-- dump date 20140619_112618 -- class Genbank::misc_feature -- table misc_feature_note -- id note 85962000001 Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus...; Region: Terminator_NusB; cd00619 85962000002 putative RNA binding site [nucleotide binding]; other site 85962000003 lumazine synthase (6,7-dimethyl-8-ribityllumazine synthase, LS), catalyzes the penultimate step in the biosynthesis of riboflavin (vitamin B2); type-I; Region: Lumazine_synthase-I; cd09209 85962000004 homopentamer interface [polypeptide binding]; other site 85962000005 active site 85962000006 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 85962000007 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 85962000008 active site clefts [active] 85962000009 zinc binding site [ion binding]; other site 85962000010 dimer interface [polypeptide binding]; other site 85962000011 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 85962000012 active site 85962000013 dimer interface [polypeptide binding]; other site 85962000014 Pantoate-beta-alanine ligase; Region: PanC; cd00560 85962000015 active site 85962000016 ATP-binding site [chemical binding]; other site 85962000017 pantoate-binding site; other site 85962000018 HXXH motif; other site 85962000019 similar to hypothetical protein; hypothetical protein; identified by GeneMark 85962000020 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962000021 chaperonin GroEL; Reviewed; Region: groEL; PRK12850 85962000022 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 85962000023 ring oligomerisation interface [polypeptide binding]; other site 85962000024 ATP/Mg binding site [chemical binding]; other site 85962000025 stacking interactions; other site 85962000026 hinge regions; other site 85962000027 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 85962000028 oligomerisation interface [polypeptide binding]; other site 85962000029 mobile loop; other site 85962000030 roof hairpin; other site 85962000031 DNA primase; Validated; Region: dnaG; PRK05667 85962000032 CHC2 zinc finger; Region: zf-CHC2; pfam01807 85962000033 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 85962000034 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 85962000035 active site 85962000036 metal binding site [ion binding]; metal-binding site 85962000037 interdomain interaction site; other site 85962000038 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 85962000039 ThiI is required for thiazole synthesis in the thiamine biosynthesis pathway. It belongs to the Adenosine Nucleotide Hydrolysis suoerfamily and predicted to bind to Adenosine nucleotide; Region: ThiI; cd01712 85962000040 Ligand Binding Site [chemical binding]; other site 85962000041 TrbC/VIRB2 family; Region: TrbC; pfam04956 85962000042 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 85962000043 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 85962000044 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 85962000045 Walker A motif; other site 85962000046 ATP binding site [chemical binding]; other site 85962000047 Walker B motif; other site 85962000048 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3014 85962000049 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cd00588 85962000050 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 85962000051 active site 85962000052 phosphorylation site [posttranslational modification] 85962000053 intermolecular recognition site; other site 85962000054 dimerization interface [polypeptide binding]; other site 85962000055 carboxynorspermidine decarboxylase; Region: nspC; TIGR01047 85962000056 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Carboxynorspermidine Decarboxylase; Region: PLPDE_III_CANSDC; cd06829 85962000057 dimer interface [polypeptide binding]; other site 85962000058 active site 85962000059 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 85962000060 catalytic residues [active] 85962000061 substrate binding site [chemical binding]; other site 85962000062 lipid A 1-phosphatase; Reviewed; Region: PRK09597 85962000063 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 85962000064 active site 85962000065 lipid A phosphoethanolamine transferase; Reviewed; Region: PRK09598 85962000066 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 85962000067 Sulfatase; Region: Sulfatase; pfam00884 85962000068 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962000069 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 85962000070 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 85962000071 dimer interface [polypeptide binding]; other site 85962000072 active site 85962000073 citrylCoA binding site [chemical binding]; other site 85962000074 NADH binding [chemical binding]; other site 85962000075 cationic pore residues; other site 85962000076 oxalacetate/citrate binding site [chemical binding]; other site 85962000077 coenzyme A binding site [chemical binding]; other site 85962000078 catalytic triad [active] 85962000079 isocitrate dehydrogenase, NADP-dependent, prokaryotic type; Region: prok_nadp_idh; TIGR00183 85962000080 Protein of unknown function (DUF1523); Region: DUF1523; pfam07509 85962000081 Dethiobiotin synthetase [Coenzyme metabolism]; Region: BioD; COG0132 85962000082 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 85962000083 Ligand Binding Site [chemical binding]; other site 85962000084 Uncharacterized conserved protein [Function unknown]; Region: COG2127 85962000085 ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]; Region: clpA; COG0542 85962000086 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 85962000087 Walker A motif; other site 85962000088 ATP binding site [chemical binding]; other site 85962000089 Walker B motif; other site 85962000090 arginine finger; other site 85962000091 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 85962000092 Walker A motif; other site 85962000093 ATP binding site [chemical binding]; other site 85962000094 Walker B motif; other site 85962000095 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 85962000096 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 85962000097 tetramerization interface [polypeptide binding]; other site 85962000098 active site 85962000099 hypothetical protein; Provisional; Region: PRK03762 85962000100 PDZ domain; Region: PDZ_2; pfam13180 85962000101 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 85962000102 Type IV secretory pathway, TrbL components [Intracellular trafficking and secretion]; Region: TrbL; COG3846 85962000103 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 85962000104 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 85962000105 VirB7 interaction site; other site 85962000106 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 85962000107 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 85962000108 Substrate binding site; other site 85962000109 Mannose-6-phosphate isomerase; Region: MannoseP_isomer; pfam01050 85962000110 GDP-mannose 4,6-dehydratase; Region: gmd; TIGR01472 85962000111 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 85962000112 NADP-binding site; other site 85962000113 homotetramer interface [polypeptide binding]; other site 85962000114 substrate binding site [chemical binding]; other site 85962000115 homodimer interface [polypeptide binding]; other site 85962000116 active site 85962000117 GDP-fucose synthetase, extended (e) SDRs; Region: GDP_FS_SDR_e; cd05239 85962000118 GDP-4-keto-6-deoxymannose-3, 5-epimerase-4-reductase; Region: PLN02725 85962000119 NADP binding site [chemical binding]; other site 85962000120 active site 85962000121 putative substrate binding site [chemical binding]; other site 85962000122 HypE (Hydrogenase expression/formation protein). HypE is involved in Ni-Fe hydrogenase biosynthesis. HypE dehydrates its own carbamoyl moiety in an ATP-dependent process to yield the enzyme thiocyanate. The N-terminal domain of HypE is related to the...; Region: HypE; cd02197 85962000123 dimerization interface [polypeptide binding]; other site 85962000124 hydrogenase expression/formation protein HypE; Region: hypE; TIGR02124 85962000125 ATP binding site [chemical binding]; other site 85962000126 Acylphosphatase; Region: Acylphosphatase; pfam00708 85962000127 [NiFe] hydrogenase maturation protein HypF; Region: hypF; TIGR00143 85962000128 HypF finger; Region: zf-HYPF; pfam07503 85962000129 HypF finger; Region: zf-HYPF; pfam07503 85962000130 Telomere recombination; Region: Sua5_yciO_yrdC; pfam01300 85962000131 Peptidylarginine deiminase and related enzymes [Amino acid transport and metabolism]; Region: COG2957 85962000132 DNA methylase; Region: N6_N4_Mtase; pfam01555 85962000133 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 85962000134 cofactor binding site; other site 85962000135 DNA binding site [nucleotide binding] 85962000136 substrate interaction site [chemical binding]; other site 85962000137 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 85962000138 cofactor binding site; other site 85962000139 DNA binding site [nucleotide binding] 85962000140 substrate interaction site [chemical binding]; other site 85962000141 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0827 85962000142 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 85962000143 S-adenosylmethionine binding site [chemical binding]; other site 85962000144 Eco57I restriction-modification methylase; Region: Eco57I; pfam07669 85962000145 Na(+)/proline cotransporter PutP and related proteins; solute binding domain; Region: SLC5sbd_PutP; cd11475 85962000146 Na binding site [ion binding]; other site 85962000147 Proline dehydrogenase [Amino acid transport and metabolism]; Region: PutA; COG0506 85962000148 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4399; cl19827 85962000149 Proline dehydrogenase; Region: Pro_dh; pfam01619 85962000150 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 85962000151 Glutamate binding site [chemical binding]; other site 85962000152 NAD binding site [chemical binding]; other site 85962000153 catalytic residues [active] 85962000154 hypothetical protein; Provisional; Region: PRK04081 85962000155 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 85962000156 Molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: DnaK; COG0443 85962000157 Proteins of 100 residues with WXG; Region: WXG100; cl02005 85962000158 STIM1 Orai1-activating region; Region: SOAR; cd11722 85962000159 DNase/tRNase domain of colicin-like bacteriocin; Region: Colicin-DNase; cl15861 85962000160 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; pfam09346 85962000161 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 85962000162 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 85962000163 Urease accessory protein UreH [Posttranslational modification, protein turnover, chaperones]; Region: UreH; COG0829 85962000164 GTPase SAR1 and related small G proteins [General function prediction only]; Region: COG1100 85962000165 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cd00882 85962000166 G1 box; other site 85962000167 GTP/Mg2+ binding site [chemical binding]; other site 85962000168 G2 box; other site 85962000169 Switch I region; other site 85962000170 G3 box; other site 85962000171 Switch II region; other site 85962000172 G4 box; other site 85962000173 G5 box; other site 85962000174 Urease accessory protein UreF [Posttranslational modification, protein turnover, chaperones]; Region: UreF; COG0830 85962000175 Urease accessory protein UreE [Posttranslational modification, protein turnover, chaperones]; Region: UreE; COG2371 85962000176 UreE urease accessory protein. UreE is a metallochaperone assisting the insertion of a Ni2+ ion in the active site of urease, an important step in the in vivo assembly of urease, an enzyme that hydrolyses urea into ammonia and carbamic acid. The...; Region: UreE; cd00571 85962000177 dimer interface [polypeptide binding]; other site 85962000178 catalytic residues [active] 85962000179 UreI/AmiS family, proton-gated urea channel and putative amide transporters; Region: UreI_AmiS_like; cd13404 85962000180 hexamer interface [polypeptide binding]; other site 85962000181 transport channel [chemical binding]; other site 85962000182 constriction site 1 [chemical binding]; other site 85962000183 constriction site 2 [chemical binding]; other site 85962000184 urease subunit beta; Provisional; Region: ureB; PRK13985 85962000185 Urease alpha-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, fungi and plants. Their primary role is to allow the use of...; Region: Urease_alpha; cd00375 85962000186 subunit interactions [polypeptide binding]; other site 85962000187 active site 85962000188 flap region; other site 85962000189 urease subunit alpha; Provisional; Region: PRK13986 85962000190 Urease gamma-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use...; Region: Urease_gamma; cd00390 85962000191 alpha-gamma subunit interface [polypeptide binding]; other site 85962000192 beta-gamma subunit interface [polypeptide binding]; other site 85962000193 Urease beta-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use of...; Region: Urease_beta; cd00407 85962000194 gamma-beta subunit interface [polypeptide binding]; other site 85962000195 alpha-beta subunit interface [polypeptide binding]; other site 85962000196 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 85962000197 phosphoglucosamine mutase; Provisional; Region: glmM; PRK14324 85962000198 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 85962000199 active site 85962000200 substrate binding site [chemical binding]; other site 85962000201 metal binding site [ion binding]; metal-binding site 85962000202 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 85962000203 peptide chain release factor 1; Validated; Region: prfA; PRK00591 85962000204 This domain is found in peptide chain release factors; Region: PCRF; smart00937 85962000205 RF-1 domain; Region: RF-1; pfam00472 85962000206 PPE-repeat proteins [Cell motility and secretion]; Region: COG5651 85962000207 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962000208 Der GTPase activator (YihI); Region: YihI; cl01172 85962000209 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cl19050 85962000210 dimer interface [polypeptide binding]; other site 85962000211 putative CheW interface [polypeptide binding]; other site 85962000212 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 85962000213 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 85962000214 23S rRNA interface [nucleotide binding]; other site 85962000215 L3 interface [polypeptide binding]; other site 85962000216 Cytochrome c oxidase subunit VIa. 