001610 Peptidase inhibitor I78 family; Region: Inhibitor_I78; pfam11720 349215001611 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 349215001612 CheR methyltransferase, all-alpha domain; Region: CheR_N; pfam03705 349215001613 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 349215001614 S-adenosylmethionine binding site [chemical binding]; other site 349215001615 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 349215001616 Response regulator receiver domain; Region: Response_reg; pfam00072 349215001617 active site 349215001618 phosphorylation site [posttranslational modification] 349215001619 intermolecular recognition site; other site 349215001620 dimerization interface [polypeptide binding]; other site 349215001621 Uncharacterized protein conserved in bacteria (DUF2328); Region: DUF2328; pfam10090 349215001622 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 349215001623 The phosphomannomutase/phosphoglucomutase (PMM/PGM) bifunctional enzyme catalyzes the reversible conversion of 1-phospho to 6-phospho-sugars (e.g. between mannose-1-phosphate and mannose-6-phosphate or glucose-1-phosphate and glucose-6-phosphate) via a...; Region: PMM_PGM; cd03089 349215001624 active site 349215001625 substrate binding site [chemical binding]; other site 349215001626 metal binding site [ion binding]; metal-binding site 349215001627 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 349215001628 active site 349215001629 tetramer interface; other site 349215001630 DnaJ molecular chaperone homology domain; Region: DnaJ; smart00271 349215001631 HSP70 interaction site [polypeptide binding]; other site 349215001632 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 349215001633 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 349215001634 X-Prolyl Aminopeptidase 2. E.C. 3.4.11.9. Also known as X-Pro aminopeptidase, proline aminopeptidase, aminopeptidase P, and aminoacylproline aminopeptidase. Catalyses release of any N-terminal amino acid, including proline, that is linked with proline; Region: APP; cd01085 349215001635 active site 349215001636 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 349215001637 Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]; Region: HtpX; COG0501 349215001638 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 349215001639 Lipase. Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface. A typical feature of lipases is "interfacial activation", the process of...; Region: Lipase; cl14883 349215001640 nucleophilic elbow; other site 349215001641 catalytic triad; other site 349215001642 ABC-type uncharacterized transport system, duplicated ATPase component [General function prediction only]; Region: COG4172 349215001643 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 349215001644 Walker A/P-loop; other site 349215001645 ATP binding site [chemical binding]; other site 349215001646 Q-loop/lid; other site 349215001647 ABC transporter signature motif; other site 349215001648 Walker B; other site 349215001649 D-loop; other site 349215001650 H-loop/switch region; other site 349215001651 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 349215001652 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 349215001653 Walker A/P-loop; other site 349215001654 ATP binding site [chemical binding]; other site 349215001655 Q-loop/lid; other site 349215001656 ABC transporter signature motif; other site 349215001657 Walker B; other site 349215001658 D-loop; other site 349215001659 H-loop/switch region; other site 349215001660 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 349215001661 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 349215001662 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like1; cd05666 349215001663 metal binding site [ion binding]; metal-binding site 349215001664 putative dimer interface [polypeptide binding]; other site 349215001665 nickel ABC transporter, permease subunit NikC; Region: nickel_nikC; TIGR02790 349215001666 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 349215001667 dimer interface [polypeptide binding]; other site 349215001668 conserved gate region; other site 349215001669 putative PBP binding loops; other site 349215001670 ABC-ATPase subunit interface; other site 349215001671 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4174 349215001672 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 349215001673 dimer interface [polypeptide binding]; other site 349215001674 conserved gate region; other site 349215001675 ABC-ATPase subunit interface; other site 349215001676 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]; Region: COG2317 349215001677 Peptidase Gluzincin family (thermolysin-like proteinases, TLPs) includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins); Region: GluZincin; cl14813 349215001678 Zn binding site [ion binding]; other site 349215001679 TM1410 hypothetical-related protein; Region: DUF297; pfam03537 349215001680 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 349215001681 catalytic core [active] 349215001682 O-Antigen ligase; Region: Wzy_C; pfam04932 349215001683 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 349215001684 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 349215001685 Ligand binding site; other site 349215001686 oligomer interface; other site 349215001687 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 349215001688 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_14; cd08497 349215001689 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 349215001690 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK05286 349215001691 Dihydroorotate dehydrogenase (DHOD) class 2. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires...; Region: DHOD_2_like; cd04738 349215001692 quinone interaction residues [chemical binding]; other site 349215001693 active site 349215001694 catalytic residues [active] 349215001695 FMN binding site [chemical binding]; other site 349215001696 substrate binding site [chemical binding]; other site 349215001697 Phosphatidylglycerophosphate synthase [Lipid metabolism]; Region: PgsA; COG0558 349215001698 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 349215001699 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 349215001700 active site 349215001701 phosphorylation site [posttranslational modification] 349215001702 intermolecular recognition site; other site 349215001703 dimerization interface [polypeptide binding]; other site 349215001704 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 349215001705 DNA binding site [nucleotide binding] 349215001706 Mitochondrial fission ELM1; Region: Mito_fiss_Elm1; pfam06258 349215001707 Predicted nucleoside-diphosphate-sugar epimerase [Cell envelope biogenesis, outer membrane]; Region: COG3660 349215001708 Predicted nucleoside-diphosphate-sugar epimerase [Cell envelope biogenesis, outer membrane]; Region: COG3660 349215001709 Mitochondrial fission ELM1; Region: Mito_fiss_Elm1; pfam06258 349215001710 flagellum-specific ATP synthase; Validated; Region: fliI; PRK08927 349215001711 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 349215001712 Walker A motif/ATP binding site; other site 349215001713 Walker B motif; other site 349215001714 Flagellar FliJ protein; Region: FliJ; pfam02050 349215001715 putative diguanylate cyclase YedQ; Provisional; Region: PRK15426 349215001716 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 349215001717 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 349215001718 flagellar biosynthetic protein FlhF; Region: FlhF; TIGR03499 349215001719 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 349215001720 Protein of unknown function (DUF3137); Region: DUF3137; pfam11335 349215001721 Protein of unknown function (DUF3137); Region: DUF3137; pfam11335 349215001722 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 349215001723 FHIPEP family; Region: FHIPEP; pfam00771 349215001724 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 349215001725 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 349215001726 ligand binding site [chemical binding]; other site 349215001727 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 349215001728 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 349215001729 active site 349215001730 phosphorylation site [posttranslational modification] 349215001731 intermolecular recognition site; other site 349215001732 dimerization interface [polypeptide binding]; other site 349215001733 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 349215001734 Walker A motif; other site 349215001735 ATP binding site [chemical binding]; other site 349215001736 Walker B motif; other site 349215001737 arginine finger; other site 349215001738 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 349215001739 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 349215001740 flagellar motor switch protein; Reviewed; Region: PRK08916 349215001741 flagellar assembly protein H; Validated; Region: fliH; PRK06032 349215001742 flagellar motor switch protein G; Validated; Region: fliG; PRK05686 349215001743 FliG C-terminal domain; Region: FliG_C; pfam01706 349215001744 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 349215001745 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; pfam01514 349215001746 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 349215001747 FlaG protein; Region: FlaG; cl00591 349215001748 Flagellar protein FlaF; Region: FlaF; cl11454 349215001749 Flagellar protein FlbT; Region: FlbT; pfam07378 349215001750 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 349215001751 Peptidase M10 serralysin C terminal; Region: Peptidase_M10_C; pfam08548 349215001752 flagellin; Reviewed; Region: PRK12688 349215001753 flagellin; Reviewed; Region: PRK12688 349215001754 pyruvate phosphate dikinase; Provisional; Region: PRK09279 349215001755 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 349215001756 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 349215001757 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 349215001758 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 349215001759 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 349215001760 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 349215001761 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 349215001762 Glycosyltransferase family 9 (heptosyltransferase); Region: Glyco_transf_9; pfam01075 349215001763 putative active site [active] 349215001764 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 349215001765 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_14; cd08497 349215001766 Macro domain, 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 polymerases). Some macro domains recognize poly...; Region: Macro; cl00019 349215001767 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 349215001768 Adenosine kinase (AK) catalyzes the phosphorylation of ribofuranosyl-containing nucleoside analogues at the 5'-hydroxyl using ATP or GTP as the phosphate donor.The physiological function of AK is associated with the regulation of extracellular...; Region: adenosine_kinase; cd01168 349215001769 substrate binding site [chemical binding]; other site 349215001770 ATP binding site [chemical binding]; other site 349215001771 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 349215001772 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 349215001773 substrate-cofactor binding pocket; other site 349215001774 pyridoxal 5'-phosphate binding site [chemical binding]; other site 349215001775 catalytic residue [active] 349215001776 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 349215001777 Ribokinase catalyses the phosphorylation of ribose to ribose-5-phosphate using ATP. This reaction is the first step in the ribose metabolism. It traps ribose within the cell after uptake and also prepares the sugar for use in the synthesis of nucleotides...; Region: ribokinase; cd01174 349215001778 substrate binding site [chemical binding]; other site 349215001779 dimer interface [polypeptide binding]; other site 349215001780 ATP binding site [chemical binding]; other site 349215001781 Response regulator receiver domain; Region: Response_reg; pfam00072 349215001782 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 349215001783 active site 349215001784 phosphorylation site [posttranslational modification] 349215001785 intermolecular recognition site; other site 349215001786 dimerization interface [polypeptide binding]; other site 349215001787 thiamine pyrophosphate protein; Validated; Region: PRK08199 349215001788 Pyrimidine (PYR) binding domain of POX and related proteins; Region: TPP_PYR_POX_like; cd07035 349215001789 PYR/PP interface [polypeptide binding]; other site 349215001790 dimer interface [polypeptide binding]; other site 349215001791 TPP binding site [chemical binding]; other site 349215001792 Thiamine pyrophosphate enzyme, central domain; Region: TPP_enzyme_M; pfam00205 349215001793 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cd00568 349215001794 TPP-binding site [chemical binding]; other site 349215001795 PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by...; Region: PCD_DCoH_subfamily_b; cd00914 349215001796 aromatic arch; other site 349215001797 DCoH dimer interaction site [polypeptide binding]; other site 349215001798 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 349215001799 DCoH tetramer interaction site [polypeptide binding]; other site 349215001800 substrate binding site [chemical binding]; other site 349215001801 Minimal MMP-like domain found in Acidothermus cellulolyticus hypothetical protein ACEL2062 and similar protein; Region: MMP_ACEL2062; cd12952 349215001802 heat shock protein 90; Provisional; Region: PRK05218 349215001803 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 349215001804 ATP binding site [chemical binding]; other site 349215001805 Mg2+ binding site [ion binding]; other site 349215001806 G-X-G motif; other site 349215001807 pyridoxamine 5'-phosphate oxidase; Provisional; Region: PRK05679 349215001808 Pyridoxamine 5'-phosphate oxidase; Region: Pyridox_oxidase; pfam01243 349215001809 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region; Region: PNPOx_C; pfam10590 349215001810 Surface antigen [Cell envelope biogenesis, outer membrane]; Region: LipA; COG4520 349215001811 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK08159 349215001812 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 349215001813 NAD binding site [chemical binding]; other site 349215001814 homotetramer interface [polypeptide binding]; other site 349215001815 homodimer interface [polypeptide binding]; other site 349215001816 substrate binding site [chemical binding]; other site 349215001817 active site 349215001818 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 349215001819 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 349215001820 Tetramer interface [polypeptide binding]; other site 349215001821 active site 349215001822 FMN-binding site [chemical binding]; other site 349215001823 signal peptide peptidase SppA, 67K type; Region: SppA_67K; TIGR00705 349215001824 Signal peptide peptidase A (SppA) 67K type, a serine protease, has catalytic Ser-Lys dyad; Region: S49_SppA_67K_type; cd07018 349215001825 tandem repeat interface [polypeptide binding]; other site 349215001826 oligomer interface [polypeptide binding]; other site 349215001827 active site residues [active] 349215001828 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 349215001829 tandem repeat interface [polypeptide binding]; other site 349215001830 oligomer interface [polypeptide binding]; other site 349215001831 active site residues [active] 349215001832 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 349215001833 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 349215001834 motif II; other site 349215001835 1-deoxy-D-xylulose-5-phosphate synthase; Provisional; Region: PRK05444 349215001836 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 349215001837 TPP-binding site; other site 349215001838 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 349215001839 PYR/PP interface [polypeptide binding]; other site 349215001840 dimer interface [polypeptide binding]; other site 349215001841 TPP binding site [chemical binding]; other site 349215001842 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 349215001843 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; Region: GIY-YIG_unchar_3; cd10448 349215001844 GIY-YIG motif/motif A; other site 349215001845 putative active site [active] 349215001846 putative metal binding site [ion binding]; other site 349215001847 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 349215001848 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 349215001849 substrate binding pocket [chemical binding]; other site 349215001850 chain length determination region; other site 349215001851 substrate-Mg2+ binding site; other site 349215001852 catalytic residues [active] 349215001853 aspartate-rich region 1; other site 349215001854 active site lid residues [active] 349215001855 aspartate-rich region 2; other site 349215001856 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 349215001857 Deacetylases, including yeast histone deacetylase and acetoin utilization protein [Chromatin structure and dynamics / Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcuC; COG0123 349215001858 Histone deacetylases and histone-like deacetylases, classII; Region: HDAC_classII_2; cd11599 349215001859 putative active site [active] 349215001860 Zn binding site [ion binding]; other site 349215001861 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 349215001862 dimerization interface [polypeptide binding]; other site 349215001863 putative active cleft [active] 349215001864 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism]; Region: lytB; COG0761 349215001865 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 349215001866 Putative homoserine kinase type II (protein kinase fold) [General function prediction only]; Region: COG2334 349215001867 Homoserine Kinase, type II. Homoserine kinase is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and...; Region: HomoserineK_II; cd05153 349215001868 putative active site [active] 349215001869 putative substrate binding site [chemical binding]; other site 349215001870 ATP binding site [chemical binding]; other site 349215001871 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 349215001872 RNA/DNA hybrid binding site [nucleotide binding]; other site 349215001873 active site 349215001874 Transglycosylase; Region: Transgly; pfam00912 349215001875 penicillin-binding protein, 1A family; Region: PBP_1a_fam; TIGR02074 349215001876 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 349215001877 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 349215001878 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 349215001879 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 349215001880 MgtE intracellular N domain; Region: MgtE_N; pfam03448 349215001881 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 349215001882 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 349215001883 Divalent cation transporter; Region: MgtE; pfam01769 349215001884 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 349215001885 Malic enzyme, N-terminal domain; Region: malic; pfam00390 349215001886 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 349215001887 putative NAD(P) binding site [chemical binding]; other site 349215001888 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 349215001889 N-formylglutamate amidohydrolase; Region: FGase; pfam05013 349215001890 N-formylglutamate amidohydrolase; Region: FGase; pfam05013 349215001891 seryl-tRNA synthetase; Provisional; Region: PRK05431 349215001892 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 349215001893 Seryl-tRNA synthetase (SerRS) class II core catalytic domain. SerRS is responsible for the attachment of serine to the 3' OH group of ribose of the appropriate tRNA. This domain It is primarily responsible for ATP-dependent formation of the enzyme...; Region: SerRS_core; cd00770 349215001894 dimer interface [polypeptide binding]; other site 349215001895 active site 349215001896 motif 1; other site 349215001897 motif 2; other site 349215001898 motif 3; other site 349215001899 protein-L-isoaspartate O-methyltransferase; Reviewed; Region: pcm; PRK00312 349215001900 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 349215001901 S-adenosylmethionine binding site [chemical binding]; other site 349215001902 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 349215001903 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 349215001904 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 349215001905 Peptidase family M23; Region: Peptidase_M23; pfam01551 349215001906 Protein of unknown function (DUF3592); Region: DUF3592; pfam12158 349215001907 Protein of unknown function (DUF3592); Region: DUF3592; pfam12158 349215001908 Preprotein translocase subunit; Region: YajC; pfam02699 349215001909 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 349215001910 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 349215001911 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 349215001912 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 349215001913 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 349215001914 Protein export membrane protein; Region: SecD_SecF; pfam02355 349215001915 Mth938-like domain. The members of this family include: Mth938, 2P1, Xcr35, Rpa2829, and several uncharacterized sequences. Mth938 is a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. This protein crystallizes as a...; Region: Mth938-like; cd00248 349215001916 Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]; Region: TerC; COG0861 349215001917 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 349215001918 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 349215001919 active site 349215001920 metal binding site [ion binding]; metal-binding site 349215001921 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 349215001922 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 349215001923 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 349215001924 Squalene/phytoene synthase; Region: SQS_PSY; pfam00494 349215001925 substrate binding pocket [chemical binding]; other site 349215001926 substrate-Mg2+ binding site; other site 349215001927 aspartate-rich region 1; other site 349215001928 aspartate-rich region 2; other site 349215001929 FecR protein; Region: FecR; pfam04773 349215001930 Predicted acetyltransferases and hydrolases with the alpha/beta hydrolase fold [General function prediction only]; Region: LipA; COG1075 349215001931 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 349215001932 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 349215001933 NHL repeat; Region: NHL; pfam01436 349215001934 tRNA (uracil-5-)-methyltransferase Gid; Reviewed; Region: PRK05335 349215001935 Glucose inhibited division protein A; Region: GIDA; pfam01134 349215001936 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 349215001937 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 349215001938 Coenzyme A binding pocket [chemical binding]; other site 349215001939 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 349215001940 DNA polymerase IV; Reviewed; Region: PRK03103 349215001941 Y-family of DNA polymerases; Region: PolY; cd00424 349215001942 active site 349215001943 DNA binding site [nucleotide binding] 349215001944 Domain of unknown function (DUF4113); Region: DUF4113; pfam13438 349215001945 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 349215001946 tellurium resistance terB-like protein; Region: terB_like; cd07177 349215001947 metal binding site [ion binding]; metal-binding site 349215001948 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: CaiC; COG0318 349215001949 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 349215001950 acyl-activating enzyme (AAE) consensus motif; other site 349215001951 putative AMP binding site [chemical binding]; other site 349215001952 putative active site [active] 349215001953 putative CoA binding site [chemical binding]; other site 349215001954 5TMR of 5TMR-LYT; Region: 5TM-5TMR_LYT; pfam07694 349215001955 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 349215001956 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 349215001957 dimer interface [polypeptide binding]; other site 349215001958 phosphorylation site [posttranslational modification] 349215001959 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 349215001960 ATP binding site [chemical binding]; other site 349215001961 Mg2+ binding site [ion binding]; other site 349215001962 G-X-G motif; other site 349215001963 Response regulator receiver domain; Region: Response_reg; pfam00072 349215001964 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 349215001965 active site 349215001966 phosphorylation site [posttranslational modification] 349215001967 intermolecular recognition site; other site 349215001968 dimerization interface [polypeptide binding]; other site 349215001969 acetyl-CoA acetyltransferase; Provisional; Region: PRK06954 349215001970 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 349215001971 dimer interface [polypeptide binding]; other site 349215001972 active site 349215001973 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 349215001974 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 349215001975 active site 349215001976 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 349215001977 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 349215001978 NAD(P) binding site [chemical binding]; other site 349215001979 active site 349215001980 Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate...; Region: ICL_PEPM; cd00377 349215001981 Phosphoenolpyruvate phosphomutase; Region: PEP_mutase; pfam13714 349215001982 tetramer interface [polypeptide binding]; other site 349215001983 active site 349215001984 Mg2+/Mn2+ binding site [ion binding]; other site 349215001985 Escherichia coli (Ec) 2-methylcitrate synthase (2MCS)_like. 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and oxalacetate (OAA) to form 2-methylcitrate and coenzyme A (CoA) during propionate metabolism. Citrate synthase (CS) catalyzes...; Region: Ec2MCS_like; cd06108 349215001986 dimer interface [polypeptide binding]; other site 349215001987 Citrate synthase; Region: Citrate_synt; pfam00285 349215001988 active site 349215001989 citrylCoA binding site [chemical binding]; other site 349215001990 oxalacetate/citrate binding site [chemical binding]; other site 349215001991 coenzyme A binding site [chemical binding]; other site 349215001992 catalytic triad [active] 349215001993 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; Region: GIY-YIG_unchar_3; cd10448 349215001994 GIY-YIG motif/motif A; other site 349215001995 putative active site [active] 349215001996 putative metal binding site [ion binding]; other site 349215001997 Multiple antibiotic transporter [Intracellular trafficking and secretion]; Region: MarC; COG2095 349215001998 2-methylcitrate dehydratase; Provisional; Region: prpD; PRK09425 349215001999 2-methylcitrate dehydratase; Region: prpD; TIGR02330 349215002000 Domain of unknown function (DUF4393); Region: DUF4393; pfam14337 349215002001 Metal-dependent hydrolases of the beta-lactamase superfamily III [General function prediction only]; Region: ElaC; COG1234 349215002002 Glycerophosphoryl diester phosphodiesterase [Energy production and conversion]; Region: UgpQ; COG0584 349215002003 Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; Region: PI-PLCc_GDPD_SF; cl14615 349215002004 active site 349215002005 catalytic site [active] 349215002006 CAAX protease self-immunity; Region: Abi; pfam02517 349215002007 Domain of unknown function (DUF4402); Region: DUF4402; pfam14352 349215002008 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK07515 349215002009 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 349215002010 dimer interface [polypeptide binding]; other site 349215002011 active site 349215002012 CoA binding pocket [chemical binding]; other site 349215002013 acyl-CoA dehydrogenase; Reviewed; Region: fadE; PRK09463 349215002014 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 349215002015 active site 349215002016 Domain of unknown function (DUF1974); Region: DUF1974; pfam09317 349215002017 3-methylcrotonyl-CoA carboxylase, beta chain; Region: PLN02820 349215002018 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 349215002019 enoyl-CoA hydratase; Provisional; Region: PRK05995 349215002020 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 349215002021 substrate binding site [chemical binding]; other site 349215002022 oxyanion hole (OAH) forming residues; other site 349215002023 trimer interface [polypeptide binding]; other site 349215002024 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 349215002025 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 349215002026 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 349215002027 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 349215002028 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 349215002029 carboxyltransferase (CT) interaction site; other site 349215002030 biotinylation site [posttranslational modification]; other site 349215002031 Isopropylmalate/homocitrate/citramalate synthases [Amino acid transport and metabolism]; Region: LeuA; COG0119 349215002032 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain; Region: DRE_TIM_HMGL; cd07938 349215002033 active site 349215002034 catalytic residues [active] 349215002035 metal binding site [ion binding]; metal-binding site 349215002036 Isovaleryl-CoA dehydrogenase; Region: IVD; cd01156 349215002037 isovaleryl-CoA dehydrogenase; Region: PLN02519 349215002038 substrate binding site [chemical binding]; other site 349215002039 FAD binding site [chemical binding]; other site 349215002040 catalytic base [active] 349215002041 Arsenate Reductase (ArsC) family, Yffb subfamily; Yffb is an uncharacterized bacterial protein encoded by the yffb gene, related to the thioredoxin-fold arsenic reductases, ArsC. The structure of Yffb and the conservation of the catalytic cysteine...; Region: ArsC_Yffb; cd03035 349215002042 ArsC family; Region: ArsC; pfam03960 349215002043 putative catalytic residues [active] 349215002044 indolepyruvate ferredoxin oxidoreductase; Validated; Region: PRK09193 349215002045 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 349215002046 dimer interface [polypeptide binding]; other site 349215002047 PYR/PP interface [polypeptide binding]; other site 349215002048 TPP binding site [chemical binding]; other site 349215002049 substrate binding site [chemical binding]; other site 349215002050 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cl01629 349215002051 TPP-binding site [chemical binding]; other site 349215002052 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit [Energy production and conversion]; Region: PorG; COG1014 349215002053 ABC transporter transmembrane region 2; Region: ABC_membrane_2; cl00549 349215002054 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 349215002055 Walker A/P-loop; other site 349215002056 ATP binding site [chemical binding]; other site 349215002057 Q-loop/lid; other site 349215002058 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 349215002059 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 349215002060 ABC transporter signature motif; other site 349215002061 ABC transporter signature motif; other site 349215002062 Walker B; other site 349215002063 Walker B; other site 349215002064 D-loop; other site 349215002065 D-loop; other site 349215002066 H-loop/switch region; other site 349215002067 PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not...; Region: PaaI_thioesterase; cd03443 349215002068 CoenzymeA binding site [chemical binding]; other site 349215002069 subunit interaction site [polypeptide binding]; other site 349215002070 PHB binding site; other site 349215002071 Methyltransferase domain; Region: Methyltransf_23; pfam13489 349215002072 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 349215002073 S-adenosylmethionine binding site [chemical binding]; other site 349215002074 ABC transporter ATPase component; Reviewed; Region: PRK11147 349215002075 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 349215002076 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 349215002077 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 349215002078 IHF dimer interface [polypeptide binding]; other site 349215002079 IHF - DNA interface [nucleotide binding]; other site 349215002080 MASE1; Region: MASE1; pfam05231 349215002081 CHASE domain; Region: CHASE; pfam03924 349215002082 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 349215002083 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 349215002084 putative active site [active] 349215002085 heme pocket [chemical binding]; other site 349215002086 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 349215002087 dimer interface [polypeptide binding]; other site 349215002088 phosphorylation site [posttranslational modification] 349215002089 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 349215002090 ATP binding site [chemical binding]; other site 349215002091 Mg2+ binding site [ion binding]; other site 349215002092 G-X-G motif; other site 349215002093 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 349215002094 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 349215002095 active site 349215002096 phosphorylation site [posttranslational modification] 349215002097 intermolecular recognition site; other site 349215002098 dimerization interface [polypeptide binding]; other site 349215002099 Response regulator receiver domain; Region: Response_reg; pfam00072 349215002100 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 349215002101 active site 349215002102 phosphorylation site [posttranslational modification] 349215002103 intermolecular recognition site; other site 349215002104 dimerization interface [polypeptide binding]; other site 349215002105 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 349215002106 putative binding surface; other site 349215002107 active site 349215002108 von Willebrand factor type A domain; Region: VWA_2; pfam13519 349215002109 prepilin-type N-terminal cleavage/methylation domain; Region: IV_pilin_GFxxxE; TIGR02532 349215002110 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl17186 349215002111 phosphate binding site [ion binding]; other site 349215002112 ATP-dependent DNA helicase RecQ; Region: recQ; TIGR01389 349215002113 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 349215002114 ATP binding site [chemical binding]; other site 349215002115 putative Mg++ binding site [ion binding]; other site 349215002116 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 349215002117 nucleotide binding region [chemical binding]; other site 349215002118 ATP-binding site [chemical binding]; other site 349215002119 This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure; Region: RQC; smart00956 349215002120 HRDC domain; Region: HRDC; pfam00570 349215002121 Methyltransferase domain; Region: Methyltransf_31; pfam13847 349215002122 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 349215002123 S-adenosylmethionine binding site [chemical binding]; other site 349215002124 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 349215002125 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 349215002126 dimer interface [polypeptide binding]; other site 349215002127 putative functional site; other site 349215002128 putative MPT binding site; other site 349215002129 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 349215002130 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 349215002131 ligand binding site [chemical binding]; other site 349215002132 flexible hinge region; other site 349215002133 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 349215002134 putative switch regulator; other site 349215002135 non-specific DNA interactions [nucleotide binding]; other site 349215002136 DNA binding site [nucleotide binding] 349215002137 sequence specific DNA binding site [nucleotide binding]; other site 349215002138 putative cAMP binding site [chemical binding]; other site 349215002139 Nitrate/nitrite transporter [Inorganic ion transport and metabolism]; Region: NarK; COG2223 349215002140 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 349215002141 putative substrate translocation pore; other site 349215002142 nitrate/nitrite transport protein NarU; Provisional; Region: PRK15034 349215002143 Nitrate reductase alpha subunit [Energy production and conversion]; Region: NarG; COG5013 349215002144 Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to...; Region: MopB_Nitrate-R-NarG-like; cd02750 349215002145 [4Fe-4S] binding site [ion binding]; other site 349215002146 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 349215002147 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 349215002148 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 349215002149 Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to...; Region: MopB_CT_Nitrate-R-NarG-like; cd02776 349215002150 molybdopterin cofactor binding site; other site 349215002151 Nitrate reductase beta subunit [Energy production and conversion]; Region: NarY; COG1140 349215002152 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 349215002153 Nitrate reductase gamma subunit; Region: Nitrate_red_gam; pfam02665 349215002154 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 349215002155 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 349215002156 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 349215002157 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 349215002158 FeS/SAM binding site; other site 349215002159 HemN C-terminal domain; Region: HemN_C; pfam06969 349215002160 NnrS protein; Region: NnrS; pfam05940 349215002161 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 349215002162 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 349215002163 ligand binding site [chemical binding]; other site 349215002164 flexible hinge region; other site 349215002165 Crp-like helix-turn-helix domain; Region: HTH_Crp_2; pfam13545 349215002166 NnrU protein; Region: NnrU; pfam07298 349215002167 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 349215002168 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 349215002169 FeS/SAM binding site; other site 349215002170 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 349215002171 bifunctional molybdenum cofactor biosynthesis protein MoaC/MogA; Provisional; Region: moaC; PRK03604 349215002172 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 349215002173 trimer interface [polypeptide binding]; other site 349215002174 dimer interface [polypeptide binding]; other site 349215002175 putative active site [active] 349215002176 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 349215002177 MPT binding site; other site 349215002178 trimer interface [polypeptide binding]; other site 349215002179 Ubiquitin-like proteins; Region: UBQ; cl00155 349215002180 charged pocket; other site 349215002181 hydrophobic patch; other site 349215002182 