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_VIa; cl00017 85962000217 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl17341 85962000218 Predicted dehydrogenase [General function prediction only]; Region: COG0579 85962000219 NLPC_P60 stabilizing domain, N term; Region: N_NLPC_P60; pfam12912 85962000220 SH3 domain of the SH3b1 type; Region: SH3_6; pfam12913 85962000221 SH3 domain of SH3b2 type; Region: SH3_7; pfam12914 85962000222 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 85962000223 NlpC/P60 family; Region: NLPC_P60; pfam00877 85962000224 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 85962000225 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 85962000226 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 85962000227 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 85962000228 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 85962000229 DNA binding residues [nucleotide binding] 85962000230 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Validated; Region: PRK05584 85962000231 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 85962000232 DpnII restriction endonuclease; Region: DpnII; pfam04556 85962000233 Methyltransferase domain; Region: Methyltransf_26; pfam13659 85962000234 DNA methylase; Region: N6_N4_Mtase; pfam01555 85962000235 2-hydroxyacid dehydrogenase; Provisional; Region: PRK08410 85962000236 Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; Region: FDH_GDH_like; cl17240 85962000237 NAD binding site [chemical binding]; other site 85962000238 threonine synthase; Validated; Region: PRK09225 85962000239 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 85962000240 pyridoxal 5'-phosphate binding site [chemical binding]; other site 85962000241 catalytic residue [active] 85962000242 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 85962000243 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cl19050 85962000244 dimer interface [polypeptide binding]; other site 85962000245 putative CheW interface [polypeptide binding]; other site 85962000246 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases and ATP sulphurylases. The domain forms a apha/beta/apha fold which binds to Adenosine group; Region: Alpha_ANH_like; cd01986 85962000247 Ligand Binding Site [chemical binding]; other site 85962000248 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962000249 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 85962000250 WfgS and WfeV are involved in O-antigen biosynthesis; Region: GT_2_WfgS_like; cd06433 85962000251 metal-binding site 85962000252 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 85962000253 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 85962000254 dimerization interface [polypeptide binding]; other site 85962000255 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 85962000256 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cl19050 85962000257 dimer interface [polypeptide binding]; other site 85962000258 putative CheW interface [polypeptide binding]; other site 85962000259 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases [Nucleotide transport and metabolism]; Region: UshA; COG0737 85962000260 Escherichia coli CpdB and related proteins, N-terminal metallophosphatase domain; Region: MPP_CpdB_N; cd07410 85962000261 active site 85962000262 metal binding site [ion binding]; metal-binding site 85962000263 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 85962000264 S-ribosylhomocysteinase; Provisional; Region: PRK02260 85962000265 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 85962000266 homodimer interface [polypeptide binding]; other site 85962000267 substrate-cofactor binding pocket; other site 85962000268 pyridoxal 5'-phosphate binding site [chemical binding]; other site 85962000269 catalytic residue [active] 85962000270 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 85962000271 dimer interface [polypeptide binding]; other site 85962000272 pyridoxal 5'-phosphate binding site [chemical binding]; other site 85962000273 catalytic residue [active] 85962000274 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 85962000275 Nucleotide-binding domain of human HSPA9 and similar proteins; Region: HSPA9-Ssq1-like_NBD; cd10234 85962000276 nucleotide binding site [chemical binding]; other site 85962000277 NEF interaction site [polypeptide binding]; other site 85962000278 SBD interface [polypeptide binding]; other site 85962000279 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 85962000280 dimer interface [polypeptide binding]; other site 85962000281 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 85962000282 heat-inducible transcription repressor; Provisional; Region: PRK03911 85962000283 hypothetical protein; Provisional; Region: PRK05834 85962000284 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2604 85962000285 flagellin B; Provisional; Region: PRK13588 85962000286 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 85962000287 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 85962000288 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 85962000289 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 85962000290 DNA topoisomerase I; Validated; Region: PRK05582 85962000291 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 85962000292 active site 85962000293 interdomain interaction site; other site 85962000294 putative metal-binding site [ion binding]; other site 85962000295 nucleotide binding site [chemical binding]; other site 85962000296 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 85962000297 domain I; other site 85962000298 DNA binding groove [nucleotide binding] 85962000299 phosphate binding site [ion binding]; other site 85962000300 domain II; other site 85962000301 domain III; other site 85962000302 nucleotide binding site [chemical binding]; other site 85962000303 catalytic site [active] 85962000304 domain IV; other site 85962000305 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 85962000306 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 85962000307 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 85962000308 Fe-S oxidoreductases [Energy production and conversion]; Region: COG0731 85962000309 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 85962000310 FeS/SAM binding site; other site 85962000311 Helicobacter pylori protein of unknown function (DUF874); Region: DUF874; pfam05917 85962000312 Helicobacter pylori protein of unknown function (DUF874); Region: DUF874; pfam05917 85962000313 Helicobacter pylori protein of unknown function (DUF874); Region: DUF874; pfam05917 85962000314 Protein gp23 (Bacteriophage A118); Region: Phage_Gp23; pfam10669 85962000315 phosphoenolpyruvate synthase; Validated; Region: PRK06464 85962000316 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 85962000317 PEP-utilizing enzyme, mobile domain; Region: PEP-utilizers; pfam00391 85962000318 PEP-utilizing enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 85962000319 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK12305 85962000320 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; pfam07973 85962000321 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 85962000322 active site 85962000323 dimer interface [polypeptide binding]; other site 85962000324 motif 1; other site 85962000325 motif 2; other site 85962000326 motif 3; other site 85962000327 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 85962000328 anticodon binding site; other site 85962000329 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 85962000330 translation initiation factor IF-3; Region: infC; TIGR00168 85962000331 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 85962000332 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 85962000333 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 85962000334 23S rRNA binding site [nucleotide binding]; other site 85962000335 L21 binding site [polypeptide binding]; other site 85962000336 L13 binding site [polypeptide binding]; other site 85962000337 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962000338 Protein of unknown function (DUF1104); Region: DUF1104; pfam06518 85962000339 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 85962000340 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 85962000341 Serine dehydratase alpha chain; Region: SDH_alpha; pfam03313 85962000342 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 85962000343 serine transporter; Region: stp; TIGR00814 85962000344 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase [Amino acid transport and metabolism]; Region: AroG; COG3200 85962000345 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 85962000346 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 85962000347 catalytic triad [active] 85962000348 Uncharacterized conserved protein [Function unknown]; Region: COG1556 85962000349 iron-sulfur cluster-binding protein; Region: TIGR00273 85962000350 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 85962000351 4Fe-4S dicluster domain; Region: Fer4_8; pfam13183 85962000352 Domain of unknown function (DUF3390); Region: DUF3390; pfam11870 85962000353 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 85962000354 Cysteine-rich domain; Region: CCG; pfam02754 85962000355 Cysteine-rich domain; Region: CCG; pfam02754 85962000356 L-lactate transport; Region: lctP; TIGR00795 85962000357 L-lactate transport; Region: lctP; TIGR00795 85962000358 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 85962000359 DNA glycosylase MutY; Provisional; Region: PRK13910 85962000360 minor groove reading motif; other site 85962000361 helix-hairpin-helix signature motif; other site 85962000362 substrate binding pocket [chemical binding]; other site 85962000363 active site 85962000364 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cl00447 85962000365 cbb3-type cytochrome c oxidase subunit I; Provisional; Region: PRK14488 85962000366 Low-spin heme binding site [chemical binding]; other site 85962000367 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 85962000368 D-pathway; other site 85962000369 Putative water exit pathway; other site 85962000370 Binuclear center (active site) [active] 85962000371 K-pathway; other site 85962000372 Putative proton exit pathway; other site 85962000373 cytochrome c oxidase, cbb3-type, subunit II; Region: ccoO; TIGR00781 85962000374 cytochrome c oxidase, cbb3-type, CcoQ subunit, epsilon-Proteobacterial; Region: cbb3_Q_epsi; TIGR02736 85962000375 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 85962000376 N-terminal domain of cytochrome oxidase-cbb3, FixP; Region: FixP_N; pfam14715 85962000377 Cytochrome c; Region: Cytochrom_C; pfam00034 85962000378 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 85962000379 Family of unknown function (DUF4006); Region: DUF4006; pfam13179 85962000380 Predicted periplasmic solute-binding protein [General function prediction only]; Region: COG2107 85962000381 recombinase A; Provisional; Region: recA; PRK09354 85962000382 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 85962000383 hexamer interface [polypeptide binding]; other site 85962000384 Walker A motif; other site 85962000385 ATP binding site [chemical binding]; other site 85962000386 Walker B motif; other site 85962000387 enolase; Provisional; Region: eno; PRK00077 85962000388 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 85962000389 dimer interface [polypeptide binding]; other site 85962000390 metal binding site [ion binding]; metal-binding site 85962000391 substrate binding pocket [chemical binding]; other site 85962000392 AMIN domain; Region: AMIN; pfam11741 85962000393 Shikimate kinase [Amino acid transport and metabolism]; Region: AroK; COG0703 85962000394 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 85962000395 ADP binding site [chemical binding]; other site 85962000396 magnesium binding site [ion binding]; other site 85962000397 putative shikimate binding site; other site 85962000398 Cache domain; Region: Cache_1; pfam02743 85962000399 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 85962000400 A4GalT_like proteins catalyze the addition of galactose or glucose residues to the lipooligosaccharide (LOS) or lipopolysaccharide (LPS) of the bacterial cell surface; Region: GT8_A4GalT_like; cd04194 85962000401 Ligand binding site; other site 85962000402 metal-binding site 85962000403 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 85962000404 Sel1-like repeats; Region: SEL1; smart00671 85962000405 Sel1-like repeats; Region: SEL1; smart00671 85962000406 Sel1-like repeats; Region: SEL1; smart00671 85962000407 Sel1-like repeats; Region: SEL1; smart00671 85962000408 Sel1-like repeats; Region: SEL1; smart00671 85962000409 Sel1-like repeats; Region: SEL1; smart00671 85962000410 hypothetical protein; Provisional; Region: PRK12378 85962000411 Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the...; Region: ALAD_PBGS; cd00384 85962000412 dimer interface [polypeptide binding]; other site 85962000413 active site 85962000414 Schiff base residues; other site 85962000415 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 85962000416 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 85962000417 active site 85962000418 dimerization interface [polypeptide binding]; other site 85962000419 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 85962000420 DNA binding site [nucleotide binding] 85962000421 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 85962000422 peptide chain release factor 2; Region: prfB; TIGR00020 85962000423 This domain is found in peptide chain release factors; Region: PCRF; smart00937 85962000424 RF-1 domain; Region: RF-1; pfam00472 85962000425 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 85962000426 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 85962000427 dimer interface [polypeptide binding]; other site 85962000428 putative functional site; other site 85962000429 putative MPT binding site; other site 85962000430 Flagellar biosynthesis pathway, component FliR [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FliR; COG1684 85962000431 Etoposide-induced protein 2.4 (EI24); Region: EI24; pfam07264 85962000432 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 85962000433 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 85962000434 Tagatose-1,6-bisphosphate (TBP) aldolase and related Type B Class II aldolases. TBP aldolase is a tetrameric class II aldolase that catalyzes the reversible condensation of dihydroxyacetone phosphate with glyceraldehyde 3-phsophate to produce tagatose 1; Region: TBP_aldolase_IIB; cd00947 85962000435 intersubunit interface [polypeptide binding]; other site 85962000436 active site 85962000437 zinc binding site [ion binding]; other site 85962000438 Na+ binding site [ion binding]; other site 85962000439 elongation factor P; Validated; Region: PRK00529 85962000440 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 85962000441 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 85962000442 RNA binding site [nucleotide binding]; other site 85962000443 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 85962000444 RNA binding site [nucleotide binding]; other site 85962000445 pseudaminic acid synthase; Region: PseI; TIGR03586 85962000446 NeuB family; Region: NeuB; pfam03102 85962000447 C-terminal SAF domain of sialic acid synthetase; Region: SAF_NeuB_like; cd11615 85962000448 NeuB binding interface [polypeptide binding]; other site 85962000449 putative substrate binding site [chemical binding]; other site 85962000450 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 85962000451 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 85962000452 Walker A/P-loop; other site 85962000453 ATP binding site [chemical binding]; other site 85962000454 Q-loop/lid; other site 85962000455 ABC transporter signature motif; other site 85962000456 Walker B; other site 85962000457 D-loop; other site 85962000458 H-loop/switch region; other site 85962000459 apolipoprotein N-acyltransferase; Reviewed; Region: PRK12291 85962000460 apolipoprotein N-acyltransferase; Region: lnt; TIGR00546 85962000461 active site 85962000462 catalytic triad [active] 85962000463 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 85962000464 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 85962000465 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 85962000466 dimer interface [polypeptide binding]; other site 85962000467 putative anticodon binding site; other site 85962000468 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 85962000469 motif 1; other site 85962000470 active site 85962000471 motif 2; other site 85962000472 motif 3; other site 85962000473 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 85962000474 dimer interface [polypeptide binding]; other site 85962000475 active site 85962000476 glycine-pyridoxal phosphate binding site [chemical binding]; other site 85962000477 folate binding site [chemical binding]; other site 85962000478 AE_Prim_S_like: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases. The replication machineries of A/Es are distinct from that of bacteria. Primases are DNA-dependent RNA polymerases which synthesis...; Region: AE_Prim_S_like; cd00525 85962000479 nucleotide binding site [chemical binding]; other site 85962000480 Eukaryotic and archaeal DNA primase small subunit; Region: DNA_primase_S; pfam01896 85962000481 Cell division protein [Cell division and chromosome partitioning]; Region: FtsN; COG3087 85962000482 Sporulation related domain; Region: SPOR; pfam05036 85962000483 Uncharacterized conserved protein [Function unknown]; Region: COG1479 85962000484 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 85962000485 TIGR00645 family protein; Region: HI0507 85962000486 Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_1; cd09111 85962000487 PLD-like domain; Region: PLDc_2; pfam13091 85962000488 putative active site [active] 85962000489 catalytic site [active] 85962000490 Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_2; cd09113 85962000491 PLD-like domain; Region: PLDc_2; pfam13091 85962000492 putative active site [active] 85962000493 catalytic site [active] 85962000494 fumarate reductase iron-sulfur subunit; Provisional; Region: frdB; PRK13552 85962000495 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 85962000496 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 85962000497 catalytic loop [active] 85962000498 iron binding site [ion binding]; other site 85962000499 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl19102 85962000500 fumarate reductase flavoprotein subunit; Provisional; Region: PRK08626 85962000501 L-aspartate oxidase; Provisional; Region: PRK06175 85962000502 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 85962000503 fumarate reductase cytochrome b-556 subunit; Provisional; Region: PRK13553 85962000504 Quinol:fumarate reductase (QFR) Type B subfamily, transmembrane subunit; QFR couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, the opposite reaction to that catalyzed by the related protein, succinate:quinone...; Region: QFR_TypeB_TM; cd00581 85962000505 Iron-sulfur protein interface; other site 85962000506 proximal heme binding site [chemical binding]; other site 85962000507 distal heme binding site [chemical binding]; other site 85962000508 dimer interface [polypeptide binding]; other site 85962000509 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 85962000510 substrate binding site [chemical binding]; other site 85962000511 dimer interface [polypeptide binding]; other site 85962000512 catalytic triad [active] 85962000513 Enoyl-[acyl-carrier-protein]; Region: FabI; COG0623 85962000514 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 85962000515 NAD binding site [chemical binding]; other site 85962000516 homotetramer interface [polypeptide binding]; other site 85962000517 homodimer interface [polypeptide binding]; other site 85962000518 substrate binding site [chemical binding]; other site 85962000519 active site 85962000520 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Region: lipid_A_lpxD; TIGR01853 85962000521 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 85962000522 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 85962000523 trimer interface [polypeptide binding]; other site 85962000524 active site 85962000525 UDP-GlcNAc binding site [chemical binding]; other site 85962000526 lipid binding site [chemical binding]; lipid-binding site 85962000527 S-adenosylmethionine synthetase; Validated; Region: PRK05250 85962000528 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 85962000529 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 85962000530 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 85962000531 Nucleoside diphosphate kinase; Region: NDK; pfam00334 85962000532 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 85962000533 active site 85962000534 multimer interface [polypeptide binding]; other site 85962000535 Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]; Region: RpmF; COG0333 85962000536 fatty acid/phospholipid synthesis protein PlsX; Region: plsX; TIGR00182 85962000537 3-oxoacyl-(acyl-carrier-protein) synthase III; Region: fabH; TIGR00747 85962000538 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 85962000539 dimer interface [polypeptide binding]; other site 85962000540 active site 85962000541 CoA binding pocket [chemical binding]; other site 85962000542 Hepatic lectin, N-terminal domain; Region: Lectin_N; pfam03954 85962000543 AAA ATPase domain; Region: AAA_15; pfam13175 85962000544 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cd00267 85962000545 Walker B; other site 85962000546 D-loop; other site 85962000547 H-loop/switch region; other site 85962000548 antiporter inner membrane protein; Provisional; Region: PRK11670 85962000549 Domain of unknown function DUF59; Region: DUF59; pfam01883 85962000550 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 85962000551 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 85962000552 Walker A motif; other site 85962000553 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 85962000554 Glycosyl transferase family 8; Region: Glyco_transf_8; pfam01501 85962000555 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 85962000556 heat shock protein 90; Provisional; Region: PRK05218 85962000557 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 85962000558 ATP binding site [chemical binding]; other site 85962000559 Mg2+ binding site [ion binding]; other site 85962000560 G-X-G motif; other site 85962000561 Hsp90 protein; Region: HSP90; pfam00183 85962000562 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 85962000563 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 85962000564 binding surface 85962000565 TPR motif; other site 85962000566 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 85962000567 TPR motif; other site 85962000568 binding surface 85962000569 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 85962000570 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 85962000571 metal binding site [ion binding]; metal-binding site 85962000572 dimer interface [polypeptide binding]; other site 85962000573 glucose-inhibited division protein A; Region: gidA; TIGR00136 85962000574 tRNA:m(5)U-54 methyltransferase; Region: gid_trmFO; TIGR00137 85962000575 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 85962000576 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 85962000577 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 85962000578 Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is...; Region: SLC13_permease; cd01115 85962000579 transmembrane helices; other site 85962000580 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 85962000581 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: Dxr; TIGR00243 85962000582 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 85962000583 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 85962000584 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 85962000585 Beta-1,4-N-acetylgalactosaminyltransferase (CgtA); Region: CgtA; pfam06306 85962000586 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 85962000587 substrate binding site [chemical binding]; other site 85962000588 Helix-turn-helix domain; Region: HTH_28; pfam13518 85962000589 cysteine desulfurase, NifS family, epsilon proteobacteria type; Region: nifS_epsilon; TIGR03403 85962000590 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 85962000591 catalytic residue [active] 85962000592 Fe-S cluster assembly protein NifU; Region: NifU_proper; TIGR02000 85962000593 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 85962000594 trimerization site [polypeptide binding]; other site 85962000595 active site 85962000596 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 85962000597 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 85962000598 DNA repair protein RadA; Region: sms; TIGR00416 85962000599 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 85962000600 Walker A motif/ATP binding site; other site 85962000601 ATP binding site [chemical binding]; other site 85962000602 Walker B motif; other site 85962000603 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 85962000604 Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: MsrA; COG0225 85962000605 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: COG0229 85962000606 Predicted permeases [General function prediction only]; Region: COG0730 85962000607 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962000608 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 85962000609 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 85962000610 Sulfate transporter family; Region: Sulfate_transp; pfam00916 85962000611 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962000612 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 85962000613 Ligand binding site; other site 85962000614 oligomer interface; other site 85962000615 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 85962000616 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 85962000617 hypothetical protein; Provisional; Region: PRK04081 85962000618 Glutathionylspermidine synthase [Amino acid transport and metabolism]; Region: Gsp; COG0754 85962000619 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 85962000620 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 85962000621 binding surface 85962000622 TPR motif; other site 85962000623 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 85962000624 binding surface 85962000625 TPR motif; other site 85962000626 Sel1-like repeats; Region: SEL1; smart00671 85962000627 Sel1-like repeats; Region: SEL1; smart00671 85962000628 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 85962000629 Porphobilinogen deaminase [Coenzyme metabolism]; Region: HemC; COG0181 85962000630 Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12. HMBS catalyzes the conversion of...; Region: HMBS; cd00494 85962000631 domain interfaces; other site 85962000632 active site 85962000633 prolyl-tRNA synthetase, family II; Region: proS_fam_II; TIGR00409 85962000634 Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: ProRS_core_prok; cd00779 85962000635 dimer interface [polypeptide binding]; other site 85962000636 motif 1; other site 85962000637 active site 85962000638 motif 2; other site 85962000639 INS is an amino acid-editing domain inserted (INS) into the bacterial class II prolyl-tRNA synthetase (ProRS) however, this CD is not exclusively bacterial. It is also found at the N-terminus of the eukaryotic/archaea-like ProRS's of yeasts and...; Region: ProRS-INS; cd04334 85962000640 putative deacylase active site [active] 85962000641 motif 3; other site 85962000642 ProRS Prolyl-anticodon binding domain, short version found predominantly in bacteria. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding; Region: ProRS_anticodon_short; cd00861 85962000643 anticodon binding site; other site 85962000644 glutamyl-tRNA reductase; Region: hemA; TIGR01035 85962000645 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 85962000646 tRNA; other site 85962000647 putative tRNA binding site [nucleotide binding]; other site 85962000648 putative NADP binding site [chemical binding]; other site 85962000649 Glutamyl-tRNAGlu reductase, dimerization domain; Region: GlutR_dimer; pfam00745 85962000650 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 85962000651 substrate binding pocket [chemical binding]; other site 85962000652 chain length determination region; other site 85962000653 substrate-Mg2+ binding site; other site 85962000654 catalytic residues [active] 85962000655 aspartate-rich region 1; other site 85962000656 active site lid residues [active] 85962000657 aspartate-rich region 2; other site 85962000658 Domain of unknown function (DUF2018); Region: DUF2018; pfam09442 85962000659 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 85962000660 Ferritin-like domain; Region: Ferritin; pfam00210 85962000661 dimerization interface [polypeptide binding]; other site 85962000662 DPS ferroxidase diiron center [ion binding]; other site 85962000663 ion pore; other site 85962000664 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 85962000665 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 85962000666 dimer interface [polypeptide binding]; other site 85962000667 phosphorylation site [posttranslational modification] 85962000668 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 85962000669 ATP binding site [chemical binding]; other site 85962000670 Mg2+ binding site [ion binding]; other site 85962000671 G-X-G motif; other site 85962000672 flagellar rod assembly protein/muramidase FlgJ; Region: flagell_FlgJ; TIGR02541 85962000673 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 85962000674 Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]; Region: SrmB; COG0513 85962000675 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 85962000676 ATP binding site [chemical binding]; other site 85962000677 Mg++ binding site [ion binding]; other site 85962000678 motif III; other site 85962000679 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 85962000680 nucleotide binding region [chemical binding]; other site 85962000681 ATP-binding site [chemical binding]; other site 85962000682 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 85962000683 Prohibitin family; SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily; Region: SPFH_prohibitin; cd03401 85962000684 Protein of unknown function (DUF2393); Region: DUF2393; pfam09624 85962000685 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 85962000686 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 85962000687 Walker A/P-loop; other site 85962000688 ATP binding site [chemical binding]; other site 85962000689 Q-loop/lid; other site 85962000690 ABC transporter signature motif; other site 85962000691 Walker B; other site 85962000692 D-loop; other site 85962000693 H-loop/switch region; other site 85962000694 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 85962000695 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 85962000696 Walker A/P-loop; other site 85962000697 ATP binding site [chemical binding]; other site 85962000698 Q-loop/lid; other site 85962000699 ABC transporter signature motif; other site 85962000700 Walker B; other site 85962000701 D-loop; other site 85962000702 H-loop/switch region; other site 85962000703 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 85962000704 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4239 85962000705 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 85962000706 dimer interface [polypeptide binding]; other site 85962000707 conserved gate region; other site 85962000708 putative PBP binding loops; other site 85962000709 ABC-ATPase subunit interface; other site 85962000710 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962000711 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962000712 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 85962000713 GDP-binding site [chemical binding]; other site 85962000714 ACT binding site; other site 85962000715 IMP binding site; other site 85962000716 Flagellar FliJ protein; Region: FliJ; pfam02050 85962000717 Uncharacterized conserved protein [Function unknown]; Region: COG3334 85962000718 RIP metalloprotease RseP; Region: TIGR00054 85962000719 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 85962000720 active site 85962000721 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 85962000722 protein binding site [polypeptide binding]; other site 85962000723 putative substrate binding region [chemical binding]; other site 85962000724 exodeoxyribonuclease VII, large subunit; Region: xseA; TIGR00237 85962000725 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 85962000726 generic binding surface II; other site 85962000727 generic binding surface I; other site 85962000728 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 85962000729 DNA methylase; Region: N6_N4_Mtase; pfam01555 85962000730 DNA methylase; Region: N6_N4_Mtase; pfam01555 85962000731 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 85962000732 Clp amino terminal domain; Region: Clp_N; pfam02861 85962000733 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 85962000734 Walker A motif; other site 85962000735 ATP binding site [chemical binding]; other site 85962000736 Walker B motif; other site 85962000737 arginine finger; other site 85962000738 Apolipophorin-III and similar insect proteins; Region: ApoLp-III_like; cl19113 85962000739 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 85962000740 Walker A motif; other site 85962000741 ATP binding site [chemical binding]; other site 85962000742 Walker B motif; other site 85962000743 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 85962000744 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; pfam02683 85962000745 Dihydroorotase and related cyclic amidohydrolases [Nucleotide transport and metabolism]; Region: PyrC; COG0044 85962000746 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 85962000747 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 85962000748 active site 85962000749 chlorohydrolase; Provisional; Region: PRK08418 85962000750 Metallo-dependent hydrolases, subgroup D is part of the superfamily of metallo-dependent hydrolases, 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...; Region: Met_dep_hydrolase_D; cd01312 85962000751 active site 85962000752 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 85962000753 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14339 85962000754 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 85962000755 FeS/SAM binding site; other site 85962000756 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: DUF374; Region: LPLAT_DUF374-like; cd07983 85962000757 putative acyl-acceptor binding pocket; other site 85962000758 Predicted Fe-S-cluster oxidoreductase [General function prediction only]; Region: COG0727 85962000759 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 85962000760 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 85962000761 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl19102 85962000762 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 85962000763 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 85962000764 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 85962000765 nucleotide binding site [chemical binding]; other site 85962000766 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 85962000767 putative active site [active] 85962000768 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 85962000769 putative acyl-acceptor binding pocket; other site 85962000770 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 85962000771 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 85962000772 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3400 85962000773 TrkA-C domain; Region: TrkA_C; pfam02080 85962000774 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 85962000775 active site 85962000776 dimer interface [polypeptide binding]; other site 85962000777 metal binding site [ion binding]; metal-binding site 85962000778 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 85962000779 Mechanosensitive ion channel; Region: MS_channel; pfam00924 85962000780 radical SAM methylthiotransferase, MiaB/RimO family; Region: TIGR00089 85962000781 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 85962000782 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 85962000783 ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]; Region: HflB; COG0465 85962000784 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 85962000785 Walker A motif; other site 85962000786 ATP binding site [chemical binding]; other site 85962000787 Walker B motif; other site 85962000788 arginine finger; other site 85962000789 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 85962000790 Domain of unknown function (DUF4149); Region: DUF4149; pfam13664 85962000791 Vacuolating cyotoxin; Region: VacA; pfam02691 85962000792 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 85962000793 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 85962000794 PPE-repeat proteins [Cell motility and secretion]; Region: COG5651 85962000795 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 85962000796 Autotransporter beta-domain; Region: Autotransporter; pfam03797 85962000797 diaminopimelate decarboxylase; Region: lysA; TIGR01048 85962000798 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 85962000799 active site 85962000800 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 85962000801 substrate binding site [chemical binding]; other site 85962000802 catalytic residues [active] 85962000803 dimer interface [polypeptide binding]; other site 85962000804 Chorismate mutase [Amino acid transport and metabolism]; Region: PheA; COG1605 85962000805 Uncharacterized conserved protein [Function unknown]; Region: COG4866 85962000806 aminodeoxychorismate synthase; Provisional; Region: PRK07508 85962000807 chorismate binding enzyme; Region: Chorismate_bind; cl10555 85962000808 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 85962000809 substrate-cofactor binding pocket; other site 85962000810 pyridoxal 5'-phosphate binding site [chemical binding]; other site 85962000811 catalytic residue [active] 85962000812 aliphatic amidases (class 2 nitrilases); Region: aliphatic_amidase; cd07565 85962000813 multimer interface [polypeptide binding]; other site 85962000814 active site 85962000815 catalytic triad [active] 85962000816 dimer interface [polypeptide binding]; other site 85962000817 flagellar hook-associated protein FlgL; Validated; Region: flgL; PRK08412 85962000818 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 85962000819 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 85962000820 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 85962000821 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 85962000822 The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; Region: PBP2_DppA_like; cd08493 85962000823 peptide binding site [polypeptide binding]; other site 85962000824 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 85962000825 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 85962000826 dimer interface [polypeptide binding]; other site 85962000827 conserved gate region; other site 85962000828 putative PBP binding loops; other site 85962000829 ABC-ATPase subunit interface; other site 85962000830 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 85962000831 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 85962000832 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 85962000833 dimer interface [polypeptide binding]; other site 85962000834 conserved gate region; other site 85962000835 putative PBP binding loops; other site 85962000836 ABC-ATPase subunit interface; other site 85962000837 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 85962000838 nickel import ATP-binding protein NikD; Region: nickel_nikD; TIGR02770 85962000839 Walker A/P-loop; other site 85962000840 ATP binding site [chemical binding]; other site 85962000841 Q-loop/lid; other site 85962000842 ABC transporter signature motif; other site 85962000843 Walker B; other site 85962000844 D-loop; other site 85962000845 H-loop/switch region; other site 85962000846 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 85962000847 