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 349215002183 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 349215002184 GTP binding site; other site 349215002185 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 349215002186 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 349215002187 PAS domain; Region: PAS_9; pfam13426 349215002188 putative active site [active] 349215002189 heme pocket [chemical binding]; other site 349215002190 molybdopterin biosynthesis-like protein MoeZ; Validated; Region: PRK07878 349215002191 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 349215002192 ATP binding site [chemical binding]; other site 349215002193 substrate interface [chemical binding]; other site 349215002194 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 349215002195 active site residue [active] 349215002196 Predicted transcriptional regulator [Transcription]; Region: COG1959 349215002197 Transcriptional regulator; Region: Rrf2; cl17282 349215002198 anaerobic ribonucleoside-triphosphate reductase activating protein; Region: NrdG2; TIGR02495 349215002199 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 349215002200 FeS/SAM binding site; other site 349215002201 Anaerobic ribonucleoside-triphosphate reductase; Region: NRDD; pfam13597 349215002202 Class III ribonucleotide reductase; Region: RNR_III; cd01675 349215002203 effector binding site; other site 349215002204 active site 349215002205 Zn binding site [ion binding]; other site 349215002206 glycine loop; other site 349215002207 putative protease; Provisional; Region: PRK15447 349215002208 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 349215002209 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 349215002210 Peptidase family U32; Region: Peptidase_U32; pfam01136 349215002211 SCP-2 sterol transfer family; Region: SCP2; cl01225 349215002212 RTX toxins and related Ca2+-binding proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2931 349215002213 RTX toxins and related Ca2+-binding proteins [Secondary metabolites biosynthesis, transport, and catabolism]; Region: COG2931 349215002214 Haemolysin-type calcium binding protein related domain; Region: HCBP_related; pfam06594 349215002215 type I secretion C-terminal target domain (VC_A0849 subclass); Region: T1SS_VCA0849; TIGR03661 349215002216 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 349215002217 ParB-like nuclease domain; Region: ParBc; pfam02195 349215002218 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 349215002219 DNA methylase; Region: N6_N4_Mtase; pfam01555 349215002220 Y_X(10)_GDL-associated radical SAM protein; Region: rad_SAM_trio; TIGR03913 349215002221 His-Xaa-Ser system protein HsxD; Region: chp_LLNDYxLRE; TIGR03976 349215002222 His-Xaa-Ser system radical SAM maturase HxsB; Region: rSAM_paired_1; TIGR03978 349215002223 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 349215002224 FeS/SAM binding site; other site 349215002225 Domain of unknown function (DUF4008); Region: DUF4008; cl14869 349215002226 His-Xaa-Ser system radical SAM maturase HxsC; Region: rSAM_pair_HxsC; TIGR03977 349215002227 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 349215002228 FeS/SAM binding site; other site 349215002229 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 349215002230 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 349215002231 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 349215002232 catalytic residues [active] 349215002233 catalytic nucleophile [active] 349215002234 Presynaptic Site I dimer interface [polypeptide binding]; other site 349215002235 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 349215002236 Synaptic Flat tetramer interface [polypeptide binding]; other site 349215002237 Synaptic Site I dimer interface [polypeptide binding]; other site 349215002238 DNA binding site [nucleotide binding] 349215002239 Recombinase; Region: Recombinase; pfam07508 349215002240 Domain of unknown function (DUF4393); Region: DUF4393; pfam14337 349215002241 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 349215002242 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 349215002243 dimer interface [polypeptide binding]; other site 349215002244 pyridoxal 5'-phosphate binding site [chemical binding]; other site 349215002245 catalytic residue [active] 349215002246 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 349215002247 MutS domain I; Region: MutS_I; pfam01624 349215002248 MutS domain II; Region: MutS_II; pfam05188 349215002249 MutS domain III; Region: MutS_III; pfam05192 349215002250 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 349215002251 Walker A/P-loop; other site 349215002252 ATP binding site [chemical binding]; other site 349215002253 Q-loop/lid; other site 349215002254 ABC transporter signature motif; other site 349215002255 Walker B; other site 349215002256 D-loop; other site 349215002257 H-loop/switch region; other site 349215002258 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 349215002259 trimer interface [polypeptide binding]; other site 349215002260 active site 349215002261 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 349215002262 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 349215002263 S-adenosylmethionine binding site [chemical binding]; other site 349215002264 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 349215002265 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 349215002266 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 349215002267 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 349215002268 active site 349215002269 HIGH motif; other site 349215002270 dimer interface [polypeptide binding]; other site 349215002271 KMSKS motif; other site 349215002272 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 349215002273 Putative transmembrane protein (Alph_Pro_TM); Region: Alph_Pro_TM; cl09826 349215002274 Universal stress protein family; Region: Usp; pfam00582 349215002275 Ligand Binding Site [chemical binding]; other site 349215002276 Scaffold protein Nfu/NifU N terminal; Region: Nfu_N; pfam08712 349215002277 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 349215002278 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 349215002279 putative active site [active] 349215002280 putative metal binding site [ion binding]; other site 349215002281 Nitroreductase-like family 5. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and...; Region: Nitroreductase_5; cd02148 349215002282 putative FMN binding site [chemical binding]; other site 349215002283 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 349215002284 Glycoprotease family; Region: Peptidase_M22; pfam00814 349215002285 ROS/MUCR transcriptional regulator protein; Region: ROS_MUCR; pfam05443 349215002286 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 349215002287 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 349215002288 Putative bacterial sensory transduction regulator; Region: YbjN; cl15834 349215002289 Membrane fusogenic activity; Region: BMFP; pfam04380 349215002290 ADP-L-glycero-D-mannoheptose 6-epimerase (GME), extended (e) SDRs; Region: ADP_GME_SDR_e; cd05248 349215002291 ADP-L-glycero-D-manno-heptose-6-epimerase; Region: heptose_epim; TIGR02197 349215002292 NADP binding site [chemical binding]; other site 349215002293 homopentamer interface [polypeptide binding]; other site 349215002294 substrate binding site [chemical binding]; other site 349215002295 active site 349215002296 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 349215002297 Uncharacterized conserved protein [Function unknown]; Region: COG1565 349215002298 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 349215002299 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 349215002300 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; pfam02578 349215002301 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 349215002302 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 349215002303 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 349215002304 active site 349215002305 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 349215002306 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 349215002307 5S rRNA interface [nucleotide binding]; other site 349215002308 CTC domain interface [polypeptide binding]; other site 349215002309 L16 interface [polypeptide binding]; other site 349215002310 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 349215002311 putative active site [active] 349215002312 catalytic residue [active] 349215002313 GTP-binding protein YchF; Reviewed; Region: PRK09601 349215002314 YchF GTPase; Region: YchF; cd01900 349215002315 G1 box; other site 349215002316 GTP/Mg2+ binding site [chemical binding]; other site 349215002317 Switch I region; other site 349215002318 G2 box; other site 349215002319 Switch II region; other site 349215002320 G3 box; other site 349215002321 G4 box; other site 349215002322 G5 box; other site 349215002323 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 349215002324 adenosine deaminase; Provisional; Region: PRK09358 349215002325 Adenosine deaminase [Nucleotide transport and metabolism]; Region: Add; COG1816 349215002326 active site 349215002327 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 349215002328 PyridoxaL 5'-Phosphate Dependent Enzymes class IV (PLPDE_IV). This D-amino acid superfamily, one of five classes of PLPDE, consists of branched-chain amino acid aminotransferases (BCAT), D-amino acid transferases (DAAT), and...; Region: PLPDE_IV; cd00449 349215002329 homodimer interface [polypeptide binding]; other site 349215002330 substrate-cofactor binding pocket; other site 349215002331 pyridoxal 5'-phosphate binding site [chemical binding]; other site 349215002332 catalytic residue [active] 349215002333 osmolarity response regulator; Provisional; Region: ompR; PRK09468 349215002334 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 349215002335 active site 349215002336 phosphorylation site [posttranslational modification] 349215002337 intermolecular recognition site; other site 349215002338 dimerization interface [polypeptide binding]; other site 349215002339 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 349215002340 DNA binding site [nucleotide binding] 349215002341 osmolarity sensor protein; Provisional; Region: envZ; PRK09467 349215002342 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 349215002343 dimerization interface [polypeptide binding]; other site 349215002344 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 349215002345 dimer interface [polypeptide binding]; other site 349215002346 phosphorylation site [posttranslational modification] 349215002347 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 349215002348 ATP binding site [chemical binding]; other site 349215002349 Mg2+ binding site [ion binding]; other site 349215002350 G-X-G motif; other site 349215002351 tRNA-binding-domain-containing CsaA-like proteins. CsaA is a molecular chaperone with export related activities. CsaA has a putative tRNA binding activity. The functional unit of CsaA is a homodimer and this domain acts as a dimerization domain; Region: tRNA_bind_CsaA; cd02798 349215002352 dimer interface [polypeptide binding]; other site 349215002353 putative tRNA-binding site [nucleotide binding]; other site 349215002354 Phasin protein; Region: Phasin_2; pfam09361 349215002355 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 349215002356 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 349215002357 putative active site [active] 349215002358 heme pocket [chemical binding]; other site 349215002359 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 349215002360 putative active site [active] 349215002361 heme pocket [chemical binding]; other site 349215002362 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 349215002363 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 349215002364 dimer interface [polypeptide binding]; other site 349215002365 phosphorylation site [posttranslational modification] 349215002366 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 349215002367 ATP binding site [chemical binding]; other site 349215002368 Mg2+ binding site [ion binding]; other site 349215002369 G-X-G motif; other site 349215002370 CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit; Region: CO_dh; cl00815 349215002371 RecX family; Region: RecX; pfam02631 349215002372 Heat shock protein 33 (Hsp33): Cytosolic protein that acts as a molecular chaperone under oxidative conditions. In normal (reducing) cytosolic conditions, four conserved Cys residues are coordinated by a Zn ion. Under oxidative stress (such as heat...; Region: Hsp33; cd00498 349215002373 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 349215002374 dimerization interface [polypeptide binding]; other site 349215002375 domain crossover interface; other site 349215002376 redox-dependent activation switch; other site 349215002377 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 349215002378 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 349215002379 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 349215002380 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 349215002381 ligand binding site [chemical binding]; other site 349215002382 intracellular protease, PfpI family; Region: PfpI; TIGR01382 349215002383 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 349215002384 conserved cys residue [active] 349215002385 peptide chain release factor 2; Provisional; Region: PRK07342 349215002386 This domain is found in peptide chain release factors; Region: PCRF; smart00937 349215002387 RF-1 domain; Region: RF-1; pfam00472 349215002388 Toxin co-regulated pilus biosynthesis protein Q; Region: TcpQ; pfam10671 349215002389 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 349215002390 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 349215002391 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 349215002392 metal binding site [ion binding]; metal-binding site 349215002393 active site 349215002394 I-site; other site 349215002395 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 349215002396 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5394 349215002397 PHB/PHA accumulation regulator DNA-binding domain; Region: PHB_acc_N; pfam07879 349215002398 PHB accumulation regulatory domain; Region: PHB_acc; pfam05233 349215002399 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 349215002400 alpha/beta hydrolase fold; Region: Abhydrolase_1; pfam00561 349215002401 putative acyltransferase; Provisional; Region: PRK05790 349215002402 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 349215002403 dimer interface [polypeptide binding]; other site 349215002404 active site 349215002405 acetoacetyl-CoA reductase; Region: AcAcCoA_reduct; TIGR01829 349215002406 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 349215002407 NAD(P) binding site [chemical binding]; other site 349215002408 homotetramer interface [polypeptide binding]; other site 349215002409 homodimer interface [polypeptide binding]; other site 349215002410 active site 349215002411 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 349215002412 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 349215002413 ligand binding site [chemical binding]; other site 349215002414 flexible hinge region; other site 349215002415 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 349215002416 Ribbon-helix-helix domain; Region: RHH_4; pfam13467 349215002417 fumarate hydratase; Reviewed; Region: fumC; PRK00485 349215002418 Class II fumarases; Region: Fumarase_classII; cd01362 349215002419 active site 349215002420 tetramer interface [polypeptide binding]; other site 349215002421 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 349215002422 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 349215002423 6-phosphofructokinase; Region: PFKA_ATP; TIGR02482 349215002424 active site 349215002425 ADP/pyrophosphate binding site [chemical binding]; other site 349215002426 dimerization interface [polypeptide binding]; other site 349215002427 allosteric effector site; other site 349215002428 fructose-1,6-bisphosphate binding site; other site 349215002429 Bacterial PH domain; Region: DUF304; cl01348 349215002430 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2989 349215002431 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 349215002432 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 349215002433 L,D-transpeptidase catalytic domain; Region: YkuD; pfam03734 349215002434 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3108 349215002435 Peptidase M15; Region: Peptidase_M15_3; cl01194 349215002436 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 349215002437 Recombination protein O N terminal; Region: RecO_N; pfam11967 349215002438 Recombination protein O C terminal; Region: RecO_C; pfam02565 349215002439 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 349215002440 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes...; Region: TOP4c; cd00187 349215002441 CAP-like domain; other site 349215002442 active site 349215002443 primary dimer interface [polypeptide binding]; other site 349215002444 flagellar motor protein MotB; Validated; Region: motB; PRK09041 349215002445 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 349215002446 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 349215002447 ligand binding site [chemical binding]; other site 349215002448 flagellar motor protein MotA; Validated; Region: PRK09110 349215002449 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 349215002450 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 349215002451 putative active site [active] 349215002452 heme pocket [chemical binding]; other site 349215002453 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 349215002454 3-hydroxyisobutyryl-CoA hydrolase; Provisional; Region: PRK05617 349215002455 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 349215002456 substrate binding site [chemical binding]; other site 349215002457 oxyanion hole (OAH) forming residues; other site 349215002458 trimer interface [polypeptide binding]; other site 349215002459 2-enoyl-CoA Hydratase C-terminal region; Region: ECH_C; pfam13766 349215002460 Transcriptional regulators [Transcription]; Region: MarR; COG1846 349215002461 Winged helix DNA-binding domain; Region: HTH_27; pfam13463 349215002462 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 349215002463 DNA methylase; Region: N6_N4_Mtase; pfam01555 349215002464 SseB protein; Region: SseB; cl06279 349215002465 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 349215002466 Glutaryl-CoA dehydrogenase; Region: GCD; cd01151 349215002467 FAD binding site [chemical binding]; other site 349215002468 substrate binding pocket [chemical binding]; other site 349215002469 catalytic base [active] 349215002470 Ribose/Galactose Isomerase; Region: LacAB_rpiB; pfam02502 349215002471 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 349215002472 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 349215002473 dimer interface [polypeptide binding]; other site 349215002474 active site 349215002475 glycine-pyridoxal phosphate binding site [chemical binding]; other site 349215002476 folate binding site [chemical binding]; other site 349215002477 transcriptional regulator NrdR; Validated; Region: nrdR; PRK00464 349215002478 ATP cone domain; Region: ATP-cone; pfam03477 349215002479 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; cd00447 349215002480 dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]; Region: RfbB; COG1088 349215002481 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 349215002482 NAD(P) binding site [chemical binding]; other site 349215002483 active site 349215002484 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 349215002485 H(+) -translocating inorganic pyrophosphatase; Region: PLN02255; cl11452 349215002486 membrane-bound proton-translocating pyrophosphatase; Validated; Region: hppA; PRK00733 349215002487 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 349215002488 TRAM domain; Region: TRAM; pfam01938 349215002489 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 349215002490 S-adenosylmethionine binding site [chemical binding]; other site 349215002491 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 349215002492 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 349215002493 Ubiquinol-cytochrome C chaperone; Region: Ubiq_cyt_C_chap; pfam03981 349215002494 Uncharacterized ACR, COG1399; Region: DUF177; pfam02620 349215002495 Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]; Region: RpmF; COG0333 349215002496 putative phosphate acyltransferase; Provisional; Region: PRK05331 349215002497 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 349215002498 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 349215002499 dimer interface [polypeptide binding]; other site 349215002500 active site 349215002501 CoA binding pocket [chemical binding]; other site 349215002502 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 349215002503 IHF dimer interface [polypeptide binding]; other site 349215002504 IHF - DNA interface [nucleotide binding]; other site 349215002505 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Region: HTH_MlrA-like_sg2; cd04765 349215002506 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 349215002507 DNA binding residues [nucleotide binding] 349215002508 Predicted dehydrogenase [General function prediction only]; Region: COG0579 349215002509 hydroxyglutarate oxidase; Provisional; Region: PRK11728 349215002510 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; cl17220 349215002511 N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), RfaH; Region: NGN_SP_RfaH; cd09892 349215002512 transcriptional activator RfaH; Region: RfaH; TIGR01955 349215002513 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 349215002514 heterodimer interface [polypeptide binding]; other site 349215002515 homodimer interface [polypeptide binding]; other site 349215002516 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 349215002517 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 349215002518 NAD(P) binding site [chemical binding]; other site 349215002519 active site 349215002520 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 349215002521 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 349215002522 inhibitor-cofactor binding pocket; inhibition site 349215002523 pyridoxal 5'-phosphate binding site [chemical binding]; other site 349215002524 catalytic residue [active] 349215002525 Glutamine amidotransferases class-II (GATase) asparagine synthase_B type. Asparagine synthetase B catalyses the ATP-dependent conversion of aspartate to asparagine. This enzyme is a homodimer, with each monomer composed of a glutaminase domain and a...; Region: AsnB; cd00712 349215002526 active site 349215002527 asparagine synthase (glutamine-hydrolyzing); Region: asn_synth_AEB; TIGR01536 349215002528 dimer interface [polypeptide binding]; other site 349215002529 The C-terminal domain of Asparagine Synthase B. This domain is always found associated n-terminal amidotransferase domain. Family members that contain this domain catalyse the conversion of aspartate to asparagine. Asparagine synthetase B catalyzes the...; Region: Asn_Synthase_B_C; cd01991 349215002530 Ligand Binding Site [chemical binding]; other site 349215002531 Molecular Tunnel; other site 349215002532 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 349215002533 S-adenosylmethionine binding site [chemical binding]; other site 349215002534 Methionyl-tRNA formyltransferase [Translation, ribosomal structure and biogenesis]; Region: Fmt; COG0223 349215002535 Formyltransferase, catalytic core domain; Region: FMT_core; cl00395 349215002536 active site 349215002537 substrate binding site [chemical binding]; other site 349215002538 cosubstrate binding site; other site 349215002539 catalytic site [active] 349215002540 C-terminal subdomain of the formyltransferase domain on ArnA, which modifies lipid A with 4-amino-4-deoxy-l-arabinose; Region: Arna_FMT_C; cd08702 349215002541 active site 349215002542 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 349215002543 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 349215002544 Membrane protein involved in the export of O-antigen and teichoic acid [General function prediction only]; Region: RfbX; COG2244 349215002545 Wzx, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_Wzx_like; cd13128 349215002546 Nucleoside-diphosphate-sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: WcaG; COG0451 349215002547 extended (e) SDRs; Region: SDR_e; cd08946 349215002548 NAD(P) binding site [chemical binding]; other site 349215002549 active site 349215002550 substrate binding site [chemical binding]; other site 349215002551 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 349215002552 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 349215002553 exosortase A system-associated amidotransferase 1; Region: eps_aminotran_1; TIGR03108 349215002554 Glutamine amidotransferases class-II (GATase) asparagine synthase_B type. Asparagine synthetase B catalyses the ATP-dependent conversion of aspartate to asparagine. This enzyme is a homodimer, with each monomer composed of a glutaminase domain and a...; Region: AsnB; cd00712 349215002555 active site 349215002556 dimer interface [polypeptide binding]; other site 349215002557 The C-terminal domain of Asparagine Synthase B. This domain is always found associated n-terminal amidotransferase domain. Family members that contain this domain catalyse the conversion of aspartate to asparagine. Asparagine synthetase B catalyzes the...; Region: Asn_Synthase_B_C; cd01991 349215002558 Ligand Binding Site [chemical binding]; other site 349215002559 Molecular Tunnel; other site 349215002560 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 349215002561 active site 349215002562 UDP-N-acetylglucosamine 2-epimerase; Region: Epimerase_2; pfam02350 349215002563 homodimer interface [polypeptide binding]; other site 349215002564 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 349215002565 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 349215002566 O-acetylhomoserine sulfhydrylase [Amino acid transport and metabolism]; Region: MET17; COG2873 349215002567 CGS_like: Cystathionine gamma-synthase is a PLP dependent enzyme and catalyzes the committed step of methionine biosynthesis. This pathway is unique to microorganisms and plants, rendering the enzyme an attractive target for the development of...; Region: CGS_like; cd00614 349215002568 homodimer interface [polypeptide binding]; other site 349215002569 substrate-cofactor binding pocket; other site 349215002570 pyridoxal 5'-phosphate binding site [chemical binding]; other site 349215002571 catalytic residue [active] 349215002572 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 349215002573 23S rRNA interface [nucleotide binding]; other site 349215002574 L3 interface [polypeptide binding]; other site 349215002575 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 349215002576 Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]; Region: PaaY; COG0663 349215002577 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 349215002578 trimer interface [polypeptide binding]; other site 349215002579 putative metal binding site [ion binding]; other site 349215002580 poly(R)-hydroxyalkanoic acid synthase, class I; Region: PHA_synth_I; TIGR01838 349215002581 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 349215002582 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 349215002583 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 349215002584 metal binding site [ion binding]; metal-binding site 349215002585 active site 349215002586 I-site; other site 349215002587 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 349215002588 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 349215002589 ligand binding site [chemical binding]; other site 349215002590 homoserine dehydrogenase; Provisional; Region: PRK06349 349215002591 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 349215002592 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 349215002593 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 349215002594 Bacterial fructose-1,6-bisphosphatase, glpX-encoded. A dimeric enzyme dependent on Mg(2+). glpX-encoded FPBase (FBPase class II) differs from other members of the inositol-phosphatase superfamily by permutation of secondary structure elements. The core...; Region: FBPase_glpX; cd01516 349215002595 Bacterial fructose-1,6-bisphosphatase, glpX-encoded; Region: FBPase_glpX; pfam03320 349215002596 putative active site [active] 349215002597 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 349215002598 DHH family; Region: DHH; pfam01368 349215002599 DHHA1 domain; Region: DHHA1; pfam02272 349215002600 Restriction endonuclease; Region: Mrr_cat; pfam04471 349215002601 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 349215002602 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 349215002603 cofactor binding site; other site 349215002604 DNA binding site [nucleotide binding] 349215002605 substrate interaction site [chemical binding]; other site 349215002606 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; Region: HATPase_c_3; pfam13589 349215002607 Mg2+ binding site [ion binding]; other site 349215002608 G-X-G motif; other site 349215002609 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 349215002610 ATP binding site [chemical binding]; other site 349215002611 Mg2+ binding site [ion binding]; other site 349215002612 G-X-G motif; other site 349215002613 Predicted transcriptional regulator [Transcription]; Region: AlpA; COG3311 349215002614 integrase; Provisional; Region: PRK09692 349215002615 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall...; Region: INT_P4; cd00801 349215002616 active site 349215002617 Int/Topo IB signature motif; other site 349215002618 putative cation:proton antiport protein; Provisional; Region: PRK10669 349215002619 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 349215002620 TrkA-N domain; Region: TrkA_N; pfam02254 349215002621 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 349215002622 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 349215002623 dimer interface [polypeptide binding]; other site 349215002624 putative CheW interface [polypeptide binding]; other site 349215002625 Domain of unknown function (DUF4177); Region: DUF4177; pfam13783 349215002626 PTS_IIB, PTS system, Mannose/sorbose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIB_man; cl00021 349215002627 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 349215002628 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 349215002629 GatB domain; Region: GatB_Yqey; smart00845 349215002630 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 349215002631 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 349215002632 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 349215002633 Uncharacterized protein family (UPF0081); Region: UPF0081; pfam03652 349215002634 Protein of unknown function DUF45; Region: DUF45; pfam01863 349215002635 Poly-beta-hydroxyalkanoate depolymerase [Lipid metabolism]; Region: DepA; COG4553 349215002636 PHB de-polymerase C-terminus; Region: PHB_depo_C; pfam06850 349215002637 Adenosine kinase (AK) catalyzes the phosphorylation of ribofuranosyl-containing nucleoside analogues at the 5'-hydroxyl using ATP or GTP as the phosphate donor.The physiological function of AK is associated with the regulation of extracellular...; Region: adenosine_kinase; cd01168 349215002638 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 349215002639 substrate binding site [chemical binding]; other site 349215002640 ATP binding site [chemical binding]; other site 349215002641 putative aminophosphonate oxidoreductase; Region: Phn_aa_oxid; TIGR03329 349215002642 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 349215002643 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 349215002644 Phage Mu protein F like protein; Region: Phage_Mu_F; cl10072 349215002645 CobD/Cbib protein; Region: CobD_Cbib; cl00561 349215002646 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 349215002647 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; cl00409 349215002648 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 349215002649 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 349215002650 metal binding site [ion binding]; metal-binding site 349215002651 active site 349215002652 I-site; other site 349215002653 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 349215002654 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 349215002655 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 349215002656 putative active site [active] 349215002657 heme pocket [chemical binding]; other site 349215002658 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 349215002659 dimer interface [polypeptide binding]; other site 349215002660 phosphorylation site [posttranslational modification] 349215002661 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 349215002662 ATP binding site [chemical binding]; other site 349215002663 Mg2+ binding site [ion binding]; other site 349215002664 G-X-G motif; other site 349215002665 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 349215002666 metal binding site 2 [ion binding]; metal-binding site 349215002667 putative DNA binding helix; other site 349215002668 metal binding site 1 [ion binding]; metal-binding site 349215002669 dimer interface [polypeptide binding]; other site 349215002670 structural Zn2+ binding site [ion binding]; other site 349215002671 Protein of unknown function (DUF1491); Region: DUF1491; pfam07372 349215002672 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 349215002673 dimer interface [polypeptide binding]; other site 349215002674 substrate binding site [chemical binding]; other site 349215002675 metal binding sites [ion binding]; metal-binding site 349215002676 Protein of unknown function (DUF1304); Region: DUF1304; pfam06993 349215002677 peptide chain release factor 3; Provisional; Region: prfC; PRK00741 349215002678 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria; Region: RF3; cd04169 349215002679 G1 box; other site 349215002680 putative GEF interaction site [polypeptide binding]; other site 349215002681 GTP/Mg2+ binding site [chemical binding]; other site 349215002682 Switch I region; other site 349215002683 G2 box; other site 349215002684 G3 box; other site 349215002685 Switch II region; other site 349215002686 G4 box; other site 349215002687 G5 box; other site 349215002688 RF3_II: this subfamily represents the domain II of bacterial Release Factor 3 (RF3). Termination of protein synthesis by the ribosome requires two release factor (RF) classes. The class II RF3 is a GTPase that removes class I RFs (RF1 or RF2) from the...; Region: RF3_II; cd03689 349215002689 The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a...; Region: Ntn_hydrolase; cl00467 349215002690 FeS assembly SUF system regulator, gammaproteobacterial; Region: suf_reg_Xantho; TIGR02944 349215002691 Transcriptional regulator; Region: Rrf2; cl17282 349215002692 cysteine desulfurase activator complex subunit SufB; Provisional; Region: PRK11814 349215002693 putative ABC transporter; Region: ycf24; CHL00085 349215002694 FeS assembly ATPase SufC; Region: sufC; TIGR01978 349215002695 ABC-type transport system involved in Fe-S cluster assembly, ATPase component; Region: ABC_FeS_Assembly; cd03217 349215002696 Walker A/P-loop; other site 349215002697 ATP binding site [chemical binding]; other site 349215002698 Q-loop/lid; other site 349215002699 ABC transporter signature motif; other site 349215002700 Walker B; other site 349215002701 D-loop; other site 349215002702 H-loop/switch region; other site 349215002703 FeS assembly protein SufD; Region: sufD; TIGR01981 349215002704 Uncharacterized protein family (UPF0051); Region: UPF0051; pfam01458 349215002705 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 349215002706 Cysteine desulfurase (SufS)-like. This family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to cysteine desulfurase (SufS) and selenocysteine lyase. SufS...; Region: SufS_like; cd06453 349215002707 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 349215002708 catalytic residue [active] 349215002709 FeS assembly SUF system protein; Region: SUF_assoc; TIGR02945 349215002710 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 349215002711 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 349215002712 Ankyrin repeat; Region: Ank; pfam00023 349215002713 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 349215002714 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 349215002715 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 349215002716 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 349215002717 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 349215002718 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 349215002719 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 349215002720 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 349215002721 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 349215002722 tRNA-dihydrouridine synthase A; Provisional; Region: PRK11815 349215002723 Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also...; Region: DUS_like_FMN; cd02801 349215002724 FMN binding site [chemical binding]; other site 349215002725 active site 349215002726 catalytic residues [active] 349215002727 substrate binding site [chemical binding]; other site 349215002728 Bacterial SH3 domain; Region: SH3_4; pfam06347 349215002729 Bacterial SH3 domain; Region: SH3_4; pfam06347 349215002730 FabA, beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase: Bacterial protein of the type II, fatty acid synthase system that binds ACP and catalyzes both dehydration and isomerization reactions, apparently in the same active site. The FabA...; Region: FabA; cd01287 349215002731 active site 1 [active] 349215002732 dimer interface [polypeptide binding]; other site 349215002733 active site 2 [active] 349215002734 3-oxoacyl-(acyl carrier protein) synthase I; Reviewed; Region: PRK07967 349215002735 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 349215002736 dimer interface [polypeptide binding]; other site 349215002737 active site 349215002738 Enoyl-[acyl-carrier-protein]; Region: FabI; COG0623 349215002739 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 349215002740 NAD binding site [chemical binding]; other site 349215002741 homotetramer interface [polypeptide binding]; other site 349215002742 homodimer interface [polypeptide binding]; other site 349215002743 substrate binding site [chemical binding]; other site 349215002744 active site 349215002745 large-conductance mechanosensitive channel; Provisional; Region: mscL; PRK13952 349215002746 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 349215002747 cytoplasmic glycerophosphodiester phosphodiesterase; Provisional; Region: ugpQ; PRK09454 349215002748 Glycerophosphodiester phosphodiesterase domain in Escherichia coli cytosolic glycerophosphodiester phosphodiesterase UgpQ and similar proteins; Region: GDPD_EcUgpQ_like; cd08562 349215002749 putative active site [active] 349215002750 catalytic site [active] 349215002751 putative metal binding site [ion binding]; other site 349215002752 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 349215002753 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 349215002754 RNase E interface [polypeptide binding]; other site 349215002755 trimer interface [polypeptide binding]; other site 349215002756 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 349215002757 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 349215002758 RNase E interface [polypeptide binding]; other site 349215002759 trimer interface [polypeptide binding]; other site 349215002760 active site 349215002761 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 349215002762 putative nucleic acid binding region [nucleotide binding]; other site 349215002763 G-X-X-G motif; other site 349215002764 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 349215002765 RNA binding site [nucleotide binding]; other site 349215002766 domain interface; other site 349215002767 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 349215002768 catalytic core [active] 349215002769 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 349215002770 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 349215002771 active site 349215002772 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 349215002773 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 349215002774 16S/18S rRNA binding site [nucleotide binding]; other site 349215002775 S13e-L30e interaction site [polypeptide binding]; other site 349215002776 25S rRNA binding site [nucleotide binding]; other site 349215002777 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK05389 349215002778 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 349215002779 RNA binding site [nucleotide binding]; other site 349215002780 active site 349215002781 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 349215002782 translation initiation factor IF-2; Region: IF-2; TIGR00487 349215002783 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 349215002784 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 349215002785 G1 box; other site 349215002786 putative GEF interaction site [polypeptide binding]; other site 349215002787 GTP/Mg2+ binding site [chemical binding]; other site 349215002788 Switch I region; other site 349215002789 G2 box; other site 349215002790 G3 box; other site 349215002791 Switch II region; other site 349215002792 G4 box; other site 349215002793 G5 box; other site 349215002794 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 349215002795 Translation-initiation factor 2; Region: IF-2; pfam11987 349215002796 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 349215002797 Protein of unknown function (DUF448); Region: DUF448; pfam04296 349215002798 putative RNA binding cleft [nucleotide binding]; other site 349215002799 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; Region: Ribosomal_L7Ae; cl00600 349215002800 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 349215002801 NusA N-terminal domain; Region: NusA_N; pfam08529 349215002802 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 349215002803 RNA binding site [nucleotide binding]; other site 349215002804 homodimer interface [polypeptide binding]; other site 349215002805 NusA-like KH domain; Region: KH_5; pfam13184 349215002806 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 349215002807 G-X-X-G motif; other site 349215002808 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 349215002809 ribosome maturation protein RimP; Reviewed; Region: PRK00092 349215002810 Sm and related proteins; Region: Sm_like; cl00259 349215002811 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 349215002812 putative oligomer interface [polypeptide binding]; other site 349215002813 putative RNA binding site [nucleotide binding]; other site 349215002814 tRNA (guanine-N(7)-)-methyltransferase; Reviewed; Region: trmB; PRK00121 349215002815 S-adenosylmethionine synthetase; Validated; Region: PRK05250 349215002816 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 349215002817 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 349215002818 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 349215002819 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 349215002820 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 349215002821 non-specific DNA binding site [nucleotide binding]; other site 349215002822 salt bridge; other site 349215002823 sequence-specific DNA binding site [nucleotide binding]; other site 349215002824 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 349215002825 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 349215002826 putative active site [active] 349215002827 catalytic triad [active] 349215002828 putative dimer interface [polypeptide binding]; other site 349215002829 FOG: CBS domain [General function prediction only]; Region: COG0517 349215002830 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 349215002831 Transporter associated domain; Region: CorC_HlyC; smart01091 349215002832 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 349215002833 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 349215002834 PhoH-like protein; Region: PhoH; pfam02562 349215002835 PhoH-like protein; Region: PhoH; pfam02562 349215002836 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 349215002837 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 349215002838 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 349215002839 FeS/SAM binding site; other site 349215002840 TRAM domain; Region: TRAM; pfam01938 349215002841 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 349215002842 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 349215002843 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 349215002844 EamA-like transporter family; Region: EamA; cl17759 349215002845 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 349215002846 GlcN6P_deaminase: Glucosamine-6-phosphate (GlcN6P) deaminase subfamily; GlcN6P deaminase catalyzes the reversible conversion of GlcN6P to D-fructose-6-phosphate (Fru6P) and ammonium. The reaction is an aldo-keto isomerization coupled with an amination or...; Region: GlcN6P_deaminase; cd01399 349215002847 active site 349215002848 trimer interface [polypeptide binding]; other site 349215002849 allosteric site; other site 349215002850 active site lid [active] 349215002851 hexamer (dimer of trimers) interface [polypeptide binding]; other site 349215002852 HAD-superfamily class IIA hydrolase, TIGR01459; Region: HAD-SF-IIA-hyp4 349215002853 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 349215002854 active site 349215002855 motif I; other site 349215002856 motif II; other site 349215002857 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 349215002858 hypothetical protein; Provisional; Region: PRK10279 349215002859 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 349215002860 active site 349215002861 nucleophile elbow; other site 349215002862 lipid A export permease/ATP-binding protein MsbA; Region: MsbA_lipidA; TIGR02203 349215002863 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 349215002864 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 349215002865 Walker A/P-loop; other site 349215002866 ATP binding site [chemical binding]; other site 349215002867 Q-loop/lid; other site 349215002868 ABC transporter signature motif; other site 349215002869 Walker B; other site 349215002870 D-loop; other site 349215002871 H-loop/switch region; other site 349215002872 Alpha/beta hydrolase family; Region: Abhydrolase_5; pfam12695 349215002873 Serine hydrolase; Region: Ser_hydrolase; cl17834 349215002874 FOG: CBS domain [General function prediction only]; Region: COG0517 349215002875 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 349215002876 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 349215002877 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 349215002878 transmembrane helices; other site 349215002879 Uncharacterized ACR, COG1430; Region: DUF192; pfam02643 349215002880 ETC complex I subunit conserved region; Region: ETC_C1_NDUFA4; pfam04800 349215002881 Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; Region: SseA; COG2897 349215002882 Thiosulfate sulfurtransferase (TST), N-terminal, inactive domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the 1st repeat, which does not contain the catalytically active Cys residue. The role of the 1st repeat is uncertain, but it...; Region: TST_Repeat_1; cd01448 349215002883 active site residue [active] 349215002884 Thiosulfate sulfurtransferase (TST), C-terminal, catalytic domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the second repeat. Only the second repeat contains the catalytically active Cys residue; Region: TST_Repeat_2; cd01449 349215002885 active site residue [active] 349215002886 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 349215002887 cyclase homology domain; Region: CHD; cd07302 349215002888 nucleotidyl binding site; other site 349215002889 metal binding site [ion binding]; metal-binding site 349215002890 dimer interface [polypeptide binding]; other site 349215002891 Chromate transport protein ChrA [Inorganic ion transport and metabolism]; Region: ChrA; COG2059 349215002892 chromate transporter, chromate ion transporter (CHR) family; Region: 2A51; TIGR00937 349215002893 Chromate transporter; Region: Chromate_transp; pfam02417 349215002894 Protein-L-isoaspartate carboxylmethyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: Pcm; COG2518 349215002895 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 349215002896 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 349215002897 Protein of unknown function (DUF2497); Region: DUF2497; pfam10691 349215002898 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 349215002899 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 349215002900 HIGH motif; other site 349215002901 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 349215002902 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 349215002903 active site 349215002904 KMSKS motif; other site 349215002905 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 349215002906 tRNA binding surface [nucleotide binding]; other site 349215002907 anticodon binding site; other site 349215002908 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 349215002909 50S ribosomal protein L31; Reviewed; Region: rpmE; PRK00528 349215002910 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 349215002911 Class II Type A, Fructose-1,6-bisphosphate (FBP) aldolases. The enzyme catalyses the zinc-dependent, reversible aldol condensation of dihydroxyacetone phosphate with glyceraldehyde-3-phosphate to form fructose-1,6-bisphosphate. FBP aldolase is...; Region: FBP_aldolase_IIA; cd00946 349215002912 active site 349215002913 intersubunit interface [polypeptide binding]; other site 349215002914 zinc binding site [ion binding]; other site 349215002915 Na+ binding site [ion binding]; other site 349215002916 MarR family; Region: MarR_2; cl17246 349215002917 Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; Region: GapA; COG0057 349215002918 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; smart00846 349215002919 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 349215002920 SAM-dependent methyltransferases [Secondary metabolites biosynthesis, transport, and catabolism / General function prediction only]; Region: SmtA; COG0500 349215002921 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 349215002922 S-adenosylmethionine binding site [chemical binding]; other site 349215002923 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 349215002924 Transketolase [Carbohydrate transport and metabolism]; Region: TktA; COG0021 349215002925 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 349215002926 TPP-binding site [chemical binding]; other site 349215002927 dimer interface [polypeptide binding]; other site 349215002928 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 349215002929 PYR/PP interface [polypeptide binding]; other site 349215002930 dimer interface [polypeptide binding]; other site 349215002931 TPP binding site [chemical binding]; other site 349215002932 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 349215002933 Cell division protein ZapA; Region: ZapA; pfam05164 349215002934 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 349215002935 5,10-methenyltetrahydrofolate synthetase; Region: MTHFS_bact; TIGR02727 349215002936 Deinococcus radiodurans DR1281 and related proteins, metallophosphatase domain; Region: MPP_DR1281; cd07382 349215002937 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 349215002938 putative active site [active] 349215002939 metal binding site [ion binding]; metal-binding site 349215002940 homodimer binding site [polypeptide binding]; other site 349215002941 Response regulator receiver domain; Region: Response_reg; pfam00072 349215002942 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 349215002943 active site 349215002944 phosphorylation site [posttranslational modification] 349215002945 intermolecular recognition site; other site 349215002946 dimerization interface [polypeptide binding]; other site 349215002947 hypothetical protein; Validated; Region: PRK00110 349215002948 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD...; Region: RuvC_resolvase; cd00529 349215002949 active site 349215002950 putative DNA-binding cleft [nucleotide binding]; other site 349215002951 dimer interface [polypeptide binding]; other site 349215002952 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 349215002953 RuvA N terminal domain; Region: RuvA_N; pfam01330 349215002954 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 349215002955 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 349215002956 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 349215002957 Walker A motif; other site 349215002958 ATP binding site [chemical binding]; other site 349215002959 Walker B motif; other site 349215002960 arginine finger; other site 349215002961 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 349215002962 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 349215002963 active site 349215002964 TolQ protein; Region: tolQ; TIGR02796 349215002965 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 349215002966 TolR protein; Region: tolR; TIGR02801 349215002967 translocation protein TolB; Provisional; Region: tolB; PRK05137 349215002968 TolB amino-terminal domain; Region: TolB_N; pfam04052 349215002969 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 349215002970 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 349215002971 Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the Nudix hydrolase superfamily. Members of this family are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant...; Region: Ap4A_hydrolase_plant_like; cd03671 349215002972 putative active site [active] 349215002973 Ap4A binding site [chemical binding]; other site 349215002974 nudix motif; other site 349215002975 putative metal binding site [ion binding]; other site 349215002976 Putative catalytic domain of family 2 polysaccharide deacetylases (DACs) from bacteria; Region: CE4_DAC2; cd10936 349215002977 NodB motif; other site 349215002978 putative active site [active] 349215002979 putative catalytic site [active] 349215002980 Zn binding site [ion binding]; other site 349215002981 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 349215002982 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 349215002983 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 349215002984 protein binding site [polypeptide binding]; other site 349215002985 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 349215002986 Catalytic dyad [active] 349215002987 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]; Region: COG4942 349215002988 Peptidase family M23; Region: Peptidase_M23; pfam01551 349215002989 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 349215002990 Oligomerisation domain; Region: Oligomerisation; pfam02410 349215002991 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 349215002992 Cytidylyltransferase; Region: CTP_transf_2; pfam01467 349215002993 active site 349215002994 (T/H)XGH motif; other site 349215002995 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl17192 349215002996 F0F1 ATP synthase subunit B; Provisional; Region: PRK14475 349215002997 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl17192 349215002998 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 349215002999 ATP synthase subunit C; Region: ATP-synt_C; cl00466 349215003000 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 349215003001 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 349215003002 Putative F0F1-ATPase subunit (ATPase_gene1); Region: ATPase_gene1; pfam09527 349215003003 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 349215003004 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 349215003005 Walker A/P-loop; other site 349215003006 ATP binding site [chemical binding]; other site 349215003007 SMC proteins Flexible Hinge Domain; Region: SMC_hinge; pfam06470 349215003008 ATP-binding cassette domain of barmotin, a member of the SMC protein family; Region: ABC_SMC_barmotin; cd03278 349215003009 ABC transporter signature motif; other site 349215003010 Walker B; other site 349215003011 D-loop; other site 349215003012 H-loop/switch region; other site 349215003013 Thioredoxin; Region: Thioredoxin_4; pfam13462 349215003014 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 349215003015 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cl02931 349215003016 ligand binding site [chemical binding]; other site 349215003017 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 349215003018 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 349215003019 active site 349215003020 dimerization interface [polypeptide binding]; other site 349215003021 Protein of unknown function (DUF721); Region: DUF721; pfam05258 349215003022 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 349215003023 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 349215003024 minor groove reading motif; other site 349215003025 helix-hairpin-helix signature motif; other site 349215003026 substrate binding pocket [chemical binding]; other site 349215003027 active site 349215003028 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 349215003029 DNA glycosylase (MutY in bacteria and hMYH in humans) is responsible for repairing misread A*oxoG residues to C*G by removing the inappropriately paired adenine base from the DNA backbone. It belongs to the Nudix hydrolase superfamily and is important...; Region: DNA_Glycosylase_C; cd03431 349215003030 DNA binding and oxoG recognition site [nucleotide binding] 349215003031 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 349215003032 DNA methylase; Region: N6_N4_Mtase; pfam01555 349215003033 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 349215003034 RNA/DNA hybrid binding site [nucleotide binding]; other site 349215003035 active site 349215003036 aminopeptidase N; Provisional; Region: pepN; PRK14015 349215003037 Peptidase M1 family containing Aminopeptidase N; Region: M1_APN_1; cd09600 349215003038 active site 349215003039 Zn binding site [ion binding]; other site 349215003040 GTPase CgtA; Reviewed; Region: obgE; PRK12299 349215003041 GTP1/OBG; Region: GTP1_OBG; pfam01018 349215003042 Obg GTPase; Region: Obg; cd01898 349215003043 G1 box; other site 349215003044 GTP/Mg2+ binding site [chemical binding]; other site 349215003045 Switch I region; other site 349215003046 G2 box; other site 349215003047 G3 box; other site 349215003048 Switch II region; other site 349215003049 G4 box; other site 349215003050 G5 box; other site 349215003051 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 349215003052 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 349215003053 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 349215003054 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 349215003055 dimer interface [polypeptide binding]; other site 349215003056 phosphorylation site [posttranslational modification] 349215003057 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 349215003058 ATP binding site [chemical binding]; other site 349215003059 Mg2+ binding site [ion binding]; other site 349215003060 G-X-G motif; other site 349215003061 Response regulator receiver domain; Region: Response_reg; pfam00072 349215003062 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 349215003063 active site 349215003064 phosphorylation site [posttranslational modification] 349215003065 intermolecular recognition site; other site 349215003066 dimerization interface [polypeptide binding]; other site 349215003067 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 349215003068 Mechanosensitive ion channel; Region: MS_channel; pfam00924 349215003069 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 349215003070 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 349215003071 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 349215003072 Walker A/P-loop; other site 349215003073 ATP binding site [chemical binding]; other site 349215003074 Q-loop/lid; other site 349215003075 ABC transporter signature motif; other site 349215003076 Walker B; other site 349215003077 D-loop; other site 349215003078 H-loop/switch region; other site 349215003079 type I secretion system ATPase, LssB family; Region: type_I_sec_LssB; TIGR03375 349215003080 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 349215003081 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 349215003082 Walker A/P-loop; other site 349215003083 ATP binding site [chemical binding]; other site 349215003084 Q-loop/lid; other site 349215003085 ABC transporter signature motif; other site 349215003086 Walker B; other site 349215003087 D-loop; other site 349215003088 H-loop/switch region; other site 349215003089 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 349215003090 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 349215003091 HlyD family secretion protein; Region: HlyD_3; pfam13437 349215003092 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 349215003093 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 349215003094 active site 349215003095 phosphorylation site [posttranslational modification] 349215003096 intermolecular recognition site; other site 349215003097 dimerization interface [polypeptide binding]; other site 349215003098 Histidine kinase-like ATPase domain; Region: HATPase_c_2; pfam13581 349215003099 Thioredoxin; Region: Thioredoxin_4; cl17273 349215003100 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 349215003101 HlyD family secretion protein; Region: HlyD_3; pfam13437 349215003102 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 349215003103 putative transporter; Provisional; Region: PRK11660 349215003104 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 349215003105 Sulfate transporter family; Region: Sulfate_transp; pfam00916 349215003106 Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function; Region: STAS_SulP_like_sulfate_transporter; cd07042 349215003107 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 349215003108 Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis. Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing...; Region: OYE_YqiM_FMN; cd02932 349215003109 active site 349215003110 FMN binding site [chemical binding]; other site 349215003111 substrate binding site [chemical binding]; other site 349215003112 homotetramer interface [polypeptide binding]; other site 349215003113 catalytic residue [active] 349215003114 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 349215003115 metal binding site 2 [ion binding]; metal-binding site 349215003116 putative DNA binding helix; other site 349215003117 metal binding site 1 [ion binding]; metal-binding site 349215003118 dimer interface [polypeptide binding]; other site 349215003119 structural Zn2+ binding site [ion binding]; other site 349215003120 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 349215003121 Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan...; Region: Trp-synth-beta_II; cl00342 349215003122 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 349215003123 catalytic residue [active] 349215003124 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 349215003125 active site residue [active] 349215003126 Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Region: LysA; COG0019 349215003127 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 349215003128 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 349215003129 catalytic residue [active] 349215003130 CO dehydrogenase maturation factor [Cell division and chromosome partitioning]; Region: CooC; COG3640 349215003131 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 349215003132 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 349215003133 cysteine desulfurase DndA; Region: DNA_S_dndA; TIGR03235 349215003134 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 349215003135 catalytic residue [active] 349215003136 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 349215003137 Domain of unknown function DUF20; Region: UPF0118; pfam01594 349215003138 PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated; Region: PDZ; cd00136 349215003139 Peptidase family M48; Region: Peptidase_M48; cl12018 349215003140 FOG: CBS domain [General function prediction only]; Region: COG0517 349215003141 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 349215003142 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 349215003143 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 349215003144 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 349215003145 active site 349215003146 metal binding site [ion binding]; metal-binding site 349215003147 Phosphoenolpyruvate carboxylase; Region: PEPcase; cl17418 349215003148 Uncharacterized conserved protein [Function unknown]; Region: COG1434 349215003149 YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been...; Region: YdcF-like; cd06259 349215003150 putative active site [active] 349215003151 Transglycosylase SLT domain; Region: SLT_2; pfam13406 349215003152 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 349215003153 N-acetyl-D-glucosamine binding site [chemical binding]; other site 349215003154 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 349215003155 rare lipoprotein A; Region: rlpA; TIGR00413 349215003156 Sporulation related domain; Region: SPOR; pfam05036 349215003157 D-alanyl-D-alanine carboxypeptidase [Cell envelope biogenesis, outer membrane]; Region: DacC; COG1686 349215003158 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 349215003159 Penicillin-binding protein 5, C-terminal domain; Region: PBP5_C; smart00936 349215003160 thymidylate kinase; Validated; Region: tmk; PRK00698 349215003161 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 349215003162 TMP-binding site; other site 349215003163 ATP-binding site [chemical binding]; other site 349215003164 DNA polymerase III subunit delta'; Validated; Region: PRK07471 349215003165 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 349215003166 Walker A motif; other site 349215003167 ATP binding site [chemical binding]; other site 349215003168 DNA polymerase III subunit delta'; Validated; Region: PRK08485 349215003169 Walker B motif; other site 349215003170 arginine finger; other site 349215003171 methionyl-tRNA synthetase; Reviewed; Region: PRK11893 349215003172 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 349215003173 active site 349215003174 HIGH motif; other site 349215003175 KMSKS motif; other site 349215003176 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 349215003177 tRNA binding surface [nucleotide binding]; other site 349215003178 anticodon binding site; other site 349215003179 Predicted metal-dependent hydrolases with the TIM-barrel fold [General function prediction only]; Region: COG1099 349215003180 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 349215003181 active site 349215003182 putative hydrolase; Provisional; Region: PRK02113 349215003183 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 349215003184 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 349215003185 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 349215003186 PAS domain; Region: PAS_9; pfam13426 349215003187 putative active site [active] 349215003188 heme pocket [chemical binding]; other site 349215003189 PAS domain; Region: PAS_9; pfam13426 349215003190 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 349215003191 putative active site [active] 349215003192 heme pocket [chemical binding]; other site 349215003193 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 349215003194 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 349215003195 dimer interface [polypeptide binding]; other site 349215003196 putative CheW interface [polypeptide binding]; other site 349215003197 EAL domain; Region: EAL; pfam00563 349215003198 nucleoside triphosphate pyrophosphohydrolase; Reviewed; Region: mazG; PRK09562 349215003199 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) N-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs; Region: NTP-PPase_MazG_Nterm; cd11528 349215003200 homodimer interface [polypeptide binding]; other site 349215003201 metal binding site [ion binding]; metal-binding site 349215003202 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) C-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs' Region: NTP-PPase_MazG_Cterm; cd11529 349215003203 homodimer interface [polypeptide binding]; other site 349215003204 active site 349215003205 putative chemical substrate binding site [chemical binding]; other site 349215003206 metal binding site [ion binding]; metal-binding site 349215003207 pilus retraction protein PilT; Region: pilT_fam; TIGR01420 349215003208 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 349215003209 Inositol-monophosphatase-like domains. This family of phosphatases is dependent on bivalent metal ions such as Mg++, and many members are inhibited by Li+ (which is thought to displace a bivalent ion in the active site). Substrates include fructose-1; Region: IMPase_like; cd01637 349215003210 active site 349215003211 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 349215003212 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 349215003213 HflX GTPase family; Region: HflX; cd01878 349215003214 G1 box; other site 349215003215 GTP/Mg2+ binding site [chemical binding]; other site 349215003216 Switch I region; other site 349215003217 G2 box; other site 349215003218 G3 box; other site 349215003219 Switch II region; other site 349215003220 G4 box; other site 349215003221 G5 box; other site 349215003222 bacterial Hfq-like; Region: Hfq; cd01716 349215003223 hexamer interface [polypeptide binding]; other site 349215003224 Sm1 motif; other site 349215003225 RNA binding site [nucleotide binding]; other site 349215003226 Sm2 motif; other site 349215003227 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 349215003228 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 349215003229 active site 349215003230 motif I; other site 349215003231 motif II; other site 349215003232 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 349215003233 D-Alanine aminotransferase (D-AAT_like): D-amino acid aminotransferase catalyzes transamination between D-amino acids and their respective alpha-keto acids. It plays a major role in the synthesis of bacterial cell wall components like D-alanine and...; Region: D-AAT_like; cd01558 349215003234 homodimer interface [polypeptide binding]; other site 349215003235 substrate-cofactor binding pocket; other site 349215003236 pyridoxal 5'-phosphate binding site [chemical binding]; other site 349215003237 catalytic residue [active] 349215003238 potassium transporter peripheral membrane component; Reviewed; Region: trkA; PRK09496 349215003239 TrkA-N domain; Region: TrkA_N; pfam02254 349215003240 TrkA-C domain; Region: TrkA_C; pfam02080 349215003241 TrkA-N domain; Region: TrkA_N; pfam02254 349215003242 TrkA-C domain; Region: TrkA_C; pfam02080 349215003243 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 349215003244 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 349215003245 active site 349215003246 phosphorylation site [posttranslational modification] 349215003247 intermolecular recognition site; other site 349215003248 dimerization interface [polypeptide binding]; other site 349215003249 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 349215003250 Walker A motif; other site 349215003251 ATP binding site [chemical binding]; other site 349215003252 Walker B motif; other site 349215003253 arginine finger; other site 349215003254 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 349215003255 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 349215003256 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 349215003257 dimerization interface [polypeptide binding]; other site 349215003258 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 349215003259 putative active site [active] 349215003260 heme pocket [chemical binding]; other site 349215003261 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 349215003262 dimer interface [polypeptide binding]; other site 349215003263 phosphorylation site [posttranslational modification] 349215003264 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 349215003265 ATP binding site [chemical binding]; other site 349215003266 Mg2+ binding site [ion binding]; other site 349215003267 G-X-G motif; other site 349215003268 bifunctional 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase/2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase protein; Provisional; Region: ispDF; PRK09382 349215003269 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 349215003270 substrate binding site; other site 349215003271 dimer interface; other site 349215003272 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 349215003273 homotrimer interaction site [polypeptide binding]; other site 349215003274 zinc binding site [ion binding]; other site 349215003275 CDP-binding sites; other site 349215003276 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 349215003277 tetramer interfaces [polypeptide binding]; other site 349215003278 binuclear metal-binding site [ion binding]; other site 349215003279 Competence-damaged protein; Region: CinA; pfam02464 349215003280 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 349215003281 active site 349215003282 lipoyl synthase; Provisional; Region: PRK05481 349215003283 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 349215003284 FeS/SAM binding site; other site 349215003285 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 349215003286 catalytic core [active] 349215003287 Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It...; Region: cysteine_hydrolases; cl00220 349215003288 catalytic triad [active] 349215003289 conserved cis-peptide bond; other site 349215003290 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06416 349215003291 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 349215003292 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 349215003293 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 349215003294 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 349215003295 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 349215003296 dimerization interface [polypeptide binding]; other site 349215003297 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 349215003298 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 349215003299 dimer interface [polypeptide binding]; other site 349215003300 putative CheW interface [polypeptide binding]; other site 349215003301 Deoxynucleoside kinases [Nucleotide transport and metabolism]; Region: COG1428 349215003302 Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates...; Region: NK; cl17190 349215003303 active site 349215003304 Deoxynucleoside kinases [Nucleotide transport and metabolism]; Region: COG1428 349215003305 Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates...; Region: NK; cl17190 349215003306 active site 349215003307 Methyltransferase domain; Region: Methyltransf_32; pfam13679 349215003308 Methyltransferase domain; Region: Methyltransf_31; pfam13847 349215003309 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 349215003310 active site 349215003311 Deoxynucleoside kinases [Nucleotide transport and metabolism]; Region: COG1428 349215003312 Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates...; Region: NK; cl17190 349215003313 active site 349215003314 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 349215003315 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; Region: PDHac_trf_mito; TIGR01349 349215003316 E3 interaction surface; other site 349215003317 lipoyl attachment site [posttranslational modification]; other site 349215003318 e3 binding domain; Region: E3_binding; pfam02817 349215003319 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 349215003320 pyruvate dehydrogenase subunit beta; Provisional; Region: PRK11892 349215003321 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 349215003322 E3 interaction surface; other site 349215003323 lipoyl attachment site [posttranslational modification]; other site 349215003324 Pyrimidine (PYR) binding domain of the beta subunits of the E1 components of human pyruvate dehydrogenase complex (E1- PDHc) and related proteins; Region: TPP_PYR_E1-PDHc-beta_like; cd07036 349215003325 alpha subunit interface [polypeptide binding]; other site 349215003326 TPP binding site [chemical binding]; other site 349215003327 heterodimer interface [polypeptide binding]; other site 349215003328 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 349215003329 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 349215003330 Thiamine pyrophosphate (TPP) family, E1 of PDC_ADC_BCADC subfamily, TPP-binding module; composed of proteins similar to the E1 components of the human pyruvate dehydrogenase complex (PDC), the acetoin dehydrogenase complex (ADC) and the branched chain...; Region: TPP_E1_PDC_ADC_BCADC; cd02000 349215003331 tetramer interface [polypeptide binding]; other site 349215003332 TPP-binding site [chemical binding]; other site 349215003333 heterodimer interface [polypeptide binding]; other site 349215003334 phosphorylation loop region [posttranslational modification] 349215003335 Septum formation initiator; Region: DivIC; cl17659 349215003336 Protein of unknown function, DUF606; Region: DUF606; pfam04657 349215003337 enolase; Provisional; Region: eno; PRK00077 349215003338 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 349215003339 dimer interface [polypeptide binding]; other site 349215003340 metal binding site [ion binding]; metal-binding site 349215003341 substrate binding pocket [chemical binding]; other site 349215003342 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 349215003343 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 349215003344 CTP synthetase; Validated; Region: pyrG; PRK05380 349215003345 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 349215003346 Catalytic site [active] 349215003347 active site 