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 85962000848 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 85962000849 Walker A/P-loop; other site 85962000850 ATP binding site [chemical binding]; other site 85962000851 Q-loop/lid; other site 85962000852 ABC transporter signature motif; other site 85962000853 Walker B; other site 85962000854 D-loop; other site 85962000855 H-loop/switch region; other site 85962000856 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; pfam08352 85962000857 GTPase CgtA; Reviewed; Region: obgE; PRK12299 85962000858 GTP1/OBG; Region: GTP1_OBG; pfam01018 85962000859 Obg GTPase; Region: Obg; cd01898 85962000860 G1 box; other site 85962000861 GTP/Mg2+ binding site [chemical binding]; other site 85962000862 Switch I region; other site 85962000863 G2 box; other site 85962000864 G3 box; other site 85962000865 Switch II region; other site 85962000866 G4 box; other site 85962000867 G5 box; other site 85962000868 Alginate lyase; Region: Alginate_lyase; pfam05426 85962000869 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 85962000870 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 85962000871 inhibitor-cofactor binding pocket; inhibition site 85962000872 pyridoxal 5'-phosphate binding site [chemical binding]; other site 85962000873 catalytic residue [active] 85962000874 Putative F0F1-ATPase subunit (ATPase_gene1); Region: ATPase_gene1; pfam09527 85962000875 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cd07197 85962000876 active site 85962000877 catalytic triad [active] 85962000878 dimer interface [polypeptide binding]; other site 85962000879 Catalytic domain of Helicobacter pylori peptidoglycan deacetylase (HpPgdA) and similar proteins; Region: CE4_HpPgdA_like; cd10938 85962000880 active site 85962000881 catalytic site [active] 85962000882 Zn binding site [ion binding]; other site 85962000883 tetramer interface [polypeptide binding]; other site 85962000884 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 85962000885 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 85962000886 CobW/HypB/UreG, nucleotide-binding domain; Region: cobW; pfam02492 85962000887 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; pfam07683 85962000888 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 85962000889 Major Facilitator Superfamily; Region: MFS_1; pfam07690 85962000890 putative substrate translocation pore; other site 85962000891 Uncharacterized virulence-associated protein D [Function unknown]; Region: VapD; COG3309 85962000892 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962000893 heme oxygenase, HugZ family; Region: heme_ox_HugZ; TIGR04109 85962000894 Protein of unknown function (DUF2470); Region: DUF2470; pfam10615 85962000895 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 85962000896 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; pfam03485 85962000897 arginyl-tRNA synthetase; Region: argS; TIGR00456 85962000898 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 85962000899 active site 85962000900 HIGH motif; other site 85962000901 KMSK motif region; other site 85962000902 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 85962000903 tRNA binding surface [nucleotide binding]; other site 85962000904 anticodon binding site; other site 85962000905 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 85962000906 Guanylate kinase; Region: Guanylate_kin; pfam00625 85962000907 Guanosine monophosphate kinase (GMPK, EC 2.7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine...; Region: GMPK; cd00071 85962000908 catalytic site [active] 85962000909 G-X2-G-X-G-K; other site 85962000910 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]; Region: MDN1; COG5271 85962000911 nuclease NucT; Provisional; Region: PRK13912 85962000912 Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6, and similar proteins; Region: PLDc_Nuc_like; cd09116 85962000913 putative active site [active] 85962000914 catalytic site [active] 85962000915 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962000916 flagellar basal body L-ring protein; Reviewed; Region: flgH; PRK00249 85962000917 CMP-NeuAc_Synthase activates N-acetylneuraminic acid by adding CMP moiety; Region: CMP-NeuAc_Synthase; cd02513 85962000918 ligand binding site; other site 85962000919 tetramer interface; other site 85962000920 Spore coat polysaccharide biosynthesis protein, predicted glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: spsG; COG3980 85962000921 pseudaminic acid biosynthesis N-acetyl transferase; Region: PseH; TIGR03585 85962000922 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 85962000923 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 85962000924 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 85962000925 homodimer interface [polypeptide binding]; other site 85962000926 NAD binding pocket [chemical binding]; other site 85962000927 ATP binding pocket [chemical binding]; other site 85962000928 Mg binding site [ion binding]; other site 85962000929 active-site loop [active] 85962000930 ketol-acid reductoisomerase; Provisional; Region: PRK05479 85962000931 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 85962000932 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 85962000933 Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]; Region: MinD; COG2894 85962000934 Bacterial cell division requires the formation of a septum at mid-cell. The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a pivotal...; Region: MinD; cd02036 85962000935 P-loop; other site 85962000936 ADP binding residues [chemical binding]; other site 85962000937 Switch I; other site 85962000938 Switch II; other site 85962000939 cell division topological specificity factor MinE; Region: minE; TIGR01215 85962000940 DNA protecting protein DprA; Region: dprA; TIGR00732 85962000941 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 85962000942 Holliday junction resolvase-like protein; Reviewed; Region: PRK00109 85962000943 ABC transporter, phosphonate, periplasmic substrate-binding protein; Region: Phosphonate-bd; cl19131 85962000944 catalytic residue [active] 85962000945 Phage lysozyme; Region: Phage_lysozyme; pfam00959 85962000946 Predicted membrane protein [Function unknown]; Region: COG3326 85962000947 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 85962000948 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 85962000949 active site 85962000950 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 85962000951 DHH family; Region: DHH; pfam01368 85962000952 N-terminal domain of NEFA-interacting nuclear protein NIP30; Region: Nefa_Nip30_N; pfam10187 85962000953 DHHA1 domain; Region: DHHA1; pfam02272 85962000954 CTP synthetase; Validated; Region: pyrG; PRK05380 85962000955 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 85962000956 Catalytic site [active] 85962000957 active site 85962000958 UTP binding site [chemical binding]; other site 85962000959 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 85962000960 active site 85962000961 putative oxyanion hole; other site 85962000962 catalytic triad [active] 85962000963 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 85962000964 active site 85962000965 flagellar basal-body M-ring protein/flagellar hook-basal body protein (fliF); Region: fliF; TIGR00206 85962000966 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; pfam01514 85962000967 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 85962000968 flagellar motor switch protein FliG; Region: fliG; TIGR00207 85962000969 FliG N-terminal domain; Region: FliG_N; pfam14842 85962000970 FliG middle domain; Region: FliG_M; pfam14841 85962000971 FliG C-terminal domain; Region: FliG_C; pfam01706 85962000972 flagellar assembly protein H; Validated; Region: fliH; PRK06669 85962000973 Flagellar assembly protein FliH; Region: FliH; pfam02108 85962000974 1-deoxy-D-xylulose-5-phosphate synthase; Region: dxs; TIGR00204 85962000975 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 85962000976 TPP-binding site; other site 85962000977 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 85962000978 PYR/PP interface [polypeptide binding]; other site 85962000979 dimer interface [polypeptide binding]; other site 85962000980 TPP binding site [chemical binding]; other site 85962000981 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 85962000982 GTP-binding protein LepA; Provisional; Region: PRK05433 85962000983 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 85962000984 G1 box; other site 85962000985 putative GEF interaction site [polypeptide binding]; other site 85962000986 GTP/Mg2+ binding site [chemical binding]; other site 85962000987 Switch I region; other site 85962000988 G2 box; other site 85962000989 G3 box; other site 85962000990 Switch II region; other site 85962000991 G4 box; other site 85962000992 G5 box; other site 85962000993 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 85962000994 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 85962000995 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 85962000996 Domain of unknown function (DUF3883); Region: DUF3883; pfam13020 85962000997 classical (c) SDR, subgroup 5; Region: SDR_c5; cd05346 85962000998 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 85962000999 putative NAD(P) binding site [chemical binding]; other site 85962001000 homodimer interface [polypeptide binding]; other site 85962001001 homotetramer interface [polypeptide binding]; other site 85962001002 active site 85962001003 UDP-glucose-4-epimerase GalE; Region: galE; TIGR01179 85962001004 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 85962001005 NAD binding site [chemical binding]; other site 85962001006 homodimer interface [polypeptide binding]; other site 85962001007 active site 85962001008 substrate binding site [chemical binding]; other site 85962001009 tRNA pseudouridine(38-40) synthase; Region: hisT_truA; TIGR00071 85962001010 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 85962001011 dimerization interface 3.5A [polypeptide binding]; other site 85962001012 active site 85962001013 Predicted permeases [General function prediction only]; Region: COG0795 85962001014 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 85962001015 S-adenosylmethionine binding site [chemical binding]; other site 85962001016 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 85962001017 dimer interface [polypeptide binding]; other site 85962001018 putative radical transfer pathway; other site 85962001019 diiron center [ion binding]; other site 85962001020 tyrosyl radical; other site 85962001021 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 85962001022 inhibitor-cofactor binding pocket; inhibition site 85962001023 pyridoxal 5'-phosphate binding site [chemical binding]; other site 85962001024 catalytic residue [active] 85962001025 Flavin-dependent tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA [Cell cycle control, cell division, chromosome partitioning]; Region: GidA; COG0445 85962001026 biotin carboxylase; Validated; Region: PRK08462 85962001027 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 85962001028 ATP-grasp domain; Region: ATP-grasp_4; cl17255 85962001029 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 85962001030 acetyl-CoA carboxylase, biotin carboxyl carrier protein; Region: BCCP; TIGR00531 85962001031 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 85962001032 carboxyltransferase (CT) interaction site; other site 85962001033 biotinylation site [posttranslational modification]; other site 85962001034 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 85962001035 trimer interface [polypeptide binding]; other site 85962001036 active site 85962001037 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962001038 RNA methyltransferase, RsmE family; Region: TIGR00046 85962001039 ferrochelatase; Region: hemH; TIGR00109 85962001040 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 85962001041 C-terminal domain interface [polypeptide binding]; other site 85962001042 active site 85962001043 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 85962001044 active site 85962001045 N-terminal domain interface [polypeptide binding]; other site 85962001046 SoxW family; SoxW is a bacterial periplasmic TRX, containing a redox active CXXC motif, encoded by a genetic locus (sox operon) involved in thiosulfate oxidation. Sulfur bacteria oxidize sulfur compounds to provide reducing equivalents for carbon dioxide...; Region: SoxW; cd02951 85962001047 catalytic residues [active] 85962001048 ResB-like family; Region: ResB; cl09125 85962001049 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 85962001050 Glycosyltransferase family 10 (fucosyltransferase); Region: Glyco_transf_10; pfam00852 85962001051 glutamate dehydrogenase; Provisional; Region: PRK09414 85962001052 Glu/Leu/Phe/Val dehydrogenase, dimerization domain; Region: ELFV_dehydrog_N; pfam02812 85962001053 NAD(P) binding domain of glutamate dehydrogenase, subgroup 2; Region: NAD_bind_2_Glu_DH; cd05313 85962001054 NAD(P) binding site [chemical binding]; other site 85962001055 HemK family putative methylases; Region: hemK_fam; TIGR00536 85962001056 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 85962001057 Peptidase family M48; Region: Peptidase_M48; pfam01435 85962001058 Sporulation related domain; Region: SPOR; pfam05036 85962001059 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 85962001060 primosomal protein N' Region: priA; TIGR00595 85962001061 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 85962001062 ATP binding site [chemical binding]; other site 85962001063 putative Mg++ binding site [ion binding]; other site 85962001064 helicase superfamily c-terminal domain; Region: HELICc; smart00490 85962001065 