349215003348 UTP binding site [chemical binding]; other site 349215003349 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 349215003350 active site 349215003351 putative oxyanion hole; other site 349215003352 catalytic triad [active] 349215003353 Preprotein translocase SecG subunit; Region: SecG; pfam03840 349215003354 triosephosphate isomerase; Provisional; Region: PRK14567 349215003355 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 349215003356 substrate binding site [chemical binding]; other site 349215003357 dimer interface [polypeptide binding]; other site 349215003358 catalytic triad [active] 349215003359 SurA N-terminal domain; Region: SurA_N_3; cl07813 349215003360 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 349215003361 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 349215003362 Putative catalytic domain of family 2 polysaccharide deacetylases (DACs) from bacteria; Region: CE4_DAC2; cd10936 349215003363 putative active site [active] 349215003364 NodB motif; other site 349215003365 LexA repressor; Validated; Region: PRK00215 349215003366 LexA DNA binding domain; Region: LexA_DNA_bind; pfam01726 349215003367 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 349215003368 Catalytic site [active] 349215003369 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 349215003370 Competence protein; Region: Competence; pfam03772 349215003371 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 349215003372 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 349215003373 active site 349215003374 HIGH motif; other site 349215003375 nucleotide binding site [chemical binding]; other site 349215003376 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 349215003377 active site 349215003378 KMSKS motif; other site 349215003379 Peptidase family M48; Region: Peptidase_M48; cl12018 349215003380 Escherichia coli (Ec) citrate synthase (CS) GltA_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). The overall CS...; Region: EcCS_like; cd06114 349215003381 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 349215003382 dimer interface [polypeptide binding]; other site 349215003383 active site 349215003384 citrylCoA binding site [chemical binding]; other site 349215003385 NADH binding [chemical binding]; other site 349215003386 cationic pore residues; other site 349215003387 oxalacetate/citrate binding site [chemical binding]; other site 349215003388 coenzyme A binding site [chemical binding]; other site 349215003389 catalytic triad [active] 349215003390 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 349215003391 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 349215003392 Protein of unknown function (DUF1009); Region: DUF1009; pfam06230 349215003393 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 349215003394 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 349215003395 active site 349215003396 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 349215003397 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 349215003398 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 349215003399 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 349215003400 trimer interface [polypeptide binding]; other site 349215003401 active site 349215003402 UDP-GlcNAc binding site [chemical binding]; other site 349215003403 lipid binding site [chemical binding]; lipid-binding site 349215003404 periplasmic chaperone; Provisional; Region: PRK10780 349215003405 Outer membrane protein (OmpH-like); Region: OmpH; pfam03938 349215003406 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 349215003407 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 349215003408 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 349215003409 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 349215003410 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 349215003411 Surface antigen; Region: Bac_surface_Ag; pfam01103 349215003412 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 349215003413 RIP metalloprotease RseP; Region: TIGR00054 349215003414 active site 349215003415 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 349215003416 protein binding site [polypeptide binding]; other site 349215003417 PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated; Region: PDZ; cl00117 349215003418 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 349215003419 putative substrate binding region [chemical binding]; other site 349215003420 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 349215003421 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 349215003422 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 349215003423 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 349215003424 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 349215003425 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 349215003426 Undecaprenyl pyrophosphate synthase [Lipid metabolism]; Region: UppS; COG0020 349215003427 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 349215003428 catalytic residue [active] 349215003429 putative FPP diphosphate binding site; other site 349215003430 putative FPP binding hydrophobic cleft; other site 349215003431 dimer interface [polypeptide binding]; other site 349215003432 putative IPP diphosphate binding site; other site 349215003433 ribosome recycling factor; Reviewed; Region: frr; PRK00083 349215003434 Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are "recycled" and ready for another...; Region: RRF; cd00520 349215003435 hinge region; other site 349215003436 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 349215003437 putative nucleotide binding site [chemical binding]; other site 349215003438 uridine monophosphate binding site [chemical binding]; other site 349215003439 homohexameric interface [polypeptide binding]; other site 349215003440 elongation factor Ts; Provisional; Region: tsf; PRK09377 349215003441 UBA/TS-N domain; Region: UBA; pfam00627 349215003442 Elongation factor TS; Region: EF_TS; pfam00889 349215003443 Elongation factor TS; Region: EF_TS; pfam00889 349215003444 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 349215003445 rRNA interaction site [nucleotide binding]; other site 349215003446 S8 interaction site; other site 349215003447 putative laminin-1 binding site; other site 349215003448 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 349215003449 ligand binding site [chemical binding]; other site 349215003450 active site 349215003451 UGI interface [polypeptide binding]; other site 349215003452 catalytic site [active] 349215003453 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 349215003454 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 349215003455 putative active site [active] 349215003456 putative PHP Thumb interface [polypeptide binding]; other site 349215003457 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 349215003458 generic binding surface I; other site 349215003459 generic binding surface II; other site 349215003460 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 349215003461 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 349215003462 Walker A/P-loop; other site 349215003463 ATP binding site [chemical binding]; other site 349215003464 Q-loop/lid; other site 349215003465 ABC transporter signature motif; other site 349215003466 Walker B; other site 349215003467 D-loop; other site 349215003468 H-loop/switch region; other site 349215003469 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 349215003470 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 349215003471 FtsX-like permease family; Region: FtsX; pfam02687 349215003472 prolyl-tRNA synthetase; Provisional; Region: PRK08661 349215003473 Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: ProRS_core_arch_euk; cd00778 349215003474 dimer interface [polypeptide binding]; other site 349215003475 motif 1; other site 349215003476 active site 349215003477 motif 2; other site 349215003478 motif 3; other site 349215003479 HGTP anticodon binding domain, as found at the C-terminus of histidyl, glycyl, threonyl and prolyl tRNA synthetases, which are classified as a group of class II aminoacyl-tRNA synthetases (aaRS). In aaRSs, the anticodon binding domain is responsible for...; Region: HGTP_anticodon; cl00266 349215003480 anticodon binding site; other site 349215003481 Protein of unknown function (DUF1467); Region: DUF1467; pfam07330 349215003482 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 349215003483 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 349215003484 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 349215003485 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 349215003486 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 349215003487 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 349215003488 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 349215003489 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 349215003490 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 349215003491 NADH-ubiquinone oxidoreductase chain 4, amino terminus; Region: Oxidored_q5_N; pfam01059 349215003492 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 349215003493 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 349215003494 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 349215003495 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 349215003496 NADH dehydrogenase subunit 5 C-terminus; Region: NADH5_C; pfam06455 349215003497 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 349215003498 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 349215003499 NADH dehydrogenase subunit J; Provisional; Region: PRK06433 349215003500 NADH dehydrogenase subunit 6; Provisional; Region: ND6; MTH00213 349215003501 Lipid A 3-O-deacylase (PagL); Region: PagL; pfam09411 349215003502 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 349215003503 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 349215003504 active site 349215003505 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 349215003506 4Fe-4S binding domain; Region: Fer4; cl02805 349215003507 4Fe-4S binding domain; Region: Fer4; pfam00037 349215003508 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 349215003509 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 349215003510 NADH dehydrogenase subunit G; Validated; Region: PRK09130 349215003511 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 349215003512 catalytic loop [active] 349215003513 iron binding site [ion binding]; other site 349215003514 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 349215003515 MopB_Res_Cmplx1_Nad11: The second domain of the Nad11/75-kDa subunit of the NADH-quinone oxidoreductase/respiratory complex I/NADH dehydrogenase-1(NDH-1) of eukaryotes and the Nqo3/G subunit of alphaproteobacteria NDH-1. The NADH-quinone oxidoreductase...; Region: MopB_Res-Cmplx1_Nad11; cd02773 349215003516 Domain of unknown function (DUF1982); Region: DUF1982; pfam09326 349215003517 NADH dehydrogenase I subunit F; Provisional; Region: PRK13596 349215003518 SLBB domain; Region: SLBB; pfam10531 349215003519 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 349215003520 Respiratory-chain NADH dehydrogenase 24 Kd subunit; Region: Complex1_24kDa; pfam01257 349215003521 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 349215003522 putative dimer interface [polypeptide binding]; other site 349215003523 [2Fe-2S] cluster binding site [ion binding]; other site 349215003524 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 349215003525 NADH dehydrogenase subunit D; Validated; Region: PRK06075 349215003526 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 349215003527 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 349215003528 NADH dehydrogenase subunit B; Validated; Region: PRK06411 349215003529 NADH:ubiquinone oxidoreductase subunit A; Validated; Region: PRK06602 349215003530 Protein of unknown function (DUF3442); Region: DUF3442; pfam11924 349215003531 Right handed beta helix region; Region: Beta_helix; pfam13229 349215003532 Right handed beta helix region; Region: Beta_helix; pfam13229 349215003533 Right handed beta helix region; Region: Beta_helix; pfam13229 349215003534 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 349215003535 Alanine dehydrogenase NAD-binding and catalytic domains; Region: L-AlaDH; cd05305 349215003536 hexamer interface [polypeptide binding]; other site 349215003537 ligand binding site [chemical binding]; other site 349215003538 putative active site [active] 349215003539 NAD(P) binding site [chemical binding]; other site 349215003540 Tandem repeat subunit of reelin and related proteins; Region: Reelin_subrepeat_like; cl15240 349215003541 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 349215003542 IHF dimer interface [polypeptide binding]; other site 349215003543 IHF - DNA interface [nucleotide binding]; other site 349215003544 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 349215003545 Found in ATP-dependent protease La (LON); Region: LON; smart00464 349215003546 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 349215003547 Walker A motif; other site 349215003548 ATP binding site [chemical binding]; other site 349215003549 Walker B motif; other site 349215003550 arginine finger; other site 349215003551 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 349215003552 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 349215003553 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 349215003554 oligomer interface [polypeptide binding]; other site 349215003555 active site residues [active] 349215003556 trigger factor; Provisional; Region: tig; PRK01490 349215003557 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 349215003558 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 349215003559 Uncharacterized conserved protein [Function unknown]; Region: COG0062 349215003560 putative carbohydrate kinase; Provisional; Region: PRK10565 349215003561 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 349215003562 putative substrate binding site [chemical binding]; other site 349215003563 putative ATP binding site [chemical binding]; other site 349215003564 glutamine synthetase; Provisional; Region: glnA; PRK09469 349215003565 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 349215003566 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 349215003567 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis; Region: BFIT_BACH; cd03442 349215003568 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 349215003569 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 349215003570 Mg2+ binding site [ion binding]; other site 349215003571 G-X-G motif; other site 349215003572 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 349215003573 anchoring element; other site 349215003574 dimer interface [polypeptide binding]; other site 349215003575 ATP binding site [chemical binding]; other site 349215003576 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 349215003577 active site 349215003578 putative metal-binding site [ion binding]; other site 349215003579 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 349215003580 Dicarboxylate transport; Region: DctA-YdbH; cl14674 349215003581 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 349215003582 OstA-like protein; Region: OstA; pfam03968 349215003583 Organic solvent tolerance protein; Region: OstA_C; pfam04453 349215003584 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 349215003585 DEAD-like helicases superfamily; Region: DEXDc; smart00487 349215003586 ATP binding site [chemical binding]; other site 349215003587 Mg++ binding site [ion binding]; other site 349215003588 motif III; other site 349215003589 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 349215003590 nucleotide binding region [chemical binding]; other site 349215003591 ATP-binding site [chemical binding]; other site 349215003592 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 349215003593 S-adenosylmethionine binding site [chemical binding]; other site 349215003594 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 349215003595 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 349215003596 substrate-cofactor binding pocket; other site 349215003597 pyridoxal 5'-phosphate binding site [chemical binding]; other site 349215003598 catalytic residue [active] 349215003599 L-threonine 3-dehydrogenase; Validated; Region: tdh; PRK05396 349215003600 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 349215003601 NAD(P) binding site [chemical binding]; other site 349215003602 Uncharacterized conserved protein [Function unknown]; Region: COG2898 349215003603 Uncharacterized conserved protein (DUF2156); Region: DUF2156; pfam09924 349215003604 homogentisate 1,2-dioxygenase; Provisional; Region: PRK05341 349215003605 Domain of unknown function (DUF4139); Region: DUF4139; pfam13598 349215003606 Domain of unknown function (DUF4139); Region: DUF4139; pfam13598 349215003607 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 349215003608 Na(+)- and Cl(-)-dependent choline cotransporter CHT and related proteins; solute-binding domain; Region: SLC5sbd_CHT; cd11474 349215003609 Na binding site [ion binding]; other site 349215003610 putative glycosylation site [posttranslational modification]; other site 349215003611 putative glycosylation site [posttranslational modification]; other site 349215003612 Poly(3-hydroxybutyrate) depolymerase [Secondary metabolites biosynthesis, transport, and catabolism]; Region: LpqC; COG3509 349215003613 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 349215003614 Glycine cleavage system P-protein, alpha- and beta-subunits. This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2.1; Region: GDC-P; cd00613 349215003615 tetramer interface [polypeptide binding]; other site 349215003616 pyridoxal 5'-phosphate binding site [chemical binding]; other site 349215003617 catalytic residue [active] 349215003618 Glycine cleavage system protein P (pyridoxal-binding), N-terminal domain [Amino acid transport and metabolism]; Region: GcvP; COG0403 349215003619 glycine dehydrogenase subunit 1; Validated; Region: PRK00451 349215003620 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 349215003621 catalytic residue [active] 349215003622 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 349215003623 lipoyl attachment site [posttranslational modification]; other site 349215003624 glycine cleavage system aminomethyltransferase T; Reviewed; Region: gcvT; PRK00389 349215003625 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 349215003626 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 349215003627 Predicted flavoprotein [General function prediction only]; Region: COG0431 349215003628 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 349215003629 DNA-binding site [nucleotide binding]; DNA binding site 349215003630 RNA-binding motif; other site 349215003631 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 349215003632 DEAD-like helicases superfamily; Region: DEXDc; smart00487 349215003633 ATP binding site [chemical binding]; other site 349215003634 Mg++ binding site [ion binding]; other site 349215003635 motif III; other site 349215003636 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 349215003637 nucleotide binding region [chemical binding]; other site 349215003638 ATP-binding site [chemical binding]; other site 349215003639 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 349215003640 NlpC/P60 family; Region: NLPC_P60; pfam00877 349215003641 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 349215003642 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 349215003643 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 349215003644 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 349215003645 putrescine transporter; Provisional; Region: potE; PRK10655 349215003646 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 349215003647 Clp amino terminal domain; Region: Clp_N; pfam02861 349215003648 Clp amino terminal domain; Region: Clp_N; pfam02861 349215003649 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 349215003650 Walker A motif; other site 349215003651 ATP binding site [chemical binding]; other site 349215003652 Walker B motif; other site 349215003653 arginine finger; other site 349215003654 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 349215003655 Walker A motif; other site 349215003656 ATP binding site [chemical binding]; other site 349215003657 Walker B motif; other site 349215003658 arginine finger; other site 349215003659 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 349215003660 Domain of unknown function (DUF4167); Region: DUF4167; pfam13763 349215003661 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 349215003662 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 349215003663 peptide chain release factor 1; Validated; Region: prfA; PRK00591 349215003664 This domain is found in peptide chain release factors; Region: PCRF; smart00937 349215003665 RF-1 domain; Region: RF-1; pfam00472 349215003666 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 349215003667 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 349215003668 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 349215003669 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 349215003670 HSP70 interaction site [polypeptide binding]; other site 349215003671 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]; Region: COG1426 349215003672 Helix-turn-helix domain; Region: HTH_25; pfam13413 349215003673 Domain of unknown function (DUF4115); Region: DUF4115; pfam13464 349215003674 aspartate kinase; Reviewed; Region: PRK06635 349215003675 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 349215003676 putative nucleotide binding site [chemical binding]; other site 349215003677 putative catalytic residues [active] 349215003678 putative Mg ion binding site [ion binding]; other site 349215003679 putative aspartate binding site [chemical binding]; other site 349215003680 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 349215003681 putative allosteric regulatory site; other site 349215003682 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 349215003683 putative allosteric regulatory residue; other site 349215003684 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 349215003685 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 349215003686 S-adenosylmethionine binding site [chemical binding]; other site 349215003687 Hypoxia induced protein conserved region; Region: HIG_1_N; pfam04588 349215003688 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 349215003689 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 349215003690 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 349215003691 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 349215003692 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 349215003693 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 349215003694 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 349215003695 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 349215003696 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 349215003697 catalytic residues [active] 349215003698 diaminopimelate decarboxylase; Region: lysA; TIGR01048 349215003699 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 349215003700 active site 349215003701 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 349215003702 substrate binding site [chemical binding]; other site 349215003703 catalytic residues [active] 349215003704 dimer interface [polypeptide binding]; other site 349215003705 Domain of unknown function (DUF4175); Region: DUF4175; pfam13779 349215003706 Disulphide isomerase; Region: Disulph_isomer; cl05813 349215003707 Protein of unknown function (DUF3426); Region: DUF3426; pfam11906 349215003708 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 349215003709 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 349215003710 Walker A/P-loop; other site 349215003711 ATP binding site [chemical binding]; other site 349215003712 Q-loop/lid; other site 349215003713 ABC transporter signature motif; other site 349215003714 Walker B; other site 349215003715 D-loop; other site 349215003716 H-loop/switch region; other site 349215003717 Cell division protein [Cell division and chromosome partitioning]; Region: FtsX; COG2177 349215003718 YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been...; Region: YdcF-like; cd06259 349215003719 putative active site [active] 349215003720 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 349215003721 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 349215003722 putative acyl-acceptor binding pocket; other site 349215003723 Uncharacterized protein conserved in bacteria (DUF2125); Region: DUF2125; pfam09898 349215003724 Chorismate mutase type II; Region: CM_2; smart00830 349215003725 Methyltransferase domain; Region: Methyltransf_23; pfam13489 349215003726 Methyltransferase domain; Region: Methyltransf_11; pfam08241 349215003727 The MutT pyrophosphohydrolase is a prototypical Nudix hydrolase that catalyzes the hydrolysis of nucleoside and deoxynucleoside triphosphates (NTPs and dNTPs) by substitution at a beta-phosphorus to yield a nucleotide monophosphate (NMP) and inorganic...; Region: MutT_pyrophosphohydrolase; cd03425 349215003728 active site 349215003729 8-oxo-dGMP binding site [chemical binding]; other site 349215003730 nudix motif; other site 349215003731 metal binding site [ion binding]; metal-binding site 349215003732 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 349215003733 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 349215003734 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 349215003735 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 349215003736 ATP binding site [chemical binding]; other site 349215003737 putative Mg++ binding site [ion binding]; other site 349215003738 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 349215003739 SEC-C motif; Region: SEC-C; pfam02810 349215003740 methyltransferase, FkbM family; Region: fkbM_fam; TIGR01444 349215003741 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 349215003742 Domain of unknown function DUF21; Region: DUF21; pfam01595 349215003743 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 349215003744 Transporter associated domain; Region: CorC_HlyC; smart01091 349215003745 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 349215003746 active site 349215003747 dimer interface [polypeptide binding]; other site 349215003748 metal binding site [ion binding]; metal-binding site 349215003749 shikimate kinase; Reviewed; Region: aroK; PRK00131 349215003750 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 349215003751 ADP binding site [chemical binding]; other site 349215003752 magnesium binding site [ion binding]; other site 349215003753 putative shikimate binding site; other site 349215003754 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 349215003755 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 349215003756 active site 349215003757 DNA binding site [nucleotide binding] 349215003758 Int/Topo IB signature motif; other site 349215003759 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated; Region: PRK05724 349215003760 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 349215003761 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 349215003762 Ribbon-helix-helix domain; Region: RHH_4; pfam13467 349215003763 BolA-like protein; Region: BolA; pfam01722 349215003764 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 349215003765 HSP70 interaction site [polypeptide binding]; other site 349215003766 cobaltochelatase, CobS subunit; Region: PD_CobS; TIGR01650 349215003767 Cobaltochelatase CobS subunit N terminal; Region: CobS_N; pfam12556 349215003768 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 349215003769 Walker A motif; other site 349215003770 ATP binding site [chemical binding]; other site 349215003771 Walker B motif; other site 349215003772 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; Region: GIY-YIG_unchar_3; cd10448 349215003773 putative active site [active] 349215003774 GIY-YIG motif/motif A; other site 349215003775 putative metal binding site [ion binding]; other site 349215003776 Cobalamin biosynthesis protein CobT; Region: CobT; pfam06213 349215003777 norD type: Denitrifying bacteria contain both membrane bound and periplasmic nitrate reductases. Denitrification plays a major role in completing the nitrogen cycle by converting nitrate or nitrite to nitrogen gas. The pathway for microbial...; Region: vWA_norD_type; cd01454 349215003778 metal ion-dependent adhesion site (MIDAS); other site 349215003779 histidyl-tRNA synthetase; Region: hisS; TIGR00442 349215003780 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for...; Region: HisRS-like_core; cd00773 349215003781 dimer interface [polypeptide binding]; other site 349215003782 motif 1; other site 349215003783 active site 349215003784 motif 2; other site 349215003785 motif 3; other site 349215003786 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 349215003787 anticodon binding site; other site 349215003788 2-deoxyribose-5-phosphate aldolase (DERA) of the DeoC family; Region: DeoC; cd00959 349215003789 intersubunit interface [polypeptide binding]; other site 349215003790 active site 349215003791 catalytic residue [active] 349215003792 Aldehyde dehydrogenase family 16A1-like; Region: ALDH_F16; cd07111 349215003793 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 349215003794 NAD(P) binding site [chemical binding]; other site 349215003795 catalytic residues [active] 349215003796 NAD-dependent aldehyde dehydrogenases [Energy production and conversion]; Region: PutA; COG1012 349215003797 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 349215003798 NAD(P) binding site [chemical binding]; other site 349215003799 Zeta toxin; Region: Zeta_toxin; pfam06414 349215003800 Fe-S metabolism associated domain; Region: SufE; cl00951 349215003801 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 349215003802 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 349215003803 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 349215003804 Walker A motif; other site 349215003805 ATP binding site [chemical binding]; other site 349215003806 Walker B motif; other site 349215003807 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 349215003808 Exopolyphosphatase-related proteins [General function prediction only]; Region: COG0618 349215003809 Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]; Region: PhrB; COG0415 349215003810 DNA photolyase; Region: DNA_photolyase; pfam00875 349215003811 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 349215003812 dimer interface [polypeptide binding]; other site 349215003813 catalytic triad [active] 349215003814 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 349215003815 EamA-like transporter family; Region: EamA; pfam00892 349215003816 EamA-like transporter family; Region: EamA; pfam00892 349215003817 Ferredoxin [Energy production and conversion]; Region: COG1146 349215003818 4Fe-4S binding domain; Region: Fer4; pfam00037 349215003819 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 349215003820 Transcriptional regulators, similar to M. xanthus CarD [Transcription]; Region: COG1329 349215003821 RNA polymerase factor sigma-32; Reviewed; Region: rpoH2; PRK07500 349215003822 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 349215003823 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 349215003824 DNA binding residues [nucleotide binding] 349215003825 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 349215003826 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 349215003827 Coenzyme A binding pocket [chemical binding]; other site 349215003828 Putative Zn-dependent protease [General function prediction only]; Region: COG4784 349215003829 Peptidase family M48; Region: Peptidase_M48; cl12018 349215003830 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 349215003831 Staphylococcal nuclease homologues; Region: SNc; smart00318 349215003832 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cl00140 349215003833 Catalytic site; other site 349215003834 proline iminopeptidase, Neisseria-type subfamily; Region: pro_imino_pep_1; TIGR01249 349215003835 Phosphoglycerate kinase; Region: PGK; pfam00162 349215003836 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 349215003837 substrate binding site [chemical binding]; other site 349215003838 hinge regions; other site 349215003839 ADP binding site [chemical binding]; other site 349215003840 catalytic site [active] 349215003841 Uncharacterized protein conserved in bacteria (DUF2336); Region: DUF2336; pfam10098 349215003842 Tryptophan 2,3-dioxygenase; Region: Trp_dioxygenase; cl03994 349215003843 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 349215003844 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 349215003845 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 349215003846 catalytic residue [active] 349215003847 AMP nucleosidase; Provisional; Region: PRK08292 349215003848 Bacterial AMP nucleoside phosphorylase N-terminus; Region: AMNp_N; pfam10423 349215003849 Nucleoside phosphorylase [Nucleotide transport and metabolism]; Region: Pfs; COG0775 349215003850 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 349215003851 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 349215003852 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 349215003853 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 349215003854 catalytic core [active] 349215003855 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 349215003856 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 349215003857 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 349215003858 FeS/SAM binding site; other site 349215003859 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 349215003860 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 349215003861 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 349215003862 Protein of unknown function (DUF3800); Region: DUF3800; pfam12686 349215003863 signal recognition particle protein; Provisional; Region: PRK10867 349215003864 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 349215003865 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 349215003866 P loop; other site 349215003867 GTP binding site [chemical binding]; other site 349215003868 Signal peptide binding domain; Region: SRP_SPB; pfam02978 349215003869 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 349215003870 RimM protein, required for 16S rRNA processing [Translation, ribosomal structure and biogenesis]; Region: RimM; COG0806 349215003871 RimM N-terminal domain; Region: RimM; pfam01782 349215003872 PRC-barrel domain; Region: PRC; pfam05239 349215003873 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 349215003874 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 349215003875 3-isopropylmalate dehydratase large subunit; Reviewed; Region: PRK00402 349215003876 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; Region: IPMI; cd01583 349215003877 substrate binding site [chemical binding]; other site 349215003878 ligand binding site [chemical binding]; other site 349215003879 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 349215003880 Zn2+ binding site [ion binding]; other site 349215003881 Mg2+ binding site [ion binding]; other site 349215003882 isopropylmalate isomerase small subunit; Provisional; Region: leuD; PRK01641 349215003883 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 349215003884 substrate binding site [chemical binding]; other site 349215003885 3-isopropylmalate dehydrogenase; Provisional; Region: PRK00772 349215003886 tartrate dehydrogenase; Region: TTC; TIGR02089 349215003887 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 349215003888 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 349215003889 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 349215003890 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 349215003891 Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilU; COG5008 349215003892 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 349215003893 Walker A motif; other site 349215003894 ATP binding site [chemical binding]; other site 349215003895 Walker B motif; other site 349215003896 Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PilT; COG2805 349215003897 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 349215003898 Walker A motif; other site 349215003899 ATP binding site [chemical binding]; other site 349215003900 Walker B motif; other site 349215003901 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 349215003902 Bacterial Peptidase A24 N-terminal domain; Region: DiS_P_DiS; pfam06750 349215003903 Type IV leader peptidase family; Region: Peptidase_A24; pfam01478 349215003904 TPR repeat; Region: TPR_11; pfam13414 349215003905 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 349215003906 binding surface 349215003907 TPR motif; other site 349215003908 Tetratricopeptide repeat; Region: TPR_12; pfam13424 349215003909 ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatA; COG4555 349215003910 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 349215003911 Walker A/P-loop; other site 349215003912 ATP binding site [chemical binding]; other site 349215003913 Q-loop/lid; other site 349215003914 ABC transporter signature motif; other site 349215003915 Walker B; other site 349215003916 D-loop; other site 349215003917 H-loop/switch region; other site 349215003918 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 349215003919 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 349215003920 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 349215003921 Type II secretion system (T2SS), protein E, N-terminal domain; Region: T2SE_Nter; pfam05157 349215003922 Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulE; COG2804 349215003923 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 349215003924 Walker A motif; other site 349215003925 ATP binding site [chemical binding]; other site 349215003926 Walker B motif; other site 349215003927 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_beta; cd01714 349215003928 Ligand binding site [chemical binding]; other site 349215003929 Electron transfer flavoprotein domain; Region: ETF; pfam01012 349215003930 electron transfer flavoprotein subunit alpha; Provisional; Region: PLN00022 349215003931 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_alpha; cd01715 349215003932 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 349215003933 Acetyltransferase (GNAT) domain; Region: Acetyltransf_5; cl17496 349215003934 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 349215003935 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 349215003936 putative acyl-acceptor binding pocket; other site 349215003937 Protein of unknown function (DUF3126); Region: DUF3126; pfam11324 349215003938 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 349215003939 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 349215003940 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 349215003941 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; pfam02606 349215003942 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 349215003943 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 349215003944 putative acyl-acceptor binding pocket; other site 349215003945 Class-II DAHP synthetase family; Region: DAHP_synth_2; pfam01474 349215003946 nicotinate phosphoribosyltransferase; Validated; Region: PRK09243 349215003947 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 349215003948 active site 349215003949 NAD synthetase; Provisional; Region: PRK13981 349215003950 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 349215003951 multimer interface [polypeptide binding]; other site 349215003952 active site 349215003953 catalytic triad [active] 349215003954 protein interface 1 [polypeptide binding]; other site 349215003955 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 349215003956 homodimer interface [polypeptide binding]; other site 349215003957 NAD binding pocket [chemical binding]; other site 349215003958 ATP binding pocket [chemical binding]; other site 349215003959 Mg binding site [ion binding]; other site 349215003960 active-site loop [active] 349215003961 glutamyl-tRNA synthetase; Provisional; Region: PRK12558 349215003962 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 349215003963 HIGH motif; other site 349215003964 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 349215003965 active site 349215003966 KMSKS motif; other site 349215003967 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 349215003968 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 349215003969 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 349215003970 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 349215003971 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 349215003972 RNA binding surface [nucleotide binding]; other site 349215003973 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 349215003974 Autotransporter beta-domain; Region: Autotransporter; pfam03797 349215003975 This domain is the catalytic domain of ribonuclease II; Region: RNB; smart00955 349215003976 RNB domain; Region: RNB; pfam00773 349215003977 PAP2_like proteins, Aur1_like subfamily. Yeast Aur1p or Ipc1p is necessary for the addition of inositol phosphate to ceramide, an essential step in yeast sphingolipid synthesis, and is the target of several antifungal compounds such as aureobasidin; Region: PAP2_Aur1_like; cd03386 349215003978 active site 349215003979 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 349215003980 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 349215003981 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 349215003982 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 349215003983 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 349215003984 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 349215003985 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 349215003986 DNA binding residues [nucleotide binding] 349215003987 DNA primase; Validated; Region: dnaG; PRK05667 349215003988 CHC2 zinc finger; Region: zf-CHC2; pfam01807 349215003989 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 349215003990 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 349215003991 active site 349215003992 metal binding site [ion binding]; metal-binding site 349215003993 interdomain interaction site; other site 349215003994 DnaB-helicase binding domain of primase; Region: DnaB_bind; pfam10410 349215003995 Flagellar protein FlbT; Region: FlbT; cl11455 349215003996 Yqey-like protein; Region: YqeY; pfam09424 349215003997 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; smart01097 349215003998 carbamoyl phosphate synthase small subunit; Reviewed; Region: PRK12564 349215003999 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 349215004000 catalytic site [active] 349215004001 subunit interface [polypeptide binding]; other site 349215004002 Putative protein-S-isoprenylcysteine methyltransferase [Posttranslational modification, protein turnover, chaperones]; Region: STE14; COG2020 349215004003 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 349215004004 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 349215004005 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 349215004006 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 349215004007 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 349215004008 ATP-grasp domain; Region: ATP-grasp_4; cl17255 349215004009 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 349215004010 IMP binding site; other site 349215004011 dimer interface [polypeptide binding]; other site 349215004012 interdomain contacts; other site 349215004013 partial ornithine binding site; other site 349215004014 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; Region: GIY-YIG_unchar_3; cd10448 349215004015 putative active site [active] 349215004016 GIY-YIG motif/motif A; other site 349215004017 putative metal binding site [ion binding]; other site 349215004018 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 349215004019 ATP-binding cassette domain of a mitochondrial protein MTABC3 and related proteins; Region: ABC_MTABC3_MDL1_MDL2; cd03249 349215004020 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 349215004021 Walker A/P-loop; other site 349215004022 ATP binding site [chemical binding]; other site 349215004023 Q-loop/lid; other site 349215004024 ABC transporter signature motif; other site 349215004025 Walker B; other site 349215004026 D-loop; other site 349215004027 H-loop/switch region; other site 349215004028 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 349215004029 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 349215004030 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 349215004031 Transcriptional regulators [Transcription]; Region: Lrp; COG1522 349215004032 AsnC family; Region: AsnC_trans_reg; pfam01037 349215004033 Predicted nucleoside-diphosphate-sugar epimerase [Cell envelope biogenesis, outer membrane]; Region: COG3660 349215004034 Mitochondrial fission ELM1; Region: Mito_fiss_Elm1; pfam06258 349215004035 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 349215004036 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 349215004037 Transcriptional regulator [Transcription]; Region: LysR; COG0583 349215004038 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 349215004039 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 349215004040 putative effector binding pocket; other site 349215004041 dimerization interface [polypeptide binding]; other site 349215004042 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 349215004043 active site 349215004044 nucleophile elbow; other site 349215004045 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 349215004046 active site 349215004047 nucleophile elbow; other site 349215004048 aspartate aminotransferase; Provisional; Region: PRK05764 349215004049 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 349215004050 pyridoxal 5'-phosphate binding site [chemical binding]; other site 349215004051 homodimer interface [polypeptide binding]; other site 349215004052 catalytic residue [active] 349215004053 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 349215004054 Prephenate dehydratase; Region: PDT; pfam00800 349215004055 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 349215004056 putative L-Phe binding site [chemical binding]; other site 349215004057 Predicted phosphotransferase related to Ser/Thr protein kinases [General function prediction only]; Region: COG3178 349215004058 Phosphotransferase enzyme family; Region: APH; pfam01636 349215004059 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 349215004060 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Region: ELFV_dehydrog; pfam00208 349215004061 NAD(P) binding domain of amino acid dehydrogenase-like proteins; Region: NAD_bind_amino_acid_DH; cl17226 349215004062 NAD(P) binding pocket [chemical binding]; other site 349215004063 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 349215004064 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 349215004065 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 349215004066 ATP binding site [chemical binding]; other site 349215004067 putative Mg++ binding site [ion binding]; other site 349215004068 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 349215004069 nucleotide binding region [chemical binding]; other site 349215004070 ATP-binding site [chemical binding]; other site 349215004071 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 349215004072 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cl11424 349215004073 Predicted amidohydrolase [General function prediction only]; Region: COG0388 349215004074 active site 349215004075 catalytic triad [active] 349215004076 dimer interface [polypeptide binding]; other site 349215004077 Uncharacterized conserved protein [Function unknown]; Region: COG2938 349215004078 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 349215004079 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 349215004080 generic binding surface II; other site 349215004081 ssDNA binding site; other site 349215004082 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 349215004083 ATP binding site [chemical binding]; other site 349215004084 putative Mg++ binding site [ion binding]; other site 349215004085 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 349215004086 nucleotide binding region [chemical binding]; other site 349215004087 ATP-binding site [chemical binding]; other site 349215004088 Protein of unknown function (DUF2927); Region: DUF2927; pfam11150 349215004089 serine O-acetyltransferase; Region: cysE; TIGR01172 349215004090 Serine acetyltransferase, N-terminal; Region: SATase_N; cl05762 349215004091 Serine acetyltransferase (SAT): SAT catalyzes the CoA-dependent acetylation of the side chain hydroxyl group of L-serine to form O-acetylserine, as the first step of a two-step biosynthetic pathway in bacteria and plants leading to the formation of...; Region: LbH_SAT; cd03354 349215004092 trimer interface [polypeptide binding]; other site 349215004093 active site 349215004094 substrate binding site [chemical binding]; other site 349215004095 CoA binding site [chemical binding]; other site 349215004096 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 349215004097 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 349215004098 dimer interface [polypeptide binding]; other site 349215004099 pyridoxal 5'-phosphate binding site [chemical binding]; other site 349215004100 catalytic residue [active] 349215004101 Uncharacterized conserved protein [Function unknown]; Region: COG2928 349215004102 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 349215004103 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 349215004104 non-specific DNA binding site [nucleotide binding]; other site 349215004105 salt bridge; other site 349215004106 sequence-specific DNA binding site [nucleotide binding]; other site 349215004107 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 349215004108 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 349215004109 active site 349215004110 (T/H)XGH motif; other site 349215004111 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cd02883 349215004112 nudix motif; other site 349215004113 DNA gyrase subunit A; Validated; Region: PRK05560 349215004114 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes...; Region: TOP4c; cd00187 349215004115 CAP-like domain; other site 349215004116 active site 349215004117 primary dimer interface [polypeptide binding]; other site 349215004118 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 349215004119 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 349215004120 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 349215004121 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 349215004122 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 349215004123 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 349215004124 nucleotide binding site/active site [active] 349215004125 HIT family signature motif; other site 349215004126 catalytic residue [active] 349215004127 Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases [Nucleotide transport and metabolism / Carbohydrate transport and metabolism / General function prediction only]; Region: Hit; COG0537 349215004128 nucleotide binding site/active site [active] 349215004129 HIT family signature motif; other site 349215004130 catalytic residue [active] 349215004131 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 349215004132 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 349215004133 Methyltransferase domain; Region: Methyltransf_23; pfam13489 349215004134 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 349215004135 S-adenosylmethionine binding site [chemical binding]; other site 349215004136 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 349215004137 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 349215004138 dimer interface [polypeptide binding]; other site 349215004139 ssDNA binding site [nucleotide binding]; other site 349215004140 tetramer (dimer of dimers) interface [polypeptide binding]; other site 349215004141 ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]; Region: clpA; COG0542 349215004142 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 349215004143 Walker A motif; other site 349215004144 ATP binding site [chemical binding]; other site 349215004145 Walker B motif; other site 349215004146 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 349215004147 ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]; Region: clpA; COG0542 349215004148 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 349215004149 Walker A motif; other site 349215004150 ATP binding site [chemical binding]; other site 349215004151 Walker B motif; other site 349215004152 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 349215004153 Walker A motif; other site 349215004154 ATP binding site [chemical binding]; other site 349215004155 Walker B motif; other site 349215004156 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 349215004157 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 349215004158 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 349215004159 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 349215004160 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 349215004161 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 349215004162 HSP70 interaction site [polypeptide binding]; other site 349215004163 Transcriptional regulator; Region: Rrf2; cl17282 349215004164 Rrf2 family protein; Region: rrf2_super; TIGR00738 349215004165 bifunctional nitric oxide dioxygenase/dihydropteridine reductase 2; Provisional; Region: PRK13289 349215004166 Globins are heme proteins, which bind and transport oxygen. This family summarizes a diverse set of homologous protein domains, including: (1) tetrameric vertebrate hemoglobins, which are the major protein component of erythrocytes and transport oxygen...; Region: globin; cd01040 349215004167 heme-binding site [chemical binding]; other site 349215004168 FAD_NAD(P)H binding domain of flavohemoglobin. Flavohemoglobins have a globin domain containing a B-type heme fused with a ferredoxin reductase-like FAD/NAD-binding domain. Flavohemoglobins detoxify nitric oxide (NO) via an NO dioxygenase reaction. The...; Region: flavohem_like_fad_nad_binding; cd06184 349215004169 FAD binding pocket [chemical binding]; other site 349215004170 FAD binding motif [chemical binding]; other site 349215004171 phosphate binding motif [ion binding]; other site 349215004172 beta-alpha-beta structure motif; other site 349215004173 NAD binding pocket [chemical binding]; other site 349215004174 Heme binding pocket [chemical binding]; other site 349215004175 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 349215004176 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 349215004177 Uncharacterized conserved protein [Function unknown]; Region: COG5276 349215004178 YadA-like, left-handed beta-roll; Region: LbR_YadA-like; cd12820 349215004179 trimer interface [polypeptide binding]; other site 349215004180 YadA-like, left-handed beta-roll; Region: LbR_YadA-like; cd12820 349215004181 trimer interface [polypeptide binding]; other site 349215004182 Chaperone of endosialidase; Region: Peptidase_S74; pfam13884 349215004183 Disulfide bond formation protein DsbB; Region: DsbB; pfam02600 349215004184 Restriction endonuclease [Defense mechanisms]; Region: McrA; COG1403 349215004185 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 349215004186 active site 349215004187 putative hydrolase; Provisional; Region: PRK11460 349215004188 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 349215004189 glutamyl-Q tRNA(Asp) synthetase; Reviewed; Region: PRK05710 349215004190 active site 349215004191 HIGH motif; other site 349215004192 nucleotide binding site [chemical binding]; other site 349215004193 active site 349215004194 KMSKS motif; other site 349215004195 PAP2_like proteins, Aur1_like subfamily. Yeast Aur1p or Ipc1p is necessary for the addition of inositol phosphate to ceramide, an essential step in yeast sphingolipid synthesis, and is the target of several antifungal compounds such as aureobasidin; Region: PAP2_Aur1_like; cd03386 349215004196 active site 349215004197 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 349215004198 active site 349215004199 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 349215004200 non-specific DNA binding site [nucleotide binding]; other site 349215004201 salt bridge; other site 349215004202 sequence-specific DNA binding site [nucleotide binding]; other site 349215004203 nitrilase; Region: PLN02798 349215004204 Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases); Region: nit; cd07572 349215004205 putative active site [active] 349215004206 catalytic triad [active] 349215004207 dimer interface [polypeptide binding]; other site 349215004208 Glutaredoxin (GRX) family, GRX bacterial class 1 and 3 (b_1_3)-like subfamily; composed of bacterial GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the...; Region: GRX_GRXb_1_3_like; cd03418 349215004209 GSH binding site [chemical binding]; other site 349215004210 catalytic residues [active] 349215004211 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 349215004212 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 349215004213 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 349215004214 active site 349215004215 Methyltransferase domain; Region: Methyltransf_23; pfam13489 349215004216 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 349215004217 S-adenosylmethionine binding site [chemical binding]; other site 349215004218 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 349215004219 Methyltransferase domain; Region: Methyltransf_11; pfam08241 349215004220 guanosine 5'-monophosphate oxidoreductase; Provisional; Region: PRK05096 349215004221 IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of...; Region: IMPDH; cd00381 349215004222 active site 349215004223 Protein of unknown function (DUF1192); Region: DUF1192; pfam06698 349215004224 putative NAD(P)H quinone oxidoreductase, PIG3 family; Region: quinone_pig3; TIGR02824 349215004225 PIG3 p53-inducible quinone oxidoreductase; Region: p53_inducible_oxidoreductase; cd05276 349215004226 NAD(P) binding site [chemical binding]; other site 349215004227 Protein of unknown function (DUF1013); Region: DUF1013; cl11533 349215004228 Protein of unknown function (DUF465); Region: DUF465; cl01070 349215004229 aldehyde dehydrogenase family 7 member; Region: PLN02315 349215004230 NAD+-dependent alpha-aminoadipic semialdehyde dehydrogenase, ALDH family members 7A1 and 7B; Region: ALDH_F7_AASADH; cd07130 349215004231 tetrameric interface [polypeptide binding]; other site 349215004232 NAD binding site [chemical binding]; other site 349215004233 catalytic residues [active] 349215004234 Na+/phosphate symporter [Inorganic ion transport and metabolism]; Region: NptA; COG1283 349215004235 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 349215004236 Na+/Pi-cotransporter; Region: Na_Pi_cotrans; pfam02690 349215004237 PhoU domain; Region: PhoU; pfam01895 349215004238 PhoU domain; Region: PhoU; pfam01895 349215004239 Bacterial protein of unknown function (DUF924); Region: DUF924; pfam06041 349215004240 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 349215004241 cytochrome b; Provisional; Region: CYTB; MTH00145 349215004242 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 349215004243 Qi binding site; other site 349215004244 intrachain domain interface; other site 349215004245 interchain domain interface [polypeptide binding]; other site 349215004246 heme bH binding site [chemical binding]; other site 349215004247 heme bL binding site [chemical binding]; other site 349215004248 Qo binding site; other site 349215004249 Cytochrome b(C-terminus)/b6/petD: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: cytochrome_b_C; cd00290 349215004250 interchain domain interface [polypeptide binding]; other site 349215004251 intrachain domain interface; other site 349215004252 Qi binding site; other site 349215004253 Qo binding site; other site 349215004254 Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; Region: UCR_Fe-S_N; pfam10399 349215004255 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 349215004256 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 349215004257 [2Fe-2S] cluster binding site [ion binding]; other site 349215004258 Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]; Region: CspR; COG0219 349215004259 coproporphyrinogen III oxidase; Provisional; Region: PRK05330 349215004260 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; pfam01218 349215004261 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2859 349215004262 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 349215004263 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 349215004264 active site 349215004265 NTP binding site [chemical binding]; other site 349215004266 metal binding triad [ion binding]; metal-binding site 349215004267 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 349215004268 tRNA nucleotidyltransferase domain 2 putative; Region: tRNA_NucTran2_2; pfam13735 349215004269 Protein of unknown function (DUF1285); Region: DUF1285; pfam06938 349215004270 MoxR-like ATPases [General function prediction only]; Region: COG0714 349215004271 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 349215004272 Walker A motif; other site 349215004273 ATP binding site [chemical binding]; other site 349215004274 Walker B motif; other site 349215004275 arginine finger; other site 349215004276 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]; Region: COG1721 349215004277 Protein of unknown function DUF58; Region: DUF58; pfam01882 349215004278 Aerotolerance regulator N-terminal; Region: BatA; pfam07584 349215004279 A4 beta-galactosidase middle domain: a type 1 glutamine amidotransferase (GATase1)-like domain; Region: A4_beta-galactosidase_middle_domain; cd03143 349215004280 Domain of unknown function (DUF4159); Region: DUF4159; pfam13709 349215004281 Protein of unknown function (DUF1355); Region: DUF1355; cl17712 349215004282 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 349215004283 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 349215004284 active site 349215004285 phosphorylation site [posttranslational modification] 349215004286 intermolecular recognition site; other site 349215004287 dimerization interface [polypeptide binding]; other site 349215004288 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 349215004289 DNA binding residues [nucleotide binding] 349215004290 dimerization interface [polypeptide binding]; other site 349215004291 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 349215004292 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 349215004293 N-acetyl-D-glucosamine binding site [chemical binding]; other site 349215004294 catalytic residue [active] 349215004295 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 349215004296 dihydrodipicolinate synthase; Region: dapA; TIGR00674 349215004297 dimer interface [polypeptide binding]; other site 349215004298 active site 349215004299 catalytic residue [active] 349215004300 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 349215004301 SmpB-tmRNA interface; other site 349215004302 recombinase A; Provisional; Region: recA; PRK09354 349215004303 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 349215004304 hexamer interface [polypeptide binding]; other site 349215004305 Walker A motif; other site 349215004306 ATP binding site [chemical binding]; other site 349215004307 Walker B motif; other site 349215004308 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3108 349215004309 Peptidase M15; Region: Peptidase_M15_3; cl01194 349215004310 PAS domain; Region: PAS_9; pfam13426 349215004311 phosphate regulon sensor kinase PhoR; Region: phoR_proteo; TIGR02966 349215004312 PAS domain; Region: PAS; smart00091 349215004313 putative active site [active] 349215004314 heme pocket [chemical binding]; other site 349215004315 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 349215004316 dimer interface [polypeptide binding]; other site 349215004317 phosphorylation site [posttranslational modification] 349215004318 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 349215004319 ATP binding site [chemical binding]; other site 349215004320 Mg2+ binding site [ion binding]; other site 349215004321 G-X-G motif; other site 349215004322 Response regulator receiver domain; Region: Response_reg; pfam00072 349215004323 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 349215004324 active site 349215004325 phosphorylation site [posttranslational modification] 349215004326 intermolecular recognition site; other site 349215004327 dimerization interface [polypeptide binding]; other site 349215004328 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 349215004329 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 349215004330 flagellar biosynthesis protein FliR; Reviewed; Region: fliR; PRK05701 349215004331 Bacterial export proteins, family 3; Region: Bac_export_3; cl00867 349215004332 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 349215004333 Flagellar hook-basal body complex protein FliE; Region: FliE; cl09139 349215004334 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 349215004335 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 349215004336 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK06004 349215004337 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 349215004338 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257; cl15822 349215004339 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 349215004340 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 349215004341 Flagellar biosynthesis protein, FliO; Region: FliO; cl01247 349215004342 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK05699 349215004343 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_12; cd07255 349215004344 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 349215004345 putative metal binding site [ion binding]; other site 349215004346 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 349215004347 Flagellar motor protein [Cell motility and secretion]; Region: MotB; COG1360 349215004348 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 349215004349 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cl02931 349215004350 ligand binding site [chemical binding]; other site 349215004351 flagellar motor protein MotD; Reviewed; Region: PRK09038 349215004352 Uncharacterized conserved protein [Function unknown]; Region: COG3334 349215004353 flagellar motor switch protein FliM; Reviewed; Region: fliM; PRK12795 349215004354 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 349215004355 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 349215004356 flagellar hook-basal body protein; Region: FlgEFG_subfam; TIGR03506 349215004357 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 349215004358 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 349215004359 flagellar basal body rod protein FlgG; Reviewed; Region: flgG; PRK12691 349215004360 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 349215004361 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 349215004362 flagellar basal body P-ring biosynthesis protein FlgA; Reviewed; Region: flgA; PRK12786 349215004363 SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB; Region: SAF_CpaB_FlgA_like; cd11614 349215004364 Domains similar to fish antifreeze type III protein; Region: SAF; cl00555 349215004365 flagellar basal body L-ring protein; Reviewed; Region: flgH; PRK12788 349215004366 flagellar basal body L-ring protein; Reviewed; Region: flgH; PRK00249 349215004367 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 349215004368 flagellar assembly regulator FliX; Reviewed; Region: fliX; PRK12787 349215004369 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 349215004370 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 349215004371 Rod binding protein; Region: Rod-binding; cl01626 349215004372 FlgN protein; Region: FlgN; pfam05130 349215004373 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 349215004374 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 349215004375 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 349215004376 flagellar hook protein FlgE; Validated; Region: flgE; PRK05682 349215004377 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 349215004378 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 349215004379 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 349215004380 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 349215004381 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 349215004382 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 349215004383 Coenzyme A binding pocket [chemical binding]; other site 349215004384 glycyl-tRNA synthetase; Provisional; Region: PRK04173 349215004385 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 349215004386 motif 1; other site 349215004387 Glycyl-tRNA synthetase (GlyRS)-like class II core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes. It is responsible for the attachment of glycine to the 3...; Region: GlyRS-like_core; cd00774 349215004388 active site 349215004389 motif 2; other site 349215004390 motif 3; other site 349215004391 HGTP anticodon binding domain, as found at the C-terminus of histidyl, glycyl, threonyl and prolyl tRNA synthetases, which are classified as a group of class II aminoacyl-tRNA synthetases (aaRS). In aaRSs, the anticodon binding domain is responsible for...; Region: HGTP_anticodon; cl00266 349215004392 anticodon binding site; other site 349215004393 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 349215004394 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 349215004395 tandem repeat interface [polypeptide binding]; other site 349215004396 oligomer interface [polypeptide binding]; other site 349215004397 active site residues [active] 349215004398 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 349215004399 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 349215004400 S-adenosylmethionine binding site [chemical binding]; other site 349215004401 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 349215004402 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 349215004403 substrate binding pocket [chemical binding]; other site 349215004404 chain length determination region; other site 349215004405 substrate-Mg2+ binding site; other site 349215004406 catalytic residues [active] 349215004407 aspartate-rich region 1; other site 349215004408 active site lid residues [active] 349215004409 aspartate-rich region 2; other site 349215004410 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 349215004411 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 349215004412 ligand binding site [chemical binding]; other site 349215004413 Transcriptional regulators CsoR (copper-sensitive operon repressor), RcnR, and FrmR, and related domains; this domain superfamily was previously known as DUF156; Region: CsoR-like_DUF156; cd10148 349215004414 putative homodimer interface [polypeptide binding]; other site 349215004415 putative homotetramer interface [polypeptide binding]; other site 349215004416 putative allosteric switch controlling residues; other site 349215004417 putative metal binding site [ion binding]; other site 349215004418 putative homodimer-homodimer interface [polypeptide binding]; other site 349215004419 Predicted permease; Region: DUF318; cl17795 349215004420 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 349215004421 ATP binding site [chemical binding]; other site 349215004422 putative Mg++ binding site [ion binding]; other site 349215004423 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 349215004424 nucleotide binding region [chemical binding]; other site 349215004425 ATP-binding site [chemical binding]; other site 349215004426 coproporphyrinogen III oxidase; Provisional; Region: PRK09057 349215004427 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 349215004428 FeS/SAM binding site; other site 349215004429 HemN C-terminal domain; Region: HemN_C; pfam06969 349215004430 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 349215004431 active site 349215004432 dimerization interface [polypeptide binding]; other site 349215004433 ribonuclease PH; Reviewed; Region: rph; PRK00173 349215004434 Ribonuclease PH; Region: RNase_PH_bact; cd11362 349215004435 hexamer interface [polypeptide binding]; other site 349215004436 active site 349215004437 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 349215004438 Winged helix-turn-helix transcription repressor, HrcA DNA-binding; Region: HrcA_DNA-bdg; pfam03444 349215004439 GrpE; Region: GrpE; pfam01025 349215004440 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 349215004441 dimer interface [polypeptide binding]; other site 349215004442 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 349215004443 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 349215004444 Nucleotide-binding domain of human HSPA9, Escherichia coli DnaK, and similar proteins; Region: HSPA9-like_NBD; cd11733 349215004445 nucleotide binding site [chemical binding]; other site 349215004446 NEF interaction site [polypeptide binding]; other site 349215004447 SBD interface [polypeptide binding]; other site 349215004448 chaperone protein DnaJ; Provisional; Region: PRK10767 349215004449 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 349215004450 HSP70 interaction site [polypeptide binding]; other site 349215004451 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 349215004452 substrate binding site [polypeptide binding]; other site 349215004453 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 349215004454 Zn binding sites [ion binding]; other site 349215004455 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 349215004456 dimer interface [polypeptide binding]; other site 349215004457 Domain of unknown function (DUF2007); Region: DUF2007; pfam09413 349215004458 dihydrodipicolinate reductase; Provisional; Region: PRK00048 349215004459 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 349215004460 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 349215004461 Helix-turn-helix domain; Region: HTH_18; pfam12833 349215004462 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 349215004463 The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases...; Region: ATase; cd06445 349215004464 DNA binding site [nucleotide binding] 349215004465 active site 349215004466 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 349215004467 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 349215004468 minor groove reading motif; other site 349215004469 helix-hairpin-helix signature motif; other site 349215004470 substrate binding pocket [chemical binding]; other site 349215004471 active site 349215004472 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 349215004473 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 349215004474 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 349215004475 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 349215004476 GIY-YIG motif/motif A; other site 349215004477 active site 349215004478 catalytic site [active] 349215004479 putative DNA binding site [nucleotide binding]; other site 349215004480 metal binding site [ion binding]; metal-binding site 349215004481 UvrB/uvrC motif; Region: UVR; pfam02151 349215004482 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 349215004483 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 349215004484 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 349215004485 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 349215004486 IclR helix-turn-helix domain; Region: HTH_IclR; pfam09339 349215004487 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 349215004488 hypothetical protein; Provisional; Region: PRK06185 349215004489 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 349215004490 Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]; Region: CinA; COG1058 349215004491 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 349215004492 putative MPT binding site; other site 349215004493 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 349215004494 active site 349215004495 hypothetical protein; Reviewed; Region: PRK00024 349215004496 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 349215004497 MPN+ (JAMM) motif; other site 349215004498 Zinc-binding site [ion binding]; other site 349215004499 adenylosuccinate lyase; Provisional; Region: PRK07492 349215004500 Adenylsuccinate lyase (ASL)_subgroup 1; Region: Adenylsuccinate_lyase_1; cd01360 349215004501 tetramer interface [polypeptide binding]; other site 349215004502 active site 349215004503 Adenylosuccinate lyase C-terminus; Region: ADSL_C; smart00998 349215004504 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; cl01093 349215004505 cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the...; Region: cyclophilin; cd00317 349215004506 active site 349215004507 Alpha amylase catalytic domain found in oligo-1,6-glucosidase (also called isomaltase; sucrase-isomaltase; alpha-limit dextrinase) and related proteins; Region: AmyAc_OligoGlu; cd11330 349215004508 alpha,alpha-phosphotrehalase; Region: trehalose_treC; TIGR02403 349215004509 active site 349215004510 catalytic site [active] 349215004511 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 349215004512 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Region: ELFV_dehydrog; pfam00208 349215004513 NAD(P) binding domain of leucine dehydrogenase, phenylalanine dehydrogenase, and valine dehydrogenase; Region: NAD_bind_Leu_Phe_Val_DH; cd01075 349215004514 NAD binding site [chemical binding]; other site 349215004515 Phe binding site; other site 349215004516 Nicotianamine synthase protein; Region: NAS; cl17658 349215004517 2-isopropylmalate synthase; Region: PLN02321 349215004518 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 349215004519 TrkA-N domain; Region: TrkA_N; pfam02254 349215004520 5'-nucleotidase; Region: 5-nucleotidase; pfam06189 349215004521 Thymidylate synthase; Region: Thymidylat_synt; pfam00303 349215004522 Thymidylate synthase and pyrimidine hydroxymethylase: Thymidylate synthase (TS) and deoxycytidylate hydroxymethylase (dCMP-HMase) are homologs that catalyze analogous alkylation of C5 of pyrimidine nucleotides. Both enzymes are involved in the...; Region: TS_Pyrimidine_HMase; cd00351 349215004523 dimerization interface [polypeptide binding]; other site 349215004524 active site 349215004525 aconitate hydratase; Validated; Region: PRK09277 349215004526 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 349215004527 substrate binding site [chemical binding]; other site 349215004528 ligand binding site [chemical binding]; other site 349215004529 Aconitase A swivel domain. This is the major form of the TCA cycle enzyme aconitate hydratase, also known as aconitase and citrate hydro-lyase. It includes bacterial and archaeal aconitase A, and the eukaryotic cytosolic form of aconitase. This group...; Region: AcnA_IRP_Swivel; cd01580 349215004530 substrate binding site [chemical binding]; other site 349215004531 ABC-type transport system involved in cytochrome c biogenesis, ATPase component [Posttranslational modification, protein turnover, chaperones]; Region: CcmA; COG4133 349215004532 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 349215004533 Walker A/P-loop; other site 349215004534 ATP binding site [chemical binding]; other site 349215004535 Q-loop/lid; other site 349215004536 ABC transporter signature motif; other site 349215004537 Walker B; other site 349215004538 D-loop; other site 349215004539 H-loop/switch region; other site 349215004540 CcmB protein; Region: CcmB; cl17444 349215004541 heme exporter protein CcmC; Region: ccmC; TIGR01191 349215004542 Heme exporter protein D (CcmD); Region: CcmD; pfam04995 349215004543 cytochrome c-type biogenesis protein CcmE; Reviewed; Region: PRK13254 349215004544 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: CcmF; COG1138 349215004545 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 349215004546 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 349215004547 Cytochrome C biogenesis protein; Region: CcmH; pfam03918 349215004548 TPR repeat; Region: TPR_11; pfam13414 349215004549 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 349215004550 binding surface 349215004551 TPR motif; other site 349215004552 YGGT family; Region: YGGT; cl00508 349215004553 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14188 349215004554 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 349215004555 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 349215004556 homodimer interface [polypeptide binding]; other site 349215004557 NADP binding site [chemical binding]; other site 349215004558 substrate binding site [chemical binding]; other site 349215004559 isocitrate dehydrogenase; Validated; Region: PRK09222 349215004560 Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism]; Region: LeuB; COG0473 349215004561 pH-dependent sodium/proton antiporter; Reviewed; Region: nhaA; PRK09560 349215004562 thymidine phosphorylase; Reviewed; Region: deoA; PRK05820 349215004563 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 349215004564 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 349215004565 Pyrimidine nucleoside phosphorylase C-terminal domain; Region: PYNP_C; smart00941 349215004566 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 349215004567 EamA-like transporter family; Region: EamA; pfam00892 349215004568 Cell Wall Hydrolase; Region: Hydrolase_2; pfam07486 349215004569 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5410 349215004570 Terminase-like family; Region: Terminase_6; pfam03237 349215004571 Pectate lyase superfamily protein; Region: Pectate_lyase_3; pfam12708 349215004572 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 349215004573 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 349215004574 hypothetical protein; Region: PHA00661 349215004575 hypothetical protein; Region: PHA00661 349215004576 hypothetical protein; Region: PHA00662 349215004577 hypothetical protein; Provisional; Region: PRK11281 349215004578 PilZ domain; Region: PilZ; pfam07238 349215004579 hypothetical protein; Region: PHA00670 349215004580 Bacteriophage head to tail connecting protein; Region: Head-tail_con; pfam12236 349215004581 Predicted transcriptional regulator [Transcription]; Region: COG2932 349215004582 Cro/C1-type HTH DNA-binding domain; Region: HTH_26; pfam13443 349215004583 Bacterial PH domain; Region: DUF304; pfam03703 349215004584 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 349215004585 Adenosine kinase (AK) catalyzes the phosphorylation of ribofuranosyl-containing nucleoside analogues at the 5'-hydroxyl using ATP or GTP as the phosphate donor.The physiological function of AK is associated with the regulation of extracellular...; Region: adenosine_kinase; cd01168 349215004586 substrate binding site [chemical binding]; other site 349215004587 ATP binding site [chemical binding]; other site 349215004588 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 349215004589 active site 349215004590 inorganic polyphosphate/ATP-NAD kinase; Reviewed; Region: ppnK; PRK04761 349215004591 ATP-NAD kinase; Region: NAD_kinase; pfam01513 349215004592 trehalose-6-phosphate phosphatase; Provisional; Region: PRK10187; cl17105 349215004593 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 349215004594 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 349215004595 ATP binding site [chemical binding]; other site 349215004596 active site 349215004597 substrate binding site [chemical binding]; other site 349215004598 Domain of unknown function (DUF1476); Region: DUF1476; pfam07345 349215004599 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 349215004600 Glutaredoxin (GRX) family, PKC-interacting cousin of TRX (PICOT)-like subfamily; composed of PICOT and GRX-PICOT-like proteins. The non-PICOT members of this family contain only the GRX-like domain, whereas PICOT contains an N-terminal TRX-like domain...; Region: GRX_PICOT_like; cd03028 349215004601 putative GSH binding site [chemical binding]; other site 349215004602 catalytic residues [active] 349215004603 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 349215004604 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 349215004605 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 349215004606 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 349215004607 rod shape-determining protein MreD; Region: shape_MreD; TIGR03426 349215004608 rod shape-determining protein MreC; Provisional; Region: PRK13922 349215004609 rod shape-determining protein MreC; Region: MreC; pfam04085 349215004610 rod shape-determining protein MreB; Provisional; Region: PRK13927 349215004611 MreB and similar proteins; Region: MreB_like; cd10225 349215004612 nucleotide binding site [chemical binding]; other site 349215004613 Mg binding site [ion binding]; other site 349215004614 putative protofilament interaction site [polypeptide binding]; other site 349215004615 RodZ interaction site [polypeptide binding]; other site 349215004616 50S ribosomal protein L36; Validated; Region: rpmJ; PRK00831 349215004617 Protein of unknown function (DUF3307); Region: DUF3307; pfam11750 349215004618 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 349215004619 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 349215004620 ligand binding site [chemical binding]; other site 349215004621 flexible hinge region; other site 349215004622 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 349215004623 FecR protein; Region: FecR; pfam04773 349215004624 FG-GAP repeat; Region: FG-GAP; cl15299 349215004625 Integrin alpha (beta-propellor repeats); Region: Int_alpha; smart00191 349215004626 CHASE2 domain; Region: CHASE2; pfam05226 349215004627 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 349215004628 cyclase homology domain; Region: CHD; cd07302 349215004629 nucleotidyl binding site; other site 349215004630 metal binding site [ion binding]; metal-binding site 349215004631 dimer interface [polypeptide binding]; other site 349215004632 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 349215004633 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 349215004634 HlyD family secretion protein; Region: HlyD_3; pfam13437 349215004635 A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various...; Region: Peptidase_C39_likeD; cd02421 349215004636 type I secretion system ATPase, LssB family; Region: type_I_sec_LssB; TIGR03375 349215004637 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 349215004638 ATP-binding cassette domain of bacteriocin exporters, subfamily C; Region: ABCC_bacteriocin_exporters; cd03245 349215004639 Walker A/P-loop; other site 349215004640 ATP binding site [chemical binding]; other site 349215004641 Q-loop/lid; other site 349215004642 ABC transporter signature motif; other site 349215004643 Walker B; other site 349215004644 D-loop; other site 349215004645 H-loop/switch region; other site 349215004646 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 349215004647 Rubrum transdehydrogenase NAD-binding and catalytic domains; Region: Rubrum_tdh; cd05304 349215004648 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 349215004649 ligand binding site [chemical binding]; other site 349215004650 homodimer interface [polypeptide binding]; other site 349215004651 NAD(P) binding site [chemical binding]; other site 349215004652 trimer interface B [polypeptide binding]; other site 349215004653 trimer interface A [polypeptide binding]; other site 349215004654 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 349215004655 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; COG1282 349215004656 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 349215004657 phosphatidylserine decarboxylase; Region: PLN02964 349215004658 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 349215004659 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 349215004660 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 349215004661 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 349215004662 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 349215004663 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 349215004664 nucleotide binding pocket [chemical binding]; other site 349215004665 K-X-D-G motif; other site 349215004666 catalytic site [active] 349215004667 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 349215004668 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 349215004669 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 349215004670 Dimer interface [polypeptide binding]; other site 349215004671 BRCT sequence motif; other site 349215004672 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 349215004673 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 349215004674 Walker A/P-loop; other site 349215004675 ATP binding site [chemical binding]; other site 349215004676 Q-loop/lid; other site 349215004677 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 349215004678 ABC transporter signature motif; other site 349215004679 Walker B; other site 349215004680 D-loop; other site 349215004681 H-loop/switch region; other site 349215004682 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 349215004683 Protein of unknown function (DUF2419); Region: DUF2419; pfam10343 349215004684 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 349215004685 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 349215004686 Cell division GTPase [Cell division and chromosome partitioning]; Region: FtsZ; COG0206 349215004687 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 349215004688 nucleotide binding site [chemical binding]; other site 349215004689 SulA interaction site; other site 349215004690 cell division protein FtsZ, alphaProteobacterial C-terminal extension; Region: FtsZ_alphas_C; TIGR03483 349215004691 Cell division ATPase FtsA [Cell division and chromosome partitioning]; Region: ftsA; COG0849 349215004692 Cell division protein FtsA; Region: FtsA; smart00842 349215004693 Cell division protein FtsA; Region: FtsA; pfam14450 349215004694 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 349215004695 Cell division protein FtsQ; Region: FtsQ; pfam03799 349215004696 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 349215004697 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 349215004698 ATP-grasp domain; Region: ATP-grasp_4; cl17255 349215004699 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 349215004700 FAD binding domain; Region: FAD_binding_4; pfam01565 349215004701 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 349215004702 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 349215004703 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 349215004704 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 349215004705 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 349215004706 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 349215004707 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 349215004708 active site 349215004709 homodimer interface [polypeptide binding]; other site 349215004710 cell division protein FtsW; Region: ftsW; TIGR02614 349215004711 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK01390 349215004712 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 349215004713 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 349215004714 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 349215004715 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 349215004716 Mg++ binding site [ion binding]; other site 349215004717 putative catalytic motif [active] 349215004718 putative substrate binding site [chemical binding]; other site 349215004719 UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanine ligase; Provisional; Region: PRK14093 349215004720 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 349215004721 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 349215004722 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 349215004723 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 349215004724 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 349215004725 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 349215004726 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 349215004727 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 349215004728 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 349215004729 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 349215004730 Predicted secreted (periplasmic) protein [Function unknown]; Region: COG5462 349215004731 MraW methylase family; Region: Methyltransf_5; cl17771 349215004732 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 349215004733 MraZ protein; Region: MraZ; pfam02381 349215004734 cell division protein MraZ; Reviewed; Region: PRK00326 349215004735 MraZ protein; Region: MraZ; pfam02381 349215004736 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 349215004737 Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20...; Region: PGRP; cd06583 349215004738 amidase catalytic site [active] 349215004739 Zn binding residues [ion binding]; other site 349215004740 substrate binding site [chemical binding]; other site 349215004741 purine nucleoside phosphorylase; Provisional; Region: PRK08202 349215004742 Permeases of the major facilitator superfamily [General function prediction only]; Region: COG2270 349215004743 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 349215004744 putative substrate translocation pore; other site 349215004745 methionine sulfoxide reductase A; Provisional; Region: PRK14054 349215004746 Uncharacterized conserved protein [Function unknown]; Region: COG1872 349215004747 Protein of unknown function (DUF1761); Region: DUF1761; pfam08570 349215004748 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 349215004749 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 349215004750 Isopenicillin N synthase and related dioxygenases [General function prediction only]; Region: PcbC; COG3491 349215004751 non-haem dioxygenase in morphine synthesis N-terminal; Region: DIOX_N; pfam14226 349215004752 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy; pfam03171 349215004753 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 349215004754 active site 1 [active] 349215004755 dimer interface [polypeptide binding]; other site 349215004756 hexamer interface [polypeptide binding]; other site 349215004757 active site 2 [active] 349215004758 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK09078 349215004759 L-aspartate oxidase; Provisional; Region: PRK06175 349215004760 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 349215004761 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase D (SdhD) subunit-like; composed of predominantly uncharacterized bacterial proteins with similarity to the E. coli SdhD subunit. One characterized protein is the respiratory...; Region: SQR_TypeC_SdhD_like; cd03495 349215004762 putative SdhC subunit interface [polypeptide binding]; other site 349215004763 putative proximal heme binding site [chemical binding]; other site 349215004764 putative Iron-sulfur protein interface [polypeptide binding]; other site 349215004765 putative proximal quinone binding site; other site 349215004766 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase C (SdhC) subunit; composed of bacterial SdhC and eukaryotic large cytochrome b binding (CybL) proteins. SQR catalyzes the oxidation of succinate to fumarate coupled to the...; Region: SQR_TypeC_SdhC; cd03499 349215004767 proximal quinone binding site [chemical binding]; other site 349215004768 SdhD (CybS) interface [polypeptide binding]; other site 349215004769 proximal heme binding site [chemical binding]; other site 349215004770 methionine sulfoxide reductase B; Provisional; Region: PRK00222 349215004771 SelR domain; Region: SelR; pfam01641 349215004772 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 349215004773 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 349215004774 PAS domain S-box; Region: sensory_box; TIGR00229 349215004775 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 349215004776 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 349215004777 dimer interface [polypeptide binding]; other site 349215004778 phosphorylation site [posttranslational modification] 349215004779 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 349215004780 ATP binding site [chemical binding]; other site 349215004781 Mg2+ binding site [ion binding]; other site 349215004782 G-X-G motif; other site 349215004783 Response regulator receiver domain; Region: Response_reg; pfam00072 349215004784 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 349215004785 active site 349215004786 phosphorylation site [posttranslational modification] 349215004787 intermolecular recognition site; other site 349215004788 dimerization interface [polypeptide binding]; other site 349215004789 Response regulator receiver domain; Region: Response_reg; pfam00072 349215004790 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 349215004791 active site 349215004792 phosphorylation site [posttranslational modification] 349215004793 intermolecular recognition site; other site 349215004794 dimerization interface [polypeptide binding]; other site 349215004795 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 349215004796 putative binding surface; other site 349215004797 active site 349215004798 Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]; Region: PulF; COG1459 349215004799 Type II secretion system (T2SS), protein F; Region: T2SF; pfam00482 349215004800 Type II/IV secretion system protein; Region: T2SE; pfam00437 349215004801 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 349215004802 Walker A motif; other site 349215004803 ATP binding site [chemical binding]; other site 349215004804 Walker B motif; other site 349215004805 pilus (MSHA type) biogenesis protein MshL; Region: pilus_MshL; TIGR02519 349215004806 Bacterial type II and III secretion system protein; Region: Secretin; pfam00263 349215004807 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 349215004808 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 349215004809 active site 349215004810 phosphorylation site [posttranslational modification] 349215004811 intermolecular recognition site; other site 349215004812 dimerization interface [polypeptide binding]; other site 349215004813 Type IV leader peptidase family; Region: Peptidase_A24; pfam01478 349215004814 Predicted acyl-CoA transferases/carnitine dehydratase [Energy production and conversion]; Region: CaiB; COG1804 349215004815 CoA-transferase family III; Region: CoA_transf_3; pfam02515 349215004816 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 349215004817 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 349215004818 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 349215004819 putative glycerol-3-phosphate acyltransferase PlsY; Provisional; Region: PRK00220 349215004820 Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]; Region: HtpX; COG0501 349215004821 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 349215004822 DNA protecting protein DprA; Region: dprA; TIGR00732 349215004823 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 349215004824 Predicted Fe-S oxidoreductases [General function prediction only]; Region: COG0535 349215004825 FeS/SAM binding site; other site 349215004826 DNA topoisomerase I; Validated; Region: PRK06599 349215004827 TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I. Type IA DNA topoisomerases remove (relax) negative supercoils in the...; Region: TOPRIM_TopoIA_TopoI; cd03363 349215004828 active site 349215004829 interdomain interaction site; other site 349215004830 putative metal-binding site [ion binding]; other site 349215004831 nucleotide binding site [chemical binding]; other site 349215004832 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 349215004833 domain I; other site 349215004834 DNA binding groove [nucleotide binding] 349215004835 phosphate binding site [ion binding]; other site 349215004836 domain II; other site 349215004837 domain III; other site 349215004838 nucleotide binding site [chemical binding]; other site 349215004839 catalytic site [active] 349215004840 domain IV; other site 349215004841 Uncharacterized C-terminal domain of topoisomerase IA [General function prediction only]; Region: COG1754 349215004842 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 349215004843 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 349215004844 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 349215004845 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 349215004846 non-specific DNA binding site [nucleotide binding]; other site 349215004847 salt bridge; other site 349215004848 sequence-specific DNA binding site [nucleotide binding]; other site 349215004849 ribonuclease R; Region: RNase_R; TIGR02063 349215004850 RNB domain; Region: RNB; pfam00773 349215004851 S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase...; Region: S1_RNase_R; cd04471 349215004852 RNA binding site [nucleotide binding]; other site 349215004853 This domain is the catalytic domain of ribonuclease II; Region: RNB; smart00955 349215004854 RNB domain; Region: RNB; pfam00773 349215004855 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 349215004856 response regulator PleD; Reviewed; Region: pleD; PRK09581 349215004857 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 349215004858 active site 349215004859 phosphorylation site [posttranslational modification] 349215004860 intermolecular recognition site; other site 349215004861 dimerization interface [polypeptide binding]; other site 349215004862 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 349215004863 active site 349215004864 phosphorylation site [posttranslational modification] 349215004865 intermolecular recognition site; other site 349215004866 dimerization interface [polypeptide binding]; other site 349215004867 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 349215004868 metal binding site [ion binding]; metal-binding site 349215004869 active site 349215004870 I-site; other site 349215004871 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 349215004872 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 349215004873 active site 349215004874 phosphorylation site [posttranslational modification] 349215004875 intermolecular recognition site; other site 349215004876 dimerization interface [polypeptide binding]; other site 349215004877 Domain of unknown function (DUF1849); Region: DUF1849; pfam08904 349215004878 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 349215004879 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 349215004880 metal binding site [ion binding]; metal-binding site 349215004881 active site 349215004882 I-site; other site 349215004883 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 349215004884 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 349215004885 putative dimer interface [polypeptide binding]; other site 349215004886 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 349215004887 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 349215004888 dimer interface [polypeptide binding]; other site 349215004889 anticodon binding site; other site 349215004890 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of...; Region: AspRS_core; cd00777 349215004891 homodimer interface [polypeptide binding]; other site 349215004892 motif 1; other site 349215004893 active site 349215004894 motif 2; other site 349215004895 GAD domain; Region: GAD; pfam02938 349215004896 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 349215004897 active site 349215004898 motif 3; other site 349215004899 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 349215004900 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 349215004901 catalytic site [active] 349215004902 putative active site [active] 349215004903 putative substrate binding site [chemical binding]; other site 349215004904 HRDC domain; Region: HRDC; pfam00570 349215004905 Haloacid dehalogenase-like hydrolase; Region: HAD_2; pfam13419 349215004906 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 349215004907 motif II; other site 349215004908 fructokinase; Reviewed; Region: PRK09557 349215004909 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 349215004910 nucleotide binding site [chemical binding]; other site 349215004911 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 349215004912 catalytic core [active] 349215004913 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 349215004914 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 349215004915 Domain of unknown function DUF20; Region: UPF0118; pfam01594 349215004916 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 349215004917 Uncharacterized protein conserved in bacteria (DUF2066); Region: DUF2066; pfam09839 349215004918 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 349215004919 dimer interface [polypeptide binding]; other site 349215004920 phosphorylation site [posttranslational modification] 349215004921 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 349215004922 ATP binding site [chemical binding]; other site 349215004923 Mg2+ binding site [ion binding]; other site 349215004924 G-X-G motif; other site 349215004925 Response regulator receiver domain; Region: Response_reg; pfam00072 349215004926 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 349215004927 active site 349215004928 phosphorylation site [posttranslational modification] 349215004929 intermolecular recognition site; other site 349215004930 dimerization interface [polypeptide binding]; other site 349215004931 Hpt domain; Region: Hpt; pfam01627 349215004932 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 349215004933 active site 349215004934 multimer interface [polypeptide binding]; other site 349215004935 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 349215004936 Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain. AlaRS is a homodimer. It is responsible for the attachment of alanine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: AlaRS_core; cd00673 349215004937 motif 1; other site 349215004938 active site 349215004939 motif 2; other site 349215004940 motif 3; other site 349215004941 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 349215004942 GCN5-like protein 1 (GCN5L1); Region: GCN5L1; pfam06320 349215004943 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 349215004944 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 349215004945 N-acetyl-D-glucosamine binding site [chemical binding]; other site 349215004946 catalytic residue [active] 349215004947 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 349215004948 Fe-S cluster binding site [ion binding]; other site 349215004949 active site 349215004950 Dehydrogenases (flavoproteins) [Energy production and conversion]; Region: FixC; COG0644 349215004951 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 349215004952 Electron transfer flavoprotein-ubiquinone oxidoreductase; Region: ETF_QO; pfam05187 349215004953 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 349215004954 binding surface 349215004955 TPR motif; other site 349215004956 TPR repeat; Region: TPR_11; pfam13414 349215004957 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 349215004958 binding surface 349215004959 TPR motif; other site 349215004960 TPR repeat; Region: TPR_11; pfam13414 349215004961 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 349215004962 binding surface 349215004963 TPR motif; other site 349215004964 TPR repeat; Region: TPR_11; pfam13414 349215004965 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: PRK14608 349215004966 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 349215004967 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 349215004968 Sel1 repeat; Region: Sel1; pfam08238 349215004969 Sel1-like repeats; Region: SEL1; smart00671 349215004970 Sel1-like repeats; Region: SEL1; smart00671 349215004971 Sel1-like repeats; Region: SEL1; smart00671 349215004972 Putative peptidoglycan binding domain; Region: PG_binding_1; pfam01471 349215004973 Transcriptional regulator [Transcription]; Region: LysR; COG0583 349215004974 Bacterial regulatory helix-turn-helix protein, lysR family; Region: HTH_1; pfam00126 349215004975 The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain; Region: PBP2_CrgA_like; cd08422 349215004976 putative effector binding pocket; other site 349215004977 dimerization interface [polypeptide binding]; other site 349215004978 Isochorismatase family; Region: Isochorismatase; pfam00857 349215004979 YcaC related amidohydrolases; E.coli YcaC is an homooctameric hydrolase with unknown specificity. Despite its weak sequence similarity, it is structurally related to other amidohydrolases and shares conserved active site residues with them; Region: YcaC_related; cd01012 349215004980 catalytic triad [active] 349215004981 dimer interface [polypeptide binding]; other site 349215004982 conserved cis-peptide bond; other site 349215004983 N-terminal domain of Sphingobium chlorophenolicum 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and similar proteins; Region: PcpA_N_like; cd08346 349215004984 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 349215004985 Zn binding site [ion binding]; other site 349215004986 C-terminal domain of Sphingobium chlorophenolicum 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and similar proteins; Region: PcpA_C_like; cd08347 349215004987 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 349215004988 Zn binding site [ion binding]; other site 349215004989 Predicted esterase [General function prediction only]; Region: COG0400 349215004990 putative hydrolase; Provisional; Region: PRK11460 349215004991 Predicted metal-dependent hydrolase with the TIM-barrel fold [General function prediction only]; Region: COG1574 349215004992 YtcJ_like metal dependent amidohydrolases. YtcJ is a Bacillus subtilis ORF of unknown function. The Arabidopsis homolog LAF3 has been identified as a factor required for photochrome A signalling; Region: YtcJ_like; cd01300 349215004993 active site 349215004994 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3224 349215004995 Uncharacterized protein related to deoxyribodipyrimidine photolyase [General function prediction only]; Region: COG3046 349215004996 Deoxyribodipyrimidine photo-lyase-related protein; Region: DPRP; pfam04244 349215004997 Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue per...; Region: GSH_Peroxidase; cd00340 349215004998 catalytic residues [active] 349215004999 dimer interface [polypeptide binding]; other site 349215005000 short chain dehydrogenase; Provisional; Region: PRK07024 349215005001 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 349215005002 NAD(P) binding site [chemical binding]; other site 349215005003 active site 349215005004 Protein of unknown function (DUF3833); Region: DUF3833; pfam12915 349215005005 MFS/sugar transport protein; Region: MFS_2; pfam13347 349215005006 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 349215005007 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 349215005008 S-adenosylmethionine binding site [chemical binding]; other site 349215005009 Protein of unknown function (DUF1365); Region: DUF1365; pfam07103 349215005010 Predicted NAD/FAD-binding protein [General function prediction only]; Region: COG2907 349215005011 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 349215005012 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 349215005013 HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain; Region: HAMP; smart00304 349215005014 dimerization interface [polypeptide binding]; other site 349215005015 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 349215005016 dimer interface [polypeptide binding]; other site 349215005017 phosphorylation site [posttranslational modification] 349215005018 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 349215005019 ATP binding site [chemical binding]; other site 349215005020 Mg2+ binding site [ion binding]; other site 349215005021 G-X-G motif; other site 349215005022 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 349215005023 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 349215005024 active site 349215005025 phosphorylation site [posttranslational modification] 349215005026 intermolecular recognition site; other site 349215005027 dimerization interface [polypeptide binding]; other site 349215005028 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 349215005029 DNA binding site [nucleotide binding] 349215005030 Peptidase family M48; Region: Peptidase_M48; cl12018 349215005031 K+-dependent Na+/Ca+ exchanger related-protein; Region: TIGR00367 349215005032 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 349215005033 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 349215005034 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 349215005035 E3 interaction surface; other site 349215005036 lipoyl attachment site [posttranslational modification]; other site 349215005037 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 349215005038 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, alpha subunit [Energy production and conversion]; Region: AcoA; COG1071 349215005039 Thiamine pyrophosphate (TPP) family, E1 of PDC_ADC_BCADC subfamily, TPP-binding module; composed of proteins similar to the E1 components of the human pyruvate dehydrogenase complex (PDC), the acetoin dehydrogenase complex (ADC) and the branched chain...; Region: TPP_E1_PDC_ADC_BCADC; cd02000 349215005040 tetramer interface [polypeptide binding]; other site 349215005041 TPP-binding site [chemical binding]; other site 349215005042 heterodimer interface [polypeptide binding]; other site 349215005043 phosphorylation loop region [posttranslational modification] 349215005044 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 349215005045 Pyrimidine (PYR) binding domain of the beta subunits of the E1 components of human pyruvate dehydrogenase complex (E1- PDHc) and related proteins; Region: TPP_PYR_E1-PDHc-beta_like; cd07036 349215005046 alpha subunit interface [polypeptide binding]; other site 349215005047 TPP binding site [chemical binding]; other site 349215005048 heterodimer interface [polypeptide binding]; other site 349215005049 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 349215005050 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 349215005051 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 349215005052 dimerization interface [polypeptide binding]; other site 349215005053 DNA binding residues [nucleotide binding] 349215005054 beta-D-glucoside glucohydrolase; Provisional; Region: PRK15098 349215005055 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; pfam00933 349215005056 Fibronectin type III-like domain; Region: Fn3-like; pfam14310 349215005057 ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]; Region: COG4178 349215005058 ABC transporter transmembrane region 2; Region: ABC_membrane_2; cl00549 349215005059 ATP-binding cassette domain of peroxisomal transporter, subfamily D; Region: ABCD_peroxisomal_ALDP; cd03223 349215005060 O-Glycosyl hydrolase family 30; Region: Glyco_hydro_30; pfam02055 349215005061 Archaeal adenylate kinase [Nucleotide transport and metabolism]; Region: AdkA; cl17890 349215005062 AAA domain; Region: AAA_28; pfam13521 349215005063 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]; Region: YSH1; COG1236 349215005064 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 349215005065 Beta-Casp domain; Region: Beta-Casp; smart01027 349215005066 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 349215005067 Putative threonine efflux protein [Amino acid transport and metabolism]; Region: RhtB; COG1280 349215005068 Outer membrane protein W [Cell envelope biogenesis, outer membrane]; Region: OmpW; COG3047 349215005069 Diaminopimelate decarboxylase [Amino acid transport and metabolism]; Region: LysA; COG0019 349215005070 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 349215005071 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 349215005072 catalytic residue [active] 349215005073 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 349215005074 active site 349215005075 CHAP domain; Region: CHAP; cl17642 349215005076 chromosome segregation protein SMC, primarily archaeal type; Region: SMC_prok_A; TIGR02169 349215005077 von Willebrand factor type A domain; Region: VWA_2; pfam13519 349215005078 metal ion-dependent adhesion site (MIDAS); other site 349215005079 Protein of unknown function, DUF485; Region: DUF485; pfam04341 349215005080 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 349215005081 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u4; cd11480 349215005082 Na binding site [ion binding]; other site 349215005083 putative FAD-binding dehydrogenase; Reviewed; Region: PRK12834 349215005084 Predicted flavoproteins [General function prediction only]; Region: COG2081 349215005085 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 349215005086 filamentous hemagglutinin family N-terminal domain; Region: adhes_NPXG; TIGR01901 349215005087 Right handed beta helix region; Region: Beta_helix; pfam13229 349215005088 Right handed beta helix region; Region: Beta_helix; pfam13229 349215005089 nitrous oxide reductase family maturation protein NosD; Region: NosD_copper_fam; TIGR04247 349215005090 Right handed beta helix region; Region: Beta_helix; pfam13229 349215005091 nitrous oxide reductase family maturation protein NosD; Region: NosD_copper_fam; TIGR04247 349215005092 Right handed beta helix region; Region: Beta_helix; pfam13229 349215005093 Right handed beta helix region; Region: Beta_helix; pfam13229 349215005094 Hemolysin activation/secretion protein [Intracellular trafficking and secretion]; Region: FhaC; COG2831 349215005095 POTRA domain, ShlB-type; Region: POTRA_2; pfam08479 349215005096 Surface antigen; Region: Bac_surface_Ag; pfam01103 349215005097 Conserved protein/domain typically associated with flavoprotein oxygenases, DIM6/NTAB family [General function prediction only]; Region: COG1853 349215005098 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 349215005099 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 349215005100 Walker A/P-loop; other site 349215005101 ATP binding site [chemical binding]; other site 349215005102 Q-loop/lid; other site 349215005103 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 349215005104 ABC transporter signature motif; other site 349215005105 Walker B; other site 349215005106 D-loop; other site 349215005107 ABC transporter; Region: ABC_tran_2; pfam12848 349215005108 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 349215005109 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 349215005110 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 349215005111 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 349215005112 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 349215005113 HlyD family secretion protein; Region: HlyD_3; pfam13437 349215005114 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 349215005115 Methylase of chemotaxis methyl-accepting proteins [Cell motility and secretion / Signal transduction mechanisms]; Region: CheR; COG1352 349215005116 CheR methyltransferase, SAM binding domain; Region: CheR; pfam01739 349215005117 chemotaxis-specific methylesterase; Provisional; Region: PRK00742 349215005118 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 349215005119 active site 349215005120 phosphorylation site [posttranslational modification] 349215005121 intermolecular recognition site; other site 349215005122 dimerization interface [polypeptide binding]; other site 349215005123 CheB methylesterase; Region: CheB_methylest; pfam01339 349215005124 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 349215005125 Response regulator receiver domain; Region: Response_reg; pfam00072 349215005126 active site 349215005127 phosphorylation site [posttranslational modification] 349215005128 intermolecular recognition site; other site 349215005129 dimerization interface [polypeptide binding]; other site 349215005130 CheW, a small regulator protein, unique to the chemotaxis signalling in prokaryotes and archea. CheW interacts with the histidine kinase CheA, most likely with the related regulatory domain of CheA. CheW is proposed to form signalling arrays together...; Region: CheW; cd00732 349215005131 putative CheA interaction surface; other site 349215005132 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 349215005133 putative binding surface; other site 349215005134 active site 349215005135 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 349215005136 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 349215005137 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 349215005138 ATP binding site [chemical binding]; other site 349215005139 Mg2+ binding site [ion binding]; other site 349215005140 G-X-G motif; other site 349215005141 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 349215005142 CheW-like domain; Region: CheW; pfam01584 349215005143 Chemotaxis phosphatase, CheZ; Region: CheZ; cl01219 349215005144 chemotaxis regulatory protein CheY; Provisional; Region: PRK10610 349215005145 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 349215005146 active site 349215005147 phosphorylation site [posttranslational modification] 349215005148 intermolecular recognition site; other site 349215005149 dimerization interface [polypeptide binding]; other site 349215005150 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 349215005151 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 349215005152 dimer interface [polypeptide binding]; other site 349215005153 putative CheW interface [polypeptide binding]; other site 349215005154 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 349215005155 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 349215005156 active site 349215005157 phosphorylation site [posttranslational modification] 349215005158 intermolecular recognition site; other site 349215005159 dimerization interface [polypeptide binding]; other site 349215005160 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 349215005161 DNA binding site [nucleotide binding] 349215005162 Family of unknown function (DUF490); Region: DUF490; pfam04357 349215005163 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: COG0729 349215005164 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 349215005165 Surface antigen; Region: Bac_surface_Ag; pfam01103 349215005166 Transglycosylase; Region: Transgly; cl17702 349215005167 Membrane carboxypeptidase (penicillin-binding protein) [Cell envelope biogenesis, outer membrane]; Region: MrcB; COG0744 349215005168 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 349215005169 universal stress protein UspE; Provisional; Region: PRK11175 349215005170 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 349215005171 Ligand Binding Site [chemical binding]; other site 349215005172 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 349215005173 Ligand Binding Site [chemical binding]; other site 349215005174 Metal binding protein PsaA. These proteins have been shown to function as initial receptors in ABC transport of Mn2+ and as surface adhesins in some eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins that...; Region: PsaA; cd01137 349215005175 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 349215005176 metal binding site [ion binding]; metal-binding site 349215005177 manganese/iron transporter ATP-binding protein; Provisional; Region: PRK15056 349215005178 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 349215005179 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 349215005180 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 349215005181 ABC-ATPase subunit interface; other site 349215005182 dimer interface [polypeptide binding]; other site 349215005183 putative PBP binding regions; other site 349215005184 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 349215005185 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 349215005186 ABC-ATPase subunit interface; other site 349215005187 dimer interface [polypeptide binding]; other site 349215005188 putative PBP binding regions; other site 349215005189 manganese transport regulator MntR; Provisional; Region: PRK11050 349215005190 Iron dependent repressor, N-terminal DNA binding domain; Region: Fe_dep_repress; pfam01325 349215005191 Iron dependent repressor, metal binding and dimerisation domain; Region: Fe_dep_repr_C; pfam02742 349215005192 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl17221 349215005193 transmembrane helices; other site 349215005194 TrkA-C domain; Region: TrkA_C; pfam02080 349215005195 TrkA-C domain; Region: TrkA_C; pfam02080 349215005196 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 349215005197 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl17221 349215005198 HemK family putative methylases; Region: hemK_fam; TIGR00536 349215005199 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 349215005200 S-adenosylmethionine binding site [chemical binding]; other site 349215005201 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 349215005202 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 349215005203 non-specific DNA binding site [nucleotide binding]; other site 349215005204 salt bridge; other site 349215005205 sequence-specific DNA binding site [nucleotide binding]; other site 349215005206 SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]; Region: LexA; COG1974 349215005207 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 349215005208 Catalytic site [active] 349215005209 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...; Region: CysQ; cd01638 349215005210 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 349215005211 active site 349215005212 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional; Region: PRK05506 349215005213 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 349215005214 G1 box; other site 349215005215 GTP/Mg2+ binding site [chemical binding]; other site 349215005216 G2 box; other site 349215005217 Switch I region; other site 349215005218 G3 box; other site 349215005219 Switch II region; other site 349215005220 G4 box; other site 349215005221 G5 box; other site 349215005222 Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to...; Region: Translation_Factor_II_like; cl02787 349215005223 Domain III of Elongation factor (EF) Tu (EF-TU) and EF-G. Elongation factors (EF) EF-Tu and EF-G participate in the elongation phase during protein biosynthesis on the ribosome. Their functional cycles depend on GTP binding and its hydrolysis. The EF-Tu...; Region: Translation_factor_III; cl02786 349215005224 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...; Region: APSK; cd02027 349215005225 ligand-binding site [chemical binding]; other site 349215005226 sulfate adenylyltransferase, small subunit; Region: CysD; TIGR02039 349215005227 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 349215005228 Active Sites [active] 349215005229 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...; Region: CysQ; cd01638 349215005230 active site 349215005231 SapC; Region: SapC; pfam07277 349215005232 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 349215005233 DNA binding residues [nucleotide binding] 349215005234 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 349215005235 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 349215005236 active site 349215005237 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 349215005238 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 349215005239 N-acetyl-D-glucosamine binding site [chemical binding]; other site 349215005240 catalytic residue [active] 349215005241 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 349215005242 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 349215005243 anhydro-N-acetylmuramic acid kinase; Reviewed; Region: anmK; PRK09585 349215005244 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 349215005245 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 349215005246 active site 349215005247 HIGH motif; other site 349215005248 dimer interface [polypeptide binding]; other site 349215005249 KMSKS motif; other site 349215005250 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 349215005251 RNA binding surface [nucleotide binding]; other site 349215005252 Protein of unknown function; Region: DUF3971; pfam13116 349215005253 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 349215005254 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 349215005255 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 349215005256 catalytic triad [active] 349215005257 Predicted membrane protein (DUF2335); Region: DUF2335; cl02210 349215005258 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 349215005259 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 349215005260 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 349215005261 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 349215005262 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 349215005263 catalytic residue [active] 349215005264 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 349215005265 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 349215005266 catalytic loop [active] 349215005267 iron binding site [ion binding]; other site 349215005268 FAD-NAD(P)-binding; Region: NAD_binding_9; pfam13454 349215005269 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 349215005270 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 349215005271 Ligand Binding Site [chemical binding]; other site 349215005272 Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Escherichia coli Hsp31 protein; Region: GATase1_Hsp31_like; cd03141 349215005273 Putative intracellular protease/amidase [General function prediction only]; Region: ThiJ; COG0693 349215005274 potential catalytic triad [active] 349215005275 conserved cys residue [active] 349215005276 sensor protein QseC; Provisional; Region: PRK10337 349215005277 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 349215005278 dimer interface [polypeptide binding]; other site 349215005279 phosphorylation site [posttranslational modification] 349215005280 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 349215005281 ATP binding site [chemical binding]; other site 349215005282 Mg2+ binding site [ion binding]; other site 349215005283 G-X-G motif; other site 349215005284 DNA-binding transcriptional regulator BasR; Provisional; Region: PRK10643 349215005285 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 349215005286 active site 349215005287 phosphorylation site [posttranslational modification] 349215005288 intermolecular recognition site; other site 349215005289 dimerization interface [polypeptide binding]; other site 349215005290 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 349215005291 DNA binding site [nucleotide binding] 349215005292 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 349215005293 TPR motif; other site 349215005294 binding surface 349215005295 short chain dehydrogenase; Provisional; Region: PRK09072 349215005296 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 349215005297 NAD(P) binding site [chemical binding]; other site 349215005298 active site 349215005299 Adenylate forming domain, Class I; Region: AFD_class_I; cl17068 349215005300 AMP-binding enzyme; Region: AMP-binding; pfam00501 349215005301 acyl-activating enzyme (AAE) consensus motif; other site 349215005302 AMP binding site [chemical binding]; other site 349215005303 active site 349215005304 CoA binding site [chemical binding]; other site 349215005305 Heme oxygenase catalyzes the rate limiting step in the degradation of heme to bilirubin, it is essential for recycling of iron from heme. Heme is used as a substrate and cofactor for its own degradation to biliverdin, iron, and carbon monoxide. This...; Region: HemeO; cd00232 349215005306 heme binding pocket [chemical binding]; other site 349215005307 heme ligand [chemical binding]; other site 349215005308 Thermostable hemolysin; Region: T_hemolysin; pfam12261 349215005309 Protein of unknown function (DUF423); Region: DUF423; pfam04241 349215005310 Protein required for attachment to host cells; Region: Host_attach; pfam10116 349215005311 Uncharacterized protein conserved in bacteria (DUF2147); Region: DUF2147; pfam09917 349215005312 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 349215005313 putative hydrolase; Provisional; Region: PRK11460 349215005314 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 349215005315 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 349215005316 active site 349215005317 Riboflavin kinase; Region: Flavokinase; smart00904 349215005318 isoleucyl-tRNA synthetase; Provisional; Region: ileS; PRK13804 349215005319 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 349215005320 active site 349215005321 HIGH motif; other site 349215005322 nucleotide binding site [chemical binding]; other site 349215005323 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 349215005324 active site 349215005325 KMSKS motif; other site 349215005326 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 349215005327 tRNA binding surface [nucleotide binding]; other site 349215005328 anticodon binding site; other site 349215005329 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 349215005330 Protein of unknown function (DUF3035); Region: DUF3035; pfam11233 349215005331 Flavin Reductases; Region: FlaRed; cl00801 349215005332 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 349215005333 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 349215005334 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 349215005335 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 349215005336 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 349215005337 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 349215005338 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 349215005339 active site 349215005340 dimer interface [polypeptide binding]; other site 349215005341 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 349215005342 dimer interface [polypeptide binding]; other site 349215005343 active site 349215005344 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 349215005345 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 349215005346 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 349215005347 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 349215005348 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 349215005349 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 349215005350 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 349215005351 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 349215005352 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 349215005353 ATP binding site [chemical binding]; other site 349215005354 Mg2+ binding site [ion binding]; other site 349215005355 G-X-G motif; other site 349215005356 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 349215005357 ATP binding site [chemical binding]; other site 349215005358 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 349215005359 ATP12 chaperone protein; Region: ATP12; pfam07542 349215005360 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 349215005361 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 349215005362 RNA binding surface [nucleotide binding]; other site 349215005363 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 349215005364 active site 349215005365 camphor resistance protein CrcB; Provisional; Region: PRK14195 349215005366 recombination factor protein RarA; Reviewed; Region: PRK13342 349215005367 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 349215005368 Walker A motif; other site 349215005369 ATP binding site [chemical binding]; other site 349215005370 Walker B motif; other site 349215005371 arginine finger; other site 349215005372 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 349215005373 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 349215005374 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 349215005375 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 349215005376 protein binding site [polypeptide binding]; other site 349215005377 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 349215005378 protein binding site [polypeptide binding]; other site 349215005379 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 349215005380 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 349215005381 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 349215005382 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 349215005383 alphaNTD homodimer interface [polypeptide binding]; other site 349215005384 alphaNTD - beta interaction site [polypeptide binding]; other site 349215005385 alphaNTD - beta' interaction site [polypeptide binding]; other site 349215005386 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 349215005387 30S ribosomal protein S11; Validated; Region: PRK05309 349215005388 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 349215005389 Ribosomal protein S13/S18; Region: Ribosomal_S13; cl00331 349215005390 adenylate kinase; Reviewed; Region: adk; PRK00279 349215005391 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 349215005392 AMP-binding site [chemical binding]; other site 349215005393 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 349215005394 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 349215005395 SecY translocase; Region: SecY; pfam00344 349215005396 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 349215005397 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 349215005398 23S rRNA binding site [nucleotide binding]; other site 349215005399 ribosomal protein S5, bacterial/organelle type; Region: rpsE_bact; TIGR01021 349215005400 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 349215005401 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 349215005402 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 349215005403 5S rRNA interface [nucleotide binding]; other site 349215005404 23S rRNA interface [nucleotide binding]; other site 349215005405 L5 interface [polypeptide binding]; other site 349215005406 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 349215005407 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 349215005408 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 349215005409 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 349215005410 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 349215005411 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 349215005412 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 349215005413 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 349215005414 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 349215005415 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 349215005416 RNA binding site [nucleotide binding]; other site 349215005417 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 349215005418 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 349215005419 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 349215005420 putative translocon interaction site; other site 349215005421 23S rRNA interface [nucleotide binding]; other site 349215005422 signal recognition particle (SRP54) interaction site; other site 349215005423 L23 interface [polypeptide binding]; other site 349215005424 trigger factor interaction site; other site 349215005425 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 349215005426 23S rRNA interface [nucleotide binding]; other site 349215005427 5S rRNA interface [nucleotide binding]; other site 349215005428 putative antibiotic binding site [chemical binding]; other site 349215005429 L25 interface [polypeptide binding]; other site 349215005430 L27 interface [polypeptide binding]; other site 349215005431 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 349215005432 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 349215005433 G-X-X-G motif; other site 349215005434 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 349215005435 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 349215005436 protein-rRNA interface [nucleotide binding]; other site 349215005437 putative translocon binding site; other site 349215005438 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 349215005439 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 349215005440 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 349215005441 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 349215005442 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 349215005443 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 349215005444 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 349215005445 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 349215005446 elongation factor Tu; Reviewed; Region: PRK00049 349215005447 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 349215005448 G1 box; other site 349215005449 GEF interaction site [polypeptide binding]; other site 349215005450 GTP/Mg2+ binding site [chemical binding]; other site 349215005451 Switch I region; other site 349215005452 G2 box; other site 349215005453 G3 box; other site 349215005454 Switch II region; other site 349215005455 G4 box; other site 349215005456 G5 box; other site 349215005457 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 349215005458 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 349215005459 Antibiotic Binding Site [chemical binding]; other site 349215005460 elongation factor G; Reviewed; Region: PRK00007 349215005461 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 349215005462 G1 box; other site 349215005463 putative GEF interaction site [polypeptide binding]; other site 349215005464 GTP/Mg2+ binding site [chemical binding]; other site 349215005465 Switch I region; other site 349215005466 G2 box; other site 349215005467 G3 box; other site 349215005468 Switch II region; other site 349215005469 G4 box; other site 349215005470 G5 box; other site 349215005471 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 349215005472 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 349215005473 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 349215005474 30S ribosomal protein S7; Validated; Region: PRK05302 349215005475 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 349215005476 16S rRNA interaction site [nucleotide binding]; other site 349215005477 streptomycin interaction site [chemical binding]; other site 349215005478 23S rRNA interaction site [nucleotide binding]; other site 349215005479 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 349215005480 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 349215005481 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 349215005482 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 349215005483 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 349215005484 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 349215005485 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 349215005486 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 349215005487 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 349215005488 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 349215005489 DNA binding site [nucleotide binding] 349215005490 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 349215005491 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 349215005492 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl17585 349215005493 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 349215005494 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 349215005495 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 349215005496 RPB12 interaction site [polypeptide binding]; other site 349215005497 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 349215005498 RPB3 interaction site [polypeptide binding]; other site 349215005499 RPB1 interaction site [polypeptide binding]; other site 349215005500 RPB11 interaction site [polypeptide binding]; other site 349215005501 RPB10 interaction site [polypeptide binding]; other site 349215005502 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 349215005503 core dimer interface [polypeptide binding]; other site 349215005504 peripheral dimer interface [polypeptide binding]; other site 349215005505 L10 interface [polypeptide binding]; other site 349215005506 L11 interface [polypeptide binding]; other site 349215005507 putative EF-Tu interaction site [polypeptide binding]; other site 349215005508 putative EF-G interaction site [polypeptide binding]; other site 349215005509 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 349215005510 23S rRNA interface [nucleotide binding]; other site 349215005511 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 349215005512 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 349215005513 mRNA/rRNA interface [nucleotide binding]; other site 349215005514 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 349215005515 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 349215005516 L7/L12 interface [polypeptide binding]; other site 349215005517 23S rRNA interface [nucleotide binding]; other site 349215005518 L25 interface [polypeptide binding]; other site 349215005519 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 349215005520 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 349215005521 putative homodimer interface [polypeptide binding]; other site 349215005522 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 349215005523 heterodimer interface [polypeptide binding]; other site 349215005524 homodimer interface [polypeptide binding]; other site 349215005525 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; pfam00584 349215005526 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 349215005527 Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also...; Region: DUS_like_FMN; cd02801 349215005528 FMN binding site [chemical binding]; other site 349215005529 active site 349215005530 catalytic residues [active] 349215005531 substrate binding site [chemical binding]; other site 349215005532 SpoVR family protein; Provisional; Region: PRK11767 349215005533 Uncharacterized conserved protein [Function unknown]; Region: SpoVR; COG2719 349215005534 hypothetical protein; Provisional; Region: PRK05325 349215005535 PrkA family serine protein kinase; Provisional; Region: PRK15455 349215005536 AAA ATPase domain; Region: AAA_16; pfam13191 349215005537 PrkA serine protein kinase C-terminal domain; Region: PrkA; pfam06798 349215005538 elongation factor Tu; Reviewed; Region: PRK00049 349215005539 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 349215005540 G1 box; other site 349215005541 GEF interaction site [polypeptide binding]; other site 349215005542 GTP/Mg2+ binding site [chemical binding]; other site 349215005543 Switch I region; other site 349215005544 G2 box; other site 349215005545 G3 box; other site 349215005546 Switch II region; other site 349215005547 G4 box; other site 349215005548 G5 box; other site 349215005549 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 349215005550 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 349215005551 Antibiotic Binding Site [chemical binding]; other site 349215005552 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 349215005553 HAMP domain; Region: HAMP; pfam00672 349215005554 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 349215005555 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 349215005556 dimer interface [polypeptide binding]; other site 349215005557 putative CheW interface [polypeptide binding]; other site 349215005558 KAP family P-loop domain; Region: KAP_NTPase; pfam07693 349215005559 AAA domain; Region: AAA_25; pfam13481 349215005560 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 349215005561 Walker A motif; other site 349215005562 ATP binding site [chemical binding]; other site 349215005563 Walker B motif; other site 349215005564 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 349215005565 AAA domain; Region: AAA_21; pfam13304 349215005566 Walker A/P-loop; other site 349215005567 ATP binding site [chemical binding]; other site 349215005568 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 349215005569 ABC transporter signature motif; other site 349215005570 Walker B; other site 349215005571 D-loop; other site 349215005572 H-loop/switch region; other site 349215005573 HEPN domain; Region: HEPN; cl00824 349215005574 integrase; Provisional; Region: PRK09692 349215005575 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall...; Region: INT_P4; cd00801 349215005576 active site 349215005577 Int/Topo IB signature motif; other site 349215005578 S-adenosyl-l-methionine hydroxide adenosyltransferase; Region: SAM_adeno_trans; cl17774 349215005579 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 349215005580 Catalytic NodB homology domain of rhizobial NodB-like proteins; Region: CE4_NodB_like_6s_7s; cd10917 349215005581 NodB motif; other site 349215005582 active site 349215005583 metal binding site [ion binding]; metal-binding site 349215005584 Glucokinase; Region: Glucokinase; cl17310 349215005585 glucokinase, proteobacterial type; Region: glk; TIGR00749 349215005586 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 349215005587 Cation efflux family; Region: Cation_efflux; cl00316 349215005588 multidrug efflux protein; Reviewed; Region: PRK09579 349215005589 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 349215005590 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 349215005591 HlyD family secretion protein; Region: HlyD_3; pfam13437 349215005592 Response regulator receiver domain; Region: Response_reg; pfam00072 349215005593 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 349215005594 active site 349215005595 phosphorylation site [posttranslational modification] 349215005596 intermolecular recognition site; other site 349215005597 dimerization interface [polypeptide binding]; other site 349215005598 Response regulator receiver domain; Region: Response_reg; pfam00072 349215005599 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 349215005600 active site 349215005601 phosphorylation site [posttranslational modification] 349215005602 intermolecular recognition site; other site 349215005603 dimerization interface [polypeptide binding]; other site 349215005604 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 349215005605 Response regulator receiver domain; Region: Response_reg; pfam00072 349215005606 active site 349215005607 phosphorylation site [posttranslational modification] 349215005608 intermolecular recognition site; other site 349215005609 dimerization interface [polypeptide binding]; other site 349215005610 CHASE3 domain; Region: CHASE3; pfam05227 349215005611 PAS fold; Region: PAS_4; pfam08448 349215005612 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 349215005613 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 349215005614 dimer interface [polypeptide binding]; other site 349215005615 phosphorylation site [posttranslational modification] 349215005616 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 349215005617 ATP binding site [chemical binding]; other site 349215005618 Mg2+ binding site [ion binding]; other site 349215005619 G-X-G motif; other site 349215005620 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 349215005621 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cl17736 349215005622 active site 349215005623 phosphorylation site [posttranslational modification] 349215005624 intermolecular recognition site; other site 349215005625 dimerization interface [polypeptide binding]; other site 349215005626 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 349215005627 active site residue [active] 349215005628 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 349215005629 dimerization interface [polypeptide binding]; other site 349215005630 putative DNA binding site [nucleotide binding]; other site 349215005631 putative Zn2+ binding site [ion binding]; other site 349215005632 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 349215005633 Predicted periplasmic protein [General function prediction only]; Region: COG3895 349215005634 Membrane-bound lysozyme-inhibitor of c-type lysozyme; Region: MliC; pfam09864 349215005635 META domain; Region: META; pfam03724 349215005636 Methyladenine glycosylase; Region: Adenine_glyco; pfam03352 349215005637 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 349215005638 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD1; cd05283 349215005639 putative NAD(P) binding site [chemical binding]; other site 349215005640 putative substrate binding site [chemical binding]; other site 349215005641 catalytic Zn binding site [ion binding]; other site 349215005642 structural Zn binding site [ion binding]; other site 349215005643 dimer interface [polypeptide binding]; other site 349215005644 Bacterial OB fold (BOF) protein; Region: BOF; cl01196 349215005645 Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnA; COG2824 349215005646 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; pfam08274 349215005647 PhnA protein; Region: PhnA; pfam03831 349215005648 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 349215005649 Domain of unknown function DUF21; Region: DUF21; pfam01595 349215005650 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 349215005651 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 349215005652 catalase/hydroperoxidase HPI(I); Provisional; Region: PRK15061 349215005653 Heme-dependent peroxidases similar to plant peroxidases; Region: plant_peroxidase_like; cl00196 349215005654 heme binding site [chemical binding]; other site 349215005655 C-terminal non-catalytic domain of catalase-peroxidases; Region: catalase_peroxidase_2; cd08200 349215005656 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 349215005657 metal binding site 2 [ion binding]; metal-binding site 349215005658 putative DNA binding helix; other site 349215005659 metal binding site 1 [ion binding]; metal-binding site 349215005660 dimer interface [polypeptide binding]; other site 349215005661 structural Zn2+ binding site [ion binding]; other site 349215005662 Nucleoside-specific channel-forming protein, Tsx; Region: Channel_Tsx; cl04114 349215005663 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 349215005664 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 349215005665 putative active site [active] 349215005666 heme pocket [chemical binding]; other site 349215005667 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 349215005668 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 349215005669 putative active site [active] 349215005670 heme pocket [chemical binding]; other site 349215005671 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 349215005672 putative active site [active] 349215005673 heme pocket [chemical binding]; other site 349215005674 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 349215005675 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 349215005676 dimer interface [polypeptide binding]; other site 349215005677 putative CheW interface [polypeptide binding]; other site 349215005678 Protein of unknown function (DUF4238); Region: DUF4238; pfam14022 349215005679 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4694 349215005680 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 349215005681 ABC transporter signature motif; other site 349215005682 Walker B; other site 349215005683 D-loop; other site 349215005684 H-loop/switch region; other site 349215005685 HipA-like N-terminal domain; Region: HipA_N; pfam07805 349215005686 HipA-like C-terminal domain; Region: HipA_C; pfam07804 349215005687 efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family; Region: outer_NodT; TIGR01845 349215005688 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family; Region: 2A0602; TIGR00915 349215005689 Protein export membrane protein; Region: SecD_SecF; cl14618 349215005690 Protein export membrane protein; Region: SecD_SecF; cl14618 349215005691 multidrug efflux system protein MdtE; Provisional; Region: PRK09859 349215005692 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 349215005693 HlyD family secretion protein; Region: HlyD_3; pfam13437 349215005694 pfkB-type carbohydrate kinase family protein; Region: PLN02630 349215005695 PAS domain; Region: PAS_9; pfam13426 349215005696 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 349215005697 virion protein; Provisional; Region: V; PHA02564 349215005698 Bacteriophage lambda tail assembly protein I; Region: Lambda_tail_I; cl01945 349215005699 Putative phage tail protein; Region: Phage-tail_3; pfam13550 349215005700 NlpC/P60 family; Region: NLPC_P60; cl17555 349215005701 Domain of unknown function (DUF1833); Region: DUF1833; pfam08875 349215005702 Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell division and chromosome partitioning / Cytoskeleton]; Region: ATS1; COG5184 349215005703 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1_2; pfam13540 349215005704 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 349215005705 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 349215005706 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 349215005707 Regulator of chromosome condensation (RCC1) repeat; Region: RCC1; pfam00415 349215005708 tape measure domain; Region: tape_meas_nterm; TIGR02675 349215005709 phage tail tape measure protein, lambda family; Region: tape_meas_lam_C; TIGR01541 349215005710 Lambda phage tail tape-measure protein (Tape_meas_lam_C); Region: Tape_meas_lam_C; pfam09718 349215005711 Phage major capsid protein E; Region: Phage_cap_E; pfam03864 349215005712 Bacteriophage lambda head decoration protein D; Region: HDPD; pfam02924 349215005713 Signal peptide peptidase A (SppA) 36K type, a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_36K_type; cd07022 349215005714 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 349215005715 tandem repeat interface [polypeptide binding]; other site 349215005716 oligomer interface [polypeptide binding]; other site 349215005717 active site residues [active] 349215005718 phage portal protein, lambda family; Region: portal_lambda; TIGR01539 349215005719 Phage portal protein, lambda family; Region: Phage_portal_2; pfam05136 349215005720 gpW; Region: gpW; pfam02831 349215005721 Phage terminase large subunit (GpA); Region: Terminase_GpA; pfam05876 349215005722 Protein of unknown function (DUF3489); Region: DUF3489; pfam11994 349215005723 ParB-like nuclease domain; Region: ParBc; pfam02195 349215005724 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 349215005725 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 349215005726 DNA methylase; Region: N6_N4_Mtase; pfam01555 349215005727 TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG...; Region: TOPRIM_primases; cd01029 349215005728 active site 349215005729 metal binding site [ion binding]; metal-binding site 349215005730 interdomain interaction site; other site 349215005731 AAA domain; Region: AAA_25; pfam13481 349215005732 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 349215005733 Walker A motif; other site 349215005734 ATP binding site [chemical binding]; other site 349215005735 Walker B motif; other site 349215005736 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 349215005737 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 349215005738 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 349215005739 DNA binding residues [nucleotide binding] 349215005740 Predicted transcriptional regulators [Transcription]; Region: COG1733 349215005741 HxlR-like helix-turn-helix; Region: HxlR; pfam01638 349215005742 Protein of unknown function (DUF2975); Region: DUF2975; pfam11188 349215005743 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 349215005744 salt bridge; other site 349215005745 non-specific DNA binding site [nucleotide binding]; other site 349215005746 sequence-specific DNA binding site [nucleotide binding]; other site 349215005747 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 349215005748 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cd00338 349215005749 catalytic residues [active] 349215005750 catalytic nucleophile [active] 349215005751 Recombinase; Region: Recombinase; pfam07508 349215005752 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 349215005753 Protein of unknown function (DUF2924); Region: DUF2924; pfam11149 349215005754 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 349215005755 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 349215005756 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 349215005757 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 349215005758 GST_N family, Class Beta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens; Region: GST_N_Beta; cd03057 349215005759 C-terminal domain interface [polypeptide binding]; other site 349215005760 GSH binding site (G-site) [chemical binding]; other site 349215005761 dimer interface [polypeptide binding]; other site 349215005762 C-terminal, alpha helical domain of Class Beta Glutathione S-transferases; Region: GST_C_Beta; cd03188 349215005763 N-terminal domain interface [polypeptide binding]; other site 349215005764 dimer interface [polypeptide binding]; other site 349215005765 substrate binding pocket (H-site) [chemical binding]; other site 349215005766 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 349215005767 Major Facilitator Superfamily; Region: MFS_1; pfam07690 349215005768 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 349215005769 TraB family; Region: TraB; pfam01963 349215005770 DNA polymerase I; Provisional; Region: PRK05755 349215005771 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 349215005772 active site 349215005773 metal binding site 1 [ion binding]; metal-binding site 349215005774 putative 5' ssDNA interaction site; other site 349215005775 metal binding site 3; metal-binding site 349215005776 metal binding site 2 [ion binding]; metal-binding site 349215005777 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 349215005778 putative DNA binding site [nucleotide binding]; other site 349215005779 putative metal binding site [ion binding]; other site 349215005780 DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases; Region: DNA_polA_I_Ecoli_like_exo; cd06139 349215005781 active site 349215005782 catalytic site [active] 349215005783 substrate binding site [chemical binding]; other site 349215005784 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 349215005785 active site 349215005786 DNA binding site [nucleotide binding] 349215005787 catalytic site [active] 349215005788 Ion transport protein; Region: Ion_trans; pfam00520 349215005789 Protein of unknown function (DUF1223); Region: DUF1223; cl10501 349215005790 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 349215005791 active site 349215005792 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 349215005793 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 349215005794 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 349215005795 23S rRNA binding site [nucleotide binding]; other site 349215005796 L21 binding site [polypeptide binding]; other site 349215005797 L13 binding site [polypeptide binding]; other site 349215005798 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 349215005799 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 349215005800 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 349215005801 dimer interface [polypeptide binding]; other site 349215005802 motif 1; other site 349215005803 active site 349215005804 motif 2; other site 349215005805 motif 3; other site 349215005806 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 349215005807 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 349215005808 Coenzyme A binding pocket [chemical binding]; other site 349215005809 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 349215005810 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 349215005811 putative tRNA-binding site [nucleotide binding]; other site 349215005812 B3/4 domain; Region: B3_4; pfam03483 349215005813 tRNA synthetase B5 domain; Region: B5; smart00874 349215005814 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 349215005815 dimer interface [polypeptide binding]; other site 349215005816 motif 1; other site 349215005817 motif 3; other site 349215005818 motif 2; other site 349215005819 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; smart00896 349215005820 long-chain-fatty-acid--CoA ligase; Validated; Region: PRK06710 349215005821 Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD; Region: FC-FACS_FadD_like; cd05936 349215005822 acyl-activating enzyme (AAE) consensus motif; other site 349215005823 putative AMP binding site [chemical binding]; other site 349215005824 putative active site [active] 349215005825 putative CoA binding site [chemical binding]; other site 349215005826 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 349215005827 DNA-binding site [nucleotide binding]; DNA binding site 349215005828 RNA-binding motif; other site 349215005829 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 349215005830 DNA-binding site [nucleotide binding]; DNA binding site 349215005831 RNA-binding motif; other site 349215005832 GcrA cell cycle regulator; Region: GcrA; cl11564 349215005833 GTPase Era; Reviewed; Region: era; PRK00089 349215005834 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 349215005835 G1 box; other site 349215005836 GTP/Mg2+ binding site [chemical binding]; other site 349215005837 Switch I region; other site 349215005838 G2 box; other site 349215005839 Switch II region; other site 349215005840 G3 box; other site 349215005841 G4 box; other site 349215005842 G5 box; other site 349215005843 KH domain; Region: KH_2; pfam07650 349215005844 ribonuclease III; Reviewed; Region: rnc; PRK00102 349215005845 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 349215005846 dimerization interface [polypeptide binding]; other site 349215005847 active site 349215005848 metal binding site [ion binding]; metal-binding site 349215005849 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 349215005850 dsRNA binding site [nucleotide binding]; other site 349215005851 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 349215005852 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 349215005853 Catalytic site [active] 349215005854 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 349215005855 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 349215005856 Uncharacterized protein conserved in bacteria (DUF2062); Region: DUF2062; cl01261 349215005857 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 349215005858 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 349215005859 Zn2+ binding site [ion binding]; other site 349215005860 Mg2+ binding site [ion binding]; other site 349215005861 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 349215005862 synthetase active site [active] 349215005863 NTP binding site [chemical binding]; other site 349215005864 metal binding site [ion binding]; metal-binding site 349215005865 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 349215005866 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 349215005867 DNA-directed RNA polymerase subunit omega; Reviewed; Region: rpoZ; PRK00392 349215005868 Uncharacterized conserved protein [Function unknown]; Region: COG1432 349215005869 LabA_like proteins; Region: LabA; cd10911 349215005870 putative metal binding site [ion binding]; other site 349215005871 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 349215005872 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 349215005873 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 349215005874 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 349215005875 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 349215005876 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 349215005877 carboxyltransferase (CT) interaction site; other site 349215005878 biotinylation site [posttranslational modification]; other site 349215005879 Dehydroquinase class II; Region: DHquinase_II; pfam01220 349215005880 Dehydroquinase (DHQase), type II. Dehydroquinase (or 3-dehydroquinate dehydratase) catalyzes the reversible dehydration of 3-dehydroquinate to form 3-dehydroshikimate. This reaction is part of two metabolic pathways: the biosynthetic shikimate pathway...; Region: DHQase_II; cd00466 349215005881 trimer interface [polypeptide binding]; other site 349215005882 active site 349215005883 dimer interface [polypeptide binding]; other site 349215005884 Protein of unknown function (DUF461); Region: DUF461; pfam04314 349215005885 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 349215005886 DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a CXXC...; Region: DsbA_Com1_like; cd03023 349215005887 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 349215005888 catalytic residues [active] 349215005889 Peptidase family M48; Region: Peptidase_M48; cl12018 349215005890 TPR repeat; Region: TPR_11; pfam13414 349215005891 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 349215005892 TPR motif; other site 349215005893 binding surface 349215005894 TPR repeat; Region: TPR_11; pfam13414 349215005895 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 349215005896 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 349215005897 S-adenosylmethionine binding site [chemical binding]; other site 349215005898 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 349215005899 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl17186 349215005900 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein. IMPDH is an essential enzyme that catalyzes the first step unique to GTP synthesis, playing a...; Region: CBS_pair_IMPDH; cd04601 349215005901 IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of...; Region: IMPDH; cd00381 349215005902 active site 349215005903 Acetyltransferase (GNAT) domain; Region: Acetyltransf_10; pfam13673 349215005904 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 349215005905 Coenzyme A binding pocket [chemical binding]; other site 349215005906 16S rRNA methyltransferase B; Provisional; Region: PRK14902 349215005907 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 349215005908 S-adenosylmethionine binding site [chemical binding]; other site 349215005909 GMP synthase; Reviewed; Region: guaA; PRK00074 349215005910 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 349215005911 AMP/PPi binding site [chemical binding]; other site 349215005912 candidate oxyanion hole; other site 349215005913 catalytic triad [active] 349215005914 potential glutamine specificity residues [chemical binding]; other site 349215005915 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 349215005916 ATP Binding subdomain [chemical binding]; other site 349215005917 Ligand Binding sites [chemical binding]; other site 349215005918 Dimerization subdomain; other site 349215005919 Predicted Fe-S-cluster redox enzyme [General function prediction only]; Region: COG0820 349215005920 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 349215005921 FeS/SAM binding site; other site 349215005922 Acetyltransferase (GNAT) domain; Region: Acetyltransf_5; cl17496 349215005923 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 349215005924 Threonine synthase catalyzes the final step of threonine biosynthesis. The conversion of O-phosphohomoserine into threonine and inorganic phosphate is pyridoxal 5'-phosphate dependent. The Thr-synth_1 CD includes members from higher plants; Region: Thr-synth_2; cd01560 349215005925 pyridoxal 5'-phosphate binding site [chemical binding]; other site 349215005926 catalytic residue [active] 349215005927 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 349215005928 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 349215005929 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 349215005930 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 349215005931 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 349215005932 hypothetical protein; Validated; Region: PRK00228 349215005933 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 349215005934 Transglycosylase; Region: Transgly; pfam00912 349215005935 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 349215005936 dehydrogenase, PQQ-dependent, s-GDH family; Region: non_repeat_PQQ; TIGR03606 349215005937 Glucose / Sorbosone dehydrogenase; Region: GSDH; pfam07995 349215005938 D-ala-D-ala dipeptidase; Region: Peptidase_M15; cl00813 349215005939 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 349215005940 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 349215005941 Walker A/P-loop; other site 349215005942 ATP binding site [chemical binding]; other site 349215005943 Q-loop/lid; other site 349215005944 ABC transporter signature motif; other site 349215005945 Walker B; other site 349215005946 D-loop; other site 349215005947 H-loop/switch region; other site 349215005948 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 349215005949 Permease; Region: Permease; pfam02405 349215005950 Alanine racemase [Cell envelope biogenesis, outer membrane]; Region: Alr; COG0787 349215005951 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 349215005952 active site 349215005953 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 349215005954 dimer interface [polypeptide binding]; other site 349215005955 substrate binding site [chemical binding]; other site 349215005956 catalytic residues [active] 349215005957 replicative DNA helicase; Provisional; Region: PRK09165 349215005958 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 349215005959 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 349215005960 Walker A motif; other site 349215005961 ATP binding site [chemical binding]; other site 349215005962 Walker B motif; other site 349215005963 DNA binding loops [nucleotide binding] 349215005964 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 349215005965 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 349215005966 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 349215005967 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 349215005968 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 349215005969 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 349215005970 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 349215005971 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 349215005972 PAS fold; Region: PAS_3; pfam08447 349215005973 putative active site [active] 349215005974 heme pocket [chemical binding]; other site 349215005975 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 349215005976 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 349215005977 dimer interface [polypeptide binding]; other site 349215005978 putative CheW interface [polypeptide binding]; other site 349215005979 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 349215005980 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 349215005981 NAD(P) binding site [chemical binding]; other site 349215005982 homotetramer interface [polypeptide binding]; other site 349215005983 homodimer interface [polypeptide binding]; other site 349215005984 active site 349215005985 Predicted phosphatase/phosphohexomutase [General function prediction only]; Region: COG0637 349215005986 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 349215005987 motif II; other site 349215005988 acyl carrier protein; Provisional; Region: acpP; PRK00982 349215005989 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 349215005990 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 349215005991 dimer interface [polypeptide binding]; other site 349215005992 active site 349215005993 YceG-like family; Region: YceG; pfam02618 349215005994 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 349215005995 dimerization interface [polypeptide binding]; other site 349215005996 NADH dehydrogenase; Validated; Region: PRK08183 349215005997 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 349215005998 mce related protein; Region: MCE; pfam02470 349215005999 Uncharacterized protein conserved in bacteria (DUF2155); Region: DUF2155; pfam09923 349215006000 leucyl/phenylalanyl-tRNA--protein transferase; Reviewed; Region: aat; PRK00301 349215006001 Isopropylmalate/homocitrate/citramalate synthases [Amino acid transport and metabolism]; Region: LeuA; COG0119 349215006002 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain; Region: DRE_TIM_IPMS; cd07940 349215006003 active site 349215006004 catalytic residues [active] 349215006005 metal binding site [ion binding]; metal-binding site 349215006006 Uncharacterized conserved protein [Function unknown]; Region: COG2835 349215006007 Uncharacterized protein, similar to the N-terminal domain of Lon protease [General function prediction only]; Region: COG2802 349215006008 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]; Region: COG3118 349215006009 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 349215006010 catalytic residues [active] 349215006011 This CD includes bacterial (Agrobacterium tumefaciens and Caulobacter crescentus ProX, and Clostridium sticklandii PrdX) and eukaryotic (Plasmodium falciparum N-terminal ProRS editing domain) sequences. The C. sticklandii PrdX protein, a homolog of the...; Region: PrdX_deacylase; cd04335 349215006012 putative deacylase active site [active] 349215006013 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 349215006014 active site 349215006015 phosphorylation site [posttranslational modification] 349215006016 intermolecular recognition site; other site 349215006017 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 349215006018 nucleoside/Zn binding site; other site 349215006019 dimer interface [polypeptide binding]; other site 349215006020 catalytic motif [active] 349215006021 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 349215006022 oligomer interface [polypeptide binding]; other site 349215006023 active site residues [active] 349215006024 GDYXXLXY protein; Region: GDYXXLXY; cl02066 349215006025 Predicted membrane protein (DUF2157); Region: DUF2157; pfam09925 349215006026 ATP-dependent Clp protease ATP-binding subunit clpA; Region: ClpA; TIGR02639 349215006027 Clp amino terminal domain; Region: Clp_N; pfam02861 349215006028 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 349215006029 Walker A motif; other site 349215006030 ATP binding site [chemical binding]; other site 349215006031 Walker B motif; other site 349215006032 arginine finger; other site 349215006033 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 349215006034 Walker A motif; other site 349215006035 ATP binding site [chemical binding]; other site 349215006036 Walker B motif; other site 349215006037 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 349215006038 ATP-dependent Clp protease ATP-binding subunit clpA; Region: ClpA; TIGR02639 349215006039 Clp amino terminal domain; Region: Clp_N; pfam02861 349215006040 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 349215006041 Walker A motif; other site 349215006042 ATP binding site [chemical binding]; other site 349215006043 Walker B motif; other site 349215006044 arginine finger; other site 349215006045 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 349215006046 Walker A motif; other site 349215006047 ATP binding site [chemical binding]; other site 349215006048 Walker B motif; other site 349215006049 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 349215006050 Uncharacterized conserved protein [Function unknown]; Region: COG2127 349215006051 Phasin protein; Region: Phasin_2; pfam09361 349215006052 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 349215006053 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 349215006054 short chain dehydrogenase; Provisional; Region: PRK08278 349215006055 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 349215006056 NAD(P) binding site [chemical binding]; other site 349215006057 active site 349215006058 ADP-heptose synthase, bifunctional sugar kinase/adenylyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaE; COG2870 349215006059 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 349215006060 putative ribose interaction site [chemical binding]; other site 349215006061 putative ADP binding site [chemical binding]; other site 349215006062 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 349215006063 active site 349215006064 nucleotide binding site [chemical binding]; other site 349215006065 HIGH motif; other site 349215006066 KMSKS motif; other site 349215006067 Bacterial transglutaminase-like cysteine proteinase BTLCP; Region: BTLCP; cl17596 349215006068 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09102 349215006069 Class I ribonucleotide reductase; Region: RNR_I; cd01679 349215006070 active site 349215006071 dimer interface [polypeptide binding]; other site 349215006072 catalytic residues [active] 349215006073 effector binding site; other site 349215006074 R2 peptide binding site; other site 349215006075 Predicted kinase [General function prediction only]; Region: COG0645 349215006076 Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates...; Region: NK; cl17190 349215006077 active site 349215006078 pyruvate kinase; Provisional; Region: PRK06247 349215006079 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl17342 349215006080 domain interfaces; other site 349215006081 active site 349215006082 Left-handed beta-roll, including virulence factors and various other proteins; Region: LbR-like; cl17507 349215006083 trimer interface [polypeptide binding]; other site 349215006084 Chaperone of endosialidase; Region: Peptidase_S74; pfam13884 349215006085 Uncharacterized conserved protein [Function unknown]; Region: COG5276 349215006086 LVIVD repeat; Region: LVIVD; pfam08309 349215006087 LVIVD repeat; Region: LVIVD; pfam08309 349215006088 LVIVD repeat; Region: LVIVD; pfam08309 349215006089 Uncharacterized conserved protein [Function unknown]; Region: COG5276 349215006090 LVIVD repeat; Region: LVIVD; pfam08309 349215006091 Uncharacterized conserved protein [Function unknown]; Region: COG5276 349215006092 LVIVD repeat; Region: LVIVD; pfam08309 349215006093 LVIVD repeat; Region: LVIVD; pfam08309 349215006094 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 349215006095 catalytic core [active] 349215006096 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 349215006097 dimer interface [polypeptide binding]; other site 349215006098 putative radical transfer pathway; other site 349215006099 diiron center [ion binding]; other site 349215006100 tyrosyl radical; other site 349215006101 Chaperone of endosialidase; Region: Peptidase_S74; pfam13884 349215006102 Chaperone of endosialidase; Region: Peptidase_S74; pfam13884 349215006103 PhoH-like protein; Region: PhoH; pfam02562 349215006104 AAA domain; Region: AAA_22; pfam13401 349215006105 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 349215006106 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 349215006107 Cu(I) binding site [ion binding]; other site 349215006108 Outer membrane protein transport protein (OMPP1/FadL/TodX); Region: Toluene_X; pfam03349 349215006109 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 349215006110 active site 349215006111 SCP-2 sterol transfer family; Region: SCP2; pfam02036 349215006112 Predicted proline hydroxylase [Posttranslational modification, protein turnover, chaperones]; Region: EGL-9; COG3751 349215006113 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy_3; pfam13640 349215006114 Acyl-CoA dehydrogenase N terminal; Region: AcylCoA_DH_N; pfam12418 349215006115 acyl-CoA dehydrogenase; Provisional; Region: PTZ00456 349215006116 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 349215006117 active site 349215006118 Acetyl-CoA dehydrogenase C-terminal like; Region: Acyl-CoA_dh_C; pfam12806 349215006119 cytidine deaminase, homodimeric; Region: cyt_deam_dimer; TIGR01355 349215006120 Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on...; Region: cytidine_deaminase; cd01283 349215006121 active site 349215006122 catalytic motif [active] 349215006123 Zn binding site [ion binding]; other site 349215006124 3-hydroxyacyl-CoA dehydrogenase [Lipid metabolism]; Region: FadB; COG1250 349215006125 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; Region: 3HCDH_N; pfam02737 349215006126 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 349215006127 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; Region: 3HCDH; pfam00725 349215006128 Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]; Region: CaiD; COG1024 349215006129 Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase; Region: crotonase-like; cd06558 349215006130 substrate binding site [chemical binding]; other site 349215006131 oxyanion hole (OAH) forming residues; other site 349215006132 trimer interface [polypeptide binding]; other site 349215006133 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 349215006134 acetyl-CoA acetyltransferases; Region: AcCoA-C-Actrans; TIGR01930 349215006135 dimer interface [polypeptide binding]; other site 349215006136 active site 349215006137 TIGR02300 family protein; Region: FYDLN_acid 349215006138 ribosomal protein L11 methyltransferase; Reviewed; Region: prmA; PRK00517 349215006139 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 349215006140 conserved hypothetical protein; Region: MG423; TIGR00649 349215006141 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 349215006142 hypothetical protein; Provisional; Region: PRK09272 349215006143 Protein of unknown function (DUF3442); Region: DUF3442; pfam11924 349215006144 Protein of unknown function (DUF3442); Region: DUF3442; pfam11924 349215006145 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 349215006146 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 349215006147 glutaminase active site [active] 349215006148 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 349215006149 dimer interface [polypeptide binding]; other site 349215006150 active site 349215006151 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 349215006152 dimer interface [polypeptide binding]; other site 349215006153 active site 349215006154 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK14353 349215006155 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 349215006156 Substrate binding site; other site 349215006157 Mg++ binding site; other site 349215006158 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 349215006159 active site 349215006160 substrate binding site [chemical binding]; other site 349215006161 CoA binding site [chemical binding]; other site 349215006162 Protein of unknown function (DUF3108); Region: DUF3108; pfam11306 349215006163 Acetyltransferase (GNAT) domain; Region: Acetyltransf_6; pfam13480 349215006164 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 349215006165 putative trimer interface [polypeptide binding]; other site 349215006166 putative CoA binding site [chemical binding]; other site 349215006167 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 349215006168 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 349215006169 metal binding site [ion binding]; metal-binding site 349215006170 dimer interface [polypeptide binding]; other site 349215006171 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 349215006172 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 349215006173 dimerization interface 3.5A [polypeptide binding]; other site 349215006174 active site 349215006175 putative metallohydrolase, TIGR04338 family; Region: HEXXH_Rv0185 349215006176 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 349215006177 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 349215006178 putative active site [active] 349215006179 substrate binding site [chemical binding]; other site 349215006180 putative cosubstrate binding site; other site 349215006181 catalytic site [active] 349215006182 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 349215006183 substrate binding site [chemical binding]; other site 349215006184 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 349215006185 active site 349215006186 catalytic residues [active] 349215006187 metal binding site [ion binding]; metal-binding site 349215006188 RmuC family; Region: RmuC; pfam02646 349215006189 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 349215006190 Elongation factor Tu GTP binding domain; Region: GTP_EFTU; pfam00009 349215006191 G1 box; other site 349215006192 GTP/Mg2+ binding site [chemical binding]; other site 349215006193 Switch I region; other site 349215006194 G2 box; other site 349215006195 G3 box; other site 349215006196 Switch II region; other site 349215006197 G4 box; other site 349215006198 G5 box; other site 349215006199 membrane protein insertase; Provisional; Region: PRK01318 349215006200 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 349215006201 Haemolytic domain; Region: Haemolytic; pfam01809 349215006202 Ribonuclease P; Region: Ribonuclease_P; pfam00825 349215006203 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 349215006204 Outer membrane protein beta-barrel domain; Region: OMP_b-brl; pfam13505 349215006205 Nitrogen regulatory protein PII [Amino acid transport and metabolism]; Region: GlnK; COG0347 349215006206 Nitrogen regulatory protein P-II; Region: P-II; smart00938 349215006207 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 349215006208 Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family; Region: Ubi-OHases; TIGR01988 349215006209 AAA-like domain; Region: AAA_10; pfam12846 349215006210 Bacterial conjugation TrbI-like protein; Region: TrbI; cl04242 349215006211 Protein of unknown function (DUF3625); Region: DUF3625; pfam12293 349215006212 Macrophage killing protein with similarity to conjugation protein; Region: IcmL; pfam11393 349215006213 flagellar hook-associated protein FlgK; Region: flgK_ends; TIGR02492 349215006214 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 349215006215 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 349215006216 flagellar hook-associated protein FlgL; Validated; Region: flgL; PRK06008 349215006217 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 349215006218 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 349215006219 Toxin co-regulated pilus biosynthesis protein Q; Region: TcpQ; pfam10671 349215006220 Dot/Icm secretion system ATPase DotB; Region: dot_icm_DotB; TIGR02524 349215006221 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 349215006222 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 349215006223 Walker A motif; other site 349215006224 Walker A/P-loop; other site 349215006225 ATP binding site [chemical binding]; other site 349215006226 ATP binding site [chemical binding]; other site 349215006227 Walker B motif; other site 349215006228 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 349215006229 N-acetyl-D-glucosamine binding site [chemical binding]; other site 349215006230 disulfide isomerase/thiol-disulfide oxidase; Provisional; Region: dsbG; PRK11657 349215006231 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 349215006232 Uncharacterized conserved protein [Function unknown]; Region: LemA; COG1704 349215006233 Peptidase family M48; Region: Peptidase_M48; cl12018 349215006234 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 349215006235 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 349215006236 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 349215006237 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 349215006238 active site 349215006239 phosphorylation site [posttranslational modification] 349215006240 intermolecular recognition site; other site 349215006241 dimerization interface [polypeptide binding]; other site 349215006242 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 349215006243 Walker A motif; other site 349215006244 ATP binding site [chemical binding]; other site 349215006245 Walker B motif; other site 349215006246 arginine finger; other site 349215006247 Bacterial regulatory protein, Fis family; Region: HTH_8; pfam02954 349215006248 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 349215006249 trimer interface [polypeptide binding]; other site 349215006250 active site 349215006251 A bacterial subgroup of the C-type lectin-like (CTLD) domain; a subgroup of bacterial protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins; Region: CLECT_VCBS; cd03603 349215006252 ligand binding surface [chemical binding]; other site 349215006253 Concanavalin A-like lectin/glucanases superfamily; Region: Laminin_G_3; pfam13385 349215006254 Domain of unknown function (DUF4402); Region: DUF4402; pfam14352 349215006255 Entericidin EcnA/B family; Region: Entericidin; cl02322 349215006256 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 349215006257 O-Antigen ligase; Region: Wzy_C; pfam04932 349215006258 SseB protein; Region: SseB; cl06279 349215006259 Indoleamine 2,3-dioxygenase; Region: IDO; pfam01231 349215006260 Membrane-bound lytic murein transglycosylase [Cell envelope biogenesis, outer membrane]; Region: MltA; COG2821 349215006261 MltA specific insert domain; Region: MltA; smart00925 349215006262 3D domain; Region: 3D; pfam06725 349215006263 Tim44-like domain; Region: Tim44; pfam04280 349215006264 FxsA cytoplasmic membrane protein; Region: FxsA; pfam04186 349215006265 Preprotein translocase subunit SecB. SecB is a cytoplasmic component of the multisubunit membrane-bound enzyme termed Sec protein translocase, which is the main constituent of the General Secretory (type II) Pathway involved in translocation of nascent...; Region: Translocase_SecB; cl00251 349215006266 SecA binding site; other site 349215006267 Preprotein binding site; other site 349215006268 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 349215006269 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 349215006270 Walker A motif; other site 349215006271 ATP binding site [chemical binding]; other site 349215006272 Walker B motif; other site 349215006273 arginine finger; other site 349215006274 Peptidase family M41; Region: Peptidase_M41; pfam01434 349215006275 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 349215006276 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 349215006277 Walker A motif; other site 349215006278 ATP binding site [chemical binding]; other site 349215006279 Walker B motif; other site 349215006280 arginine finger; other site 349215006281 Peptidase family M41; Region: Peptidase_M41; pfam01434 349215006282 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 349215006283 DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins; Region: DNA_pol_III_epsilon_Ecoli_like; cd06131 349215006284 active site 349215006285 catalytic site [active] 349215006286 substrate binding site [chemical binding]; other site 349215006287 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_1; cd01741 349215006288 GMP synthase - Glutamine amidotransferase domain [Nucleotide transport and metabolism]; Region: GuaA; COG0518 349215006289 catalytic triad [active] 349215006290 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 349215006291 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 349215006292 CoA-binding site [chemical binding]; other site 349215006293 ATP-binding [chemical binding]; other site 349215006294 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 349215006295 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 349215006296 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 349215006297 shikimate binding site; other site 349215006298 NAD(P) binding site [chemical binding]; other site 349215006299 PEP synthetase regulatory protein; Provisional; Region: PRK05339