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 85962001066 S-adenosylmethionine binding site [chemical binding]; other site 85962001067 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 85962001068 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 85962001069 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 85962001070 Peroxiredoxin (PRX) family, Atypical 2-cys PRX subfamily; composed of PRXs containing peroxidatic and resolving cysteines, similar to the homodimeric thiol specific antioxidant (TSA) protein also known as TRX-dependent thiol peroxidase (Tpx). Tpx is a...; Region: PRX_Atyp2cys; cd03014 85962001071 dimer interface [polypeptide binding]; other site 85962001072 catalytic triad [active] 85962001073 peroxidatic and resolving cysteines [active] 85962001074 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 85962001075 putative CheA interaction surface; other site 85962001076 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 85962001077 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 85962001078 putative binding surface; other site 85962001079 active site 85962001080 FinO bacterial conjugation repressor domain; the basic protein FinO is part of the the two component FinOP system which is responsible for repressing bacterial conjugation; the FinOP system represses the transfer (tra) operon of the F-plasmid which...; Region: FinO_conjug_rep; cl15270 85962001081 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 85962001082 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 85962001083 ATP binding site [chemical binding]; other site 85962001084 Mg2+ binding site [ion binding]; other site 85962001085 G-X-G motif; other site 85962001086 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 85962001087 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 85962001088 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 85962001089 active site 85962001090 phosphorylation site [posttranslational modification] 85962001091 intermolecular recognition site; other site 85962001092 dimerization interface [polypeptide binding]; other site 85962001093 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 85962001094 putative CheA interaction surface; other site 85962001095 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 85962001096 active site 85962001097 phosphorylation site [posttranslational modification] 85962001098 intermolecular recognition site; other site 85962001099 dimerization interface [polypeptide binding]; other site 85962001100 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 85962001101 putative active site [active] 85962001102 putative metal binding site [ion binding]; other site 85962001103 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 85962001104 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 85962001105 catalytic residue [active] 85962001106 menaquinone biosynthesis decarboxylase, SCO4490 family; Region: mena_SCO4490; TIGR03701 85962001107 D-3-phosphoglycerate dehydrogenase; Region: PGDH; TIGR01327 85962001108 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_4; cd12173 85962001109 ligand binding site [chemical binding]; other site 85962001110 NAD binding site [chemical binding]; other site 85962001111 dimerization interface [polypeptide binding]; other site 85962001112 catalytic site [active] 85962001113 C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH); Region: ACT_3PGDH-xct; cd04902 85962001114 putative L-serine binding site [chemical binding]; other site 85962001115 ribosomal protein S1; Region: rpsA; TIGR00717 85962001116 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 85962001117 RNA binding site [nucleotide binding]; other site 85962001118 Ribosomal protein S1-like RNA-binding domain; Region: S1; smart00316 85962001119 RNA binding site [nucleotide binding]; other site 85962001120 S1 RNA binding domain; Region: S1; pfam00575 85962001121 RNA binding site [nucleotide binding]; other site 85962001122 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 85962001123 RNA binding site [nucleotide binding]; other site 85962001124 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; cd00164 85962001125 RNA binding site [nucleotide binding]; other site 85962001126 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Region: lytB_ispH; cd13944 85962001127 Fe-S cluster binding site [ion binding]; other site 85962001128 substrate binding site [chemical binding]; other site 85962001129 catalytic site [active] 85962001130 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 85962001131 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 85962001132 hinge; other site 85962001133 active site 85962001134 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 85962001135 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 85962001136 putative tRNA-binding site [nucleotide binding]; other site 85962001137 tRNA synthetase B5 domain; Region: B5; pfam03484 85962001138 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 85962001139 dimer interface [polypeptide binding]; other site 85962001140 motif 1; other site 85962001141 motif 3; other site 85962001142 motif 2; other site 85962001143 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 85962001144 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 85962001145 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 85962001146 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 85962001147 dimer interface [polypeptide binding]; other site 85962001148 motif 1; other site 85962001149 active site 85962001150 motif 2; other site 85962001151 motif 3; other site 85962001152 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 85962001153 nucleotide binding site/active site [active] 85962001154 HIT family signature motif; other site 85962001155 catalytic residue [active] 85962001156 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 85962001157 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 85962001158 catalytic residue [active] 85962001159 Protein of unknown function (DUF3972); Region: DUF3972; pfam13118 85962001160 The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its...; Region: MopB_DMSOR-BSOR-TMAOR; cd02769 85962001161 molybdopterin guanine dinucleotide-containing S/N-oxide reductases; Region: bisC_fam; TIGR00509 85962001162 molybdopterin cofactor binding site [chemical binding]; other site 85962001163 substrate binding site [chemical binding]; other site 85962001164 The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its...; Region: MopB_CT_DMSOR-BSOR-TMAOR; cd02793 85962001165 molybdopterin cofactor binding site; other site 85962001166 GMP synthase; Reviewed; Region: guaA; PRK00074 85962001167 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 85962001168 AMP/PPi binding site [chemical binding]; other site 85962001169 candidate oxyanion hole; other site 85962001170 catalytic triad [active] 85962001171 potential glutamine specificity residues [chemical binding]; other site 85962001172 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 85962001173 ATP Binding subdomain [chemical binding]; other site 85962001174 Ligand Binding sites [chemical binding]; other site 85962001175 Dimerization subdomain; other site 85962001176 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 85962001177 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG1943 85962001178 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 85962001179 Mechanosensitive ion channel; Region: MS_channel; pfam00924 85962001180 Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]; Region: Cfa; COG2230 85962001181 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 85962001182 S-adenosylmethionine binding site [chemical binding]; other site 85962001183 methionyl-tRNA synthetase; Reviewed; Region: PRK12267 85962001184 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 85962001185 active site 85962001186 HIGH motif; other site 85962001187 KMSKS motif; other site 85962001188 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 85962001189 anticodon binding site; other site 85962001190 tRNA binding surface [nucleotide binding]; other site 85962001191 tRNA-binding-domain-containing Escherichia coli methionyl-tRNA synthetase (EcMetRS)-like proteins. This family includes EcMetRS and Aquifex aeolicus Trbp111 (AaTrbp111). This domain has general tRNA binding properties. MetRS aminoacylates methionine...; Region: tRNA_bind_EcMetRS_like; cd02800 85962001192 dimer interface [polypeptide binding]; other site 85962001193 putative tRNA-binding site [nucleotide binding]; other site 85962001194 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 85962001195 Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]; Region: SrmB; COG0513 85962001196 tRNA (mo5U34)-methyltransferase; Region: TIGR00452 85962001197 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 85962001198 S-adenosylmethionine binding site [chemical binding]; other site 85962001199 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cd03440 85962001200 active site 2 [active] 85962001201 active site 1 [active] 85962001202 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 85962001203 This family is most closely related to the GT1 family of glycosyltransferases. UDP-glucose-diacylglycerol glucosyltransferase (UGDG; also known as 1,2-diacylglycerol 3-glucosyltransferase) catalyzes the transfer of glucose from UDP-glucose to 1; Region: GT1_UGDG_like; cd03817 85962001204 putative ADP-binding pocket [chemical binding]; other site 85962001205 Arginine decarboxylase (spermidine biosynthesis) [Amino acid transport and metabolism]; Region: SpeA; COG1166 85962001206 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase; Region: PLPDE_III_ADC; cd06830 85962001207 dimer interface [polypeptide binding]; other site 85962001208 active site 85962001209 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 85962001210 catalytic residues [active] 85962001211 substrate binding site [chemical binding]; other site 85962001212 Uncharacterized protein with a von Willebrand factor type A (vWA) domain [General function prediction only]; Region: COG4867 85962001213 Single-stranded DNA-specific exonuclease [DNA replication, recombination, and repair]; Region: RecJ; COG0608 85962001214 DHH family; Region: DHH; pfam01368 85962001215 Uncharacterized conserved protein [Function unknown]; Region: COG1479 85962001216 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 85962001217 Uncharacterized protein encoded in toxicity protection region of plasmid R478, contains von Willebrand factor (vWF) domain [General function prediction only]; Region: TerY; COG4245 85962001218 metal ion-dependent adhesion site (MIDAS); other site 85962001219 Protein phosphatase 2C; Region: PP2C_2; pfam13672 85962001220 active site 85962001221 Type IV secretory pathway, VirD2 components (relaxase) [Intracellular trafficking and secretion]; Region: VirD2; COG3843 85962001222 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG1943 85962001223 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 85962001224 Helix-turn-helix domain; Region: HTH_OrfB_IS605; pfam12323 85962001225 Probable transposase; Region: OrfB_IS605; pfam01385 85962001226 Putative transposase DNA-binding domain; Region: OrfB_Zn_ribbon; pfam07282 85962001227 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 85962001228 Topoisomerase IA [DNA replication, recombination, and repair]; Region: TopA; COG0550 85962001229 TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IA family of DNA topoisomerases (TopoIA). This subgroup contains proteins similar to the Type I DNA topoisomerases: E. coli...; Region: TOPRIM_TopoIA; cd01028 85962001230 active site 85962001231 interdomain interaction site; other site 85962001232 putative metal-binding site [ion binding]; other site 85962001233 nucleotide binding site [chemical binding]; other site 85962001234 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 85962001235 domain I; other site 85962001236 DNA binding groove [nucleotide binding] 85962001237 phosphate binding site [ion binding]; other site 85962001238 domain II; other site 85962001239 domain III; other site 85962001240 nucleotide binding site [chemical binding]; other site 85962001241 catalytic site [active] 85962001242 domain IV; other site 85962001243 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 85962001244 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 85962001245 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 85962001246 Walker A motif; other site 85962001247 ATP binding site [chemical binding]; other site 85962001248 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 85962001249 Protein of unknown function (DUF3991); Region: DUF3991; pfam13154 85962001250 Toprim-like; Region: Toprim_2; pfam13155 85962001251 AAA domain; Region: AAA_11; pfam13086 85962001252 Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair]; Region: COG1112 85962001253 AAA domain; Region: AAA_30; pfam13604 85962001254 AAA domain; Region: AAA_12; pfam13087 85962001255 Protein of unknown function (DUF3086); Region: DUF3086; pfam11285 85962001256 Protein of unknown function (DUF342); Region: DUF342; cl19219 85962001257 GTPase subunit of restriction endonuclease [Defense mechanisms]; Region: McrB; COG1401 85962001258 Domain of unknown function (DUF2357); Region: DUF2357; pfam09823 85962001259 AAA domain; Region: AAA_33; pfam13671 85962001260 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 85962001261 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 85962001262 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 85962001263 Walker A motif; other site 85962001264 ATP binding site [chemical binding]; other site 85962001265 Walker B motif; other site 85962001266 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 85962001267 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 85962001268 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 85962001269 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 85962001270 Methyltransferase domain; Region: Methyltransf_26; pfam13659 85962001271 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 85962001272 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 85962001273 Type III restriction enzyme, res subunit; Region: ResIII; pfam04851 85962001274 Domain of unknown function (DUF334); Region: DUF334; pfam03904 85962001275 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2604 85962001276 tellurium resistance terB-like protein; Region: terB_like; cl11965 85962001277 metal binding site [ion binding]; metal-binding site 85962001278 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 85962001279 Heterodisulfide reductase, subunit B [Energy production and conversion]; Region: HdrB; COG2048 85962001280 oligoendopeptidase, pepF/M3 family; Region: M3_fam_3; TIGR02290 85962001281 Peptidase family M3B Oligopeptidase F (PepF); Region: M3B_PepF_5; cd09610 85962001282 active site 85962001283 Zn binding site [ion binding]; other site 85962001284 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 85962001285 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962001286 molybdenum ABC transporter, periplasmic molybdate-binding protein; Region: modA; TIGR01256 85962001287 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 85962001288 dimer interface [polypeptide binding]; other site 85962001289 conserved gate region; other site 85962001290 putative PBP binding loops; other site 85962001291 ABC-ATPase subunit interface; other site 85962001292 Predicted ATPase involved in cell division [Cell division and chromosome partitioning]; Region: FtsE; COG2884 85962001293 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 85962001294 Walker A/P-loop; other site 85962001295 ATP binding site [chemical binding]; other site 85962001296 Q-loop/lid; other site 85962001297 ABC transporter signature motif; other site 85962001298 Walker B; other site 85962001299 D-loop; other site 85962001300 H-loop/switch region; other site 85962001301 glutamyl-tRNA synthetase, bacterial family; Region: gltX_bact; TIGR00464 85962001302 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 85962001303 active site 85962001304 HIGH motif; other site 85962001305 KMSKS motif; other site 85962001306 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962001307 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0827 85962001308 Methyltransferase domain; Region: Methyltransf_26; pfam13659 85962001309 TaqI-like C-terminal specificity domain; Region: TaqI_C; pfam12950 85962001310 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 85962001311 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 85962001312 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 85962001313 G1 box; other site 85962001314 putative GEF interaction site [polypeptide binding]; other site 85962001315 GTP/Mg2+ binding site [chemical binding]; other site 85962001316 Switch I region; other site 85962001317 G2 box; other site 85962001318 G3 box; other site 85962001319 Switch II region; other site 85962001320 G4 box; other site 85962001321 G5 box; other site 85962001322 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 85962001323 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 85962001324 Catalytic GIY-YIG domain of coliphage T4 non-specific endonuclease II, type II restriction endonuclease R.Hpy188I, and similar proteins; Region: GIY-YIG_EndoII_Hpy188I_like; cd10436 85962001325 GIY-YIG motif/motif A; other site 85962001326 DNA binding site [nucleotide binding] 85962001327 active site 85962001328 catalytic site [active] 85962001329 metal binding site [ion binding]; metal-binding site 85962001330 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 85962001331 Catalase-like heme-binding proteins similar to the uncharacterized srpA; Region: srpA_like; cd08153 85962001332 putative heme binding pocket [chemical binding]; other site 85962001333 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 85962001334 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 85962001335 Protein of unknown function (DUF3519); Region: DUF3519; pfam12033 85962001336 Protein of unknown function (DUF3519); Region: DUF3519; pfam12033 85962001337 F0F1 ATP synthase subunit B; Provisional; Region: PRK14471; cl17192 85962001338 Cation transport protein; Region: TrkH; cl17365 85962001339 Kef-type K+ transport systems, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: Kch; COG1226 85962001340 TrkA-N domain; Region: TrkA_N; pfam02254 85962001341 TrkA-C domain; Region: TrkA_C; pfam02080 85962001342 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 85962001343 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 85962001344 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 85962001345 Mg++ binding site [ion binding]; other site 85962001346 putative catalytic motif [active] 85962001347 putative substrate binding site [chemical binding]; other site 85962001348 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK03815 85962001349 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 85962001350 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 85962001351 Protein of unknown function (DUF493); Region: DUF493; pfam04359 85962001352 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 85962001353 active site 85962001354 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 85962001355 Na2 binding site [ion binding]; other site 85962001356 putative substrate binding site 1 [chemical binding]; other site 85962001357 Na binding site 1 [ion binding]; other site 85962001358 putative substrate binding site 2 [chemical binding]; other site 85962001359 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 85962001360 Na2 binding site [ion binding]; other site 85962001361 putative substrate binding site 1 [chemical binding]; other site 85962001362 Na binding site 1 [ion binding]; other site 85962001363 putative substrate binding site 2 [chemical binding]; other site 85962001364 The outer membrane phospholipase A (OMPLA) is an integral membrane enzyme that catalyses the hydrolysis of acylester bonds in phospholipids using calcium as a cofactor. The enzyme has a fold of transmembrane beta-barrels and is widespread among...; Region: OMPLA; cd00541 85962001365 dimerization interface [polypeptide binding]; other site 85962001366 substrate binding site [chemical binding]; other site 85962001367 active site 85962001368 calcium binding site [ion binding]; other site 85962001369 DNA polymerase III, beta subunit; Region: dnan; TIGR00663 85962001370 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 85962001371 putative DNA binding surface [nucleotide binding]; other site 85962001372 dimer interface [polypeptide binding]; other site 85962001373 beta-clamp/translesion DNA polymerase binding surface; other site 85962001374 beta-clamp/clamp loader binding surface; other site 85962001375 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 85962001376 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 85962001377 ATP binding site [chemical binding]; other site 85962001378 Mg2+ binding site [ion binding]; other site 85962001379 G-X-G motif; other site 85962001380 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 85962001381 anchoring element; other site 85962001382 dimer interface [polypeptide binding]; other site 85962001383 ATP binding site [chemical binding]; other site 85962001384 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 85962001385 active site 85962001386 putative metal-binding site [ion binding]; other site 85962001387 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 85962001388 R.Pab1 restriction endonuclease; Region: RE_R_Pab1; pfam09522 85962001389 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 85962001390 Peptidase family M23; Region: Peptidase_M23; pfam01551 85962001391 nudix-type nucleoside diphosphatase, YffH/AdpP family; Region: TIGR00052 85962001392 ADP-ribose pyrophosphatase (ADPRase) catalyzes the hydrolysis of ADP-ribose and a variety of additional ADP-sugar conjugates to AMP and ribose-5-phosphate. Like other members of the Nudix hydrolase superfamily, it requires a divalent cation, such as Mg2+; Region: ADPRase_NUDT5; cd03424 85962001393 dimer interface [polypeptide binding]; other site 85962001394 ADP-ribose binding site [chemical binding]; other site 85962001395 active site 85962001396 nudix motif; other site 85962001397 metal binding site [ion binding]; metal-binding site 85962001398 Plasminogen-binding protein pgbA N-terminal; Region: PGBA_N; pfam15436 85962001399 Plasminogen-binding protein pgbA C-terminal; Region: PGBA_C; pfam15437 85962001400 Plasminogen-binding protein pgbA C-terminal; Region: PGBA_C; pfam15437 85962001401 FAD binding domain; Region: FAD_binding_4; pfam01565 85962001402 glycolate oxidase, subunit GlcD; Region: glcD; TIGR00387 85962001403 FAD linked oxidases, C-terminal domain; Region: FAD-oxidase_C; pfam02913 85962001404 dihydrodipicolinate reductase; Region: dapB; TIGR00036 85962001405 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 85962001406 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 85962001407 glutamine synthetase, type I; Region: GlnA; TIGR00653 85962001408 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 85962001409 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 85962001410 Uncharacterized conserved protein [Function unknown]; Region: COG1479 85962001411 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 85962001412 Uncharacterized conserved protein [Function unknown]; Region: COG3586 85962001413 ribosomal protein L9; Region: L9; TIGR00158 85962001414 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 85962001415 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 85962001416 ATP-dependent protease subunit HslV; Provisional; Region: PRK05456 85962001417 active site 85962001418 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 85962001419 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 85962001420 Walker A motif; other site 85962001421 ATP binding site [chemical binding]; other site 85962001422 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 85962001423 Walker B motif; other site 85962001424 arginine finger; other site 85962001425 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 85962001426 GTPase [General function prediction only]; Region: Era; COG1159 85962001427 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 85962001428 G1 box; other site 85962001429 GTP/Mg2+ binding site [chemical binding]; other site 85962001430 Switch I region; other site 85962001431 G2 box; other site 85962001432 Switch II region; other site 85962001433 G3 box; other site 85962001434 G4 box; other site 85962001435 G5 box; other site 85962001436 KH domain; Region: KH_2; pfam07650 85962001437 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3034 85962001438 Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of...; Region: NTF2_like; cl09109 85962001439 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 85962001440 Sel1-like repeats; Region: SEL1; smart00671 85962001441 Protein of unknown function (DUF1682); Region: DUF1682; pfam07946 85962001442 Type IV secretory pathway, VirD4 components [Intracellular trafficking and secretion]; Region: VirD4; COG3505 85962001443 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion. These proteins aid the transfer of DNA from the plasmid into the host bacterial chromosome. They contain an ATP binding domain. VirD4 is involved in DNA transfer...; Region: TraG_VirD4; cd01126 85962001444 Walker A motif; other site 85962001445 ATP binding site [chemical binding]; other site 85962001446 Walker B motif; other site 85962001447 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 85962001448 ATP binding site [chemical binding]; other site 85962001449 Walker A motif; other site 85962001450 hexamer interface [polypeptide binding]; other site 85962001451 Walker B motif; other site 85962001452 CagZ; Region: CagZ; pfam09053 85962001453 CagY type 1 repeat; Region: CagY_I; pfam14585 85962001454 CagY type 1 repeat; Region: CagY_I; pfam14585 85962001455 CagY type 1 repeat; Region: CagY_I; pfam14585 85962001456 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: SbcC; COG0419 85962001457 DC-EC Repeat; Region: CagY_M; pfam07337 85962001458 DC-EC Repeat; Region: CagY_M; pfam07337 85962001459 DC-EC Repeat; Region: CagY_M; pfam07337 85962001460 DC-EC Repeat; Region: CagY_M; pfam07337 85962001461 DC-EC Repeat; Region: CagY_M; pfam07337 85962001462 DC-EC Repeat; Region: CagY_M; pfam07337 85962001463 DC-EC Repeat; Region: CagY_M; pfam07337 85962001464 DC-EC Repeat; Region: CagY_M; pfam07337 85962001465 DC-EC Repeat; Region: CagY_M; pfam07337 85962001466 DC-EC Repeat; Region: CagY_M; pfam07337 85962001467 Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion]; Region: VirB10; COG2948 85962001468 Bacterial conjugation TrbI-like protein; Region: TrbI; pfam03743 85962001469 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cl11423 85962001470 conjugal transfer protein TrbB; Provisional; Region: PRK13728; cl17283 85962001471 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 85962001472 VirB7 interaction site; other site 85962001473 Niemann-Pick C type protein family; Region: 2A060601; TIGR00917 85962001474 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 85962001475 Cag pathogenicity island protein Cag12; Region: Cag12; pfam13117 85962001476 similar to hypothetical protein; hypothetical protein; identified by GeneMark 85962001477 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK06945 85962001478 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 85962001479 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 85962001480 CagA exotoxin; Region: CagA; pfam03507 85962001481 CagA exotoxin; Region: CagA; pfam03507 85962001482 glutamate racemase; Region: glut_race; TIGR00067 85962001483 transcription termination factor Rho; Region: rho; TIGR00767 85962001484 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 85962001485 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 85962001486 RNA binding site [nucleotide binding]; other site 85962001487 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 85962001488 multimer interface [polypeptide binding]; other site 85962001489 Walker A motif; other site 85962001490 ATP binding site [chemical binding]; other site 85962001491 Walker B motif; other site 85962001492 Ribosomal protein L31; Region: Ribosomal_L31; pfam01197 85962001493 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 85962001494 putative SAM binding site [chemical binding]; other site 85962001495 putative homodimer interface [polypeptide binding]; other site 85962001496 rRNA methylase, putative, group 3; Region: rRNA_methyl_3; TIGR00186 85962001497 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 85962001498 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 85962001499 acetyl-CoA carboxylase, carboxyl transferase, alpha subunit; Region: accA; TIGR00513 85962001500 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK08439 85962001501 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 85962001502 dimer interface [polypeptide binding]; other site 85962001503 active site 85962001504 acyl carrier protein; Provisional; Region: acpP; PRK00982 85962001505 similar to hypothetical protein; hypothetical protein; identified by GeneMark 85962001506 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 85962001507 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 85962001508 NAD(P) binding site [chemical binding]; other site 85962001509 active site 85962001510 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 85962001511 Acinetobacter rhombotarget A; Region: GlyGly_RbtA; TIGR04212 85962001512 Predicted membrane protein [Function unknown]; Region: COG3059 85962001513 diaminopimelate epimerase; Region: DapF; TIGR00652 85962001514 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 85962001515 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 85962001516 Domain of unknown function DUF20; Region: UPF0118; pfam01594 85962001517 Iron-sulfur cluster-binding domain; Region: SPASM; pfam13186 85962001518 GTP-binding protein YchF; Reviewed; Region: PRK09601 85962001519 YchF GTPase; Region: YchF; cd01900 85962001520 G1 box; other site 85962001521 GTP/Mg2+ binding site [chemical binding]; other site 85962001522 Switch I region; other site 85962001523 G2 box; other site 85962001524 Switch II region; other site 85962001525 G3 box; other site 85962001526 G4 box; other site 85962001527 G5 box; other site 85962001528 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 85962001529 multifunctional aminopeptidase A; Provisional; Region: PRK00913 85962001530 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 85962001531 interface (dimer of trimers) [polypeptide binding]; other site 85962001532 Substrate-binding/catalytic site; other site 85962001533 Zn-binding sites [ion binding]; other site 85962001534 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 85962001535 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 85962001536 active site 85962001537 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 85962001538 Ribose/Galactose Isomerase; Region: LacAB_rpiB; cl00485 85962001539 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the...; Region: S2P-M50_like_1; cd06158 85962001540 Peptidase family M50; Region: Peptidase_M50; pfam02163 85962001541 active site 85962001542 putative substrate binding region [chemical binding]; other site 85962001543 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 85962001544 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 85962001545 Catalytic site [active] 85962001546 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14191 85962001547 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 85962001548 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 85962001549 homodimer interface [polypeptide binding]; other site 85962001550 NADP binding site [chemical binding]; other site 85962001551 substrate binding site [chemical binding]; other site 85962001552 Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]; Region: MdoB; COG1368 85962001553 exosortase/archaeosortase family protein; Region: exo_archaeo; TIGR04178 85962001554 Sulfatase; Region: Sulfatase; pfam00884 85962001555 Predicted neuraminidase (sialidase) [Carbohydrate transport and metabolism]; Region: COG4692 85962001556 BNR repeat-like domain; Region: BNR_2; pfam13088 85962001557 Dihydroorotase (DHOase) catalyzes the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in the pyrimidine biosynthesis. In contrast to the large polyfunctional CAD proteins of higher organisms, this group of DHOases is...; Region: DHOase; cd01294 85962001558 active site 85962001559 substrate binding pocket [chemical binding]; other site 85962001560 dimer interface [polypeptide binding]; other site 85962001561 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 85962001562 TonB family C-terminal domain; Region: tonB_Cterm; TIGR01352 85962001563 flagellar motor switch protein; Validated; Region: PRK08433 85962001564 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 85962001565 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 85962001566 minor groove reading motif; other site 85962001567 helix-hairpin-helix signature motif; other site 85962001568 substrate binding pocket [chemical binding]; other site 85962001569 active site 85962001570 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 85962001571 Protein of unknown function; Region: DUF3971; pfam13116 85962001572 AsmA-like C-terminal region; Region: AsmA_1; pfam13109 85962001573 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 85962001574 dimerization interface [polypeptide binding]; other site 85962001575 2-oxoglutarate-acceptor oxidoreductase subunit OorD; Reviewed; Region: oorD; PRK09626 85962001576 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl19102 85962001577 2-oxoglutarate-acceptor oxidoreductase subunit OorA; Reviewed; Region: oorA; PRK09627 85962001578 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 85962001579 dimer interface [polypeptide binding]; other site 85962001580 PYR/PP interface [polypeptide binding]; other site 85962001581 TPP binding site [chemical binding]; other site 85962001582 substrate binding site [chemical binding]; other site 85962001583 2-oxoglutarate-acceptor oxidoreductase subunit OorB; Reviewed; Region: oorB; PRK09628 85962001584 Thiamine pyrophosphate (TPP family), 2-oxoglutarate ferredoxin oxidoreductase (OGFOR) subfamily, TPP-binding module; OGFOR catalyzes the oxidative decarboxylation of 2-oxo-acids, with ferredoxin acting as an electron acceptor. In the TCA cycle, OGFOR...; Region: TPP_OGFOR; cd03375 85962001585 TPP-binding site [chemical binding]; other site 85962001586 2-oxoglutarate-acceptor oxidoreductase subunit OorC; Reviewed; Region: oorC; PRK08441 85962001587 Restriction endonuclease [Defense mechanisms]; Region: COG3587 85962001588 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 85962001589 ATP binding site [chemical binding]; other site 85962001590 putative Mg++ binding site [ion binding]; other site 85962001591 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 85962001592 DNA methylase; Region: N6_N4_Mtase; cl17433 85962001593 DNA methylase; Region: N6_N4_Mtase; pfam01555 85962001594 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 85962001595 Disulfide bond formation protein DsbB [Posttranslational modification, protein turnover, chaperones]; Region: DsbB; COG1495 85962001596 tumor necrosis factor alpha-inducing protein; Reviewed; Region: PRK12303 85962001597 Membrane carboxypeptidase (penicillin-binding protein) [Cell envelope biogenesis, outer membrane]; Region: MrcB; COG0744 85962001598 Transglycosylase; Region: Transgly; pfam00912 85962001599 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 85962001600 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 85962001601 8-amino-7-oxononanoate synthase; Region: bioF; TIGR00858 85962001602 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 85962001603 catalytic residue [active] 85962001604 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 85962001605 dimer interface [polypeptide binding]; other site 85962001606 putative CheW interface [polypeptide binding]; other site 85962001607 Chemoreceptor zinc-binding domain; Region: CZB; pfam13682 85962001608 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 85962001609 ATP-binding cassette domain of multidrug resistance protein-like transporters; Region: ABCC_MRP_Like; cd03228 85962001610 Walker A/P-loop; other site 85962001611 ATP binding site [chemical binding]; other site 85962001612 Q-loop/lid; other site 85962001613 ABC transporter signature motif; other site 85962001614 Walker B; other site 85962001615 D-loop; other site 85962001616 H-loop/switch region; other site 85962001617 flagellin A; Reviewed; Region: PRK12584 85962001618 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 85962001619 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 85962001620 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 85962001621 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 85962001622 3-methyladenine DNA glycosylase; Provisional; Region: PRK13913 85962001623 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 85962001624 minor groove reading motif; other site 85962001625 helix-hairpin-helix signature motif; other site 85962001626 active site 85962001627 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 85962001628 substrate binding site [chemical binding]; other site 85962001629 active site 85962001630 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 85962001631 Outer membrane efflux protein; Region: OEP; pfam02321 85962001632 Outer membrane efflux protein; Region: OEP; pfam02321 85962001633 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 85962001634 HlyD family secretion protein; Region: HlyD_3; pfam13437 85962001635 AcrB/AcrD/AcrF family; Region: ACR_tran; pfam00873 85962001636 MMPL family; Region: MMPL; cl14618 85962001637 MMPL family; Region: MMPL; cl14618 85962001638 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962001639 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 85962001640 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 85962001641 Walker A/P-loop; other site 85962001642 ATP binding site [chemical binding]; other site 85962001643 Q-loop/lid; other site 85962001644 ABC transporter signature motif; other site 85962001645 Walker B; other site 85962001646 D-loop; other site 85962001647 H-loop/switch region; other site 85962001648 V antigen (LcrV) protein; Region: LcrV; pfam04792 85962001649 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 85962001650 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 85962001651 nucleotide binding pocket [chemical binding]; other site 85962001652 K-X-D-G motif; other site 85962001653 catalytic site [active] 85962001654 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 85962001655 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 85962001656 Helix-hairpin-helix domain; Region: HHH_5; pfam14520 85962001657 H3TH domains of structure-specific 5' nucleases (or flap endonuclease-1-like) involved in DNA replication, repair, and recombination; Region: H3TH_StructSpec-5'-nucleases; cl14815 85962001658 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 85962001659 Dimer interface [polypeptide binding]; other site 85962001660 BRCT sequence motif; other site 85962001661 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cd00588 85962001662 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 85962001663 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 85962001664 active site 85962001665 phosphorylation site [posttranslational modification] 85962001666 intermolecular recognition site; other site 85962001667 dimerization interface [polypeptide binding]; other site 85962001668 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 85962001669 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 85962001670 dimer interface [polypeptide binding]; other site 85962001671 anticodon binding site; other site 85962001672 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 85962001673 homodimer interface [polypeptide binding]; other site 85962001674 motif 1; other site 85962001675 active site 85962001676 motif 2; other site 85962001677 GAD domain; Region: GAD; pfam02938 85962001678 motif 3; other site 85962001679 adenylate kinase; Reviewed; Region: adk; PRK00279 85962001680 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 85962001681 AMP-binding site [chemical binding]; other site 85962001682 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 85962001683 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 85962001684 dimer interface [polypeptide binding]; other site 85962001685 substrate binding site [chemical binding]; other site 85962001686 metal binding sites [ion binding]; metal-binding site 85962001687 MutS2 family protein; Region: mutS2; TIGR01069 85962001688 ATPase domain of DNA mismatch repair MUTS family; Region: MUTSac; smart00534 85962001689 Walker A/P-loop; other site 85962001690 ATP binding site [chemical binding]; other site 85962001691 Q-loop/lid; other site 85962001692 ABC transporter signature motif; other site 85962001693 Walker B; other site 85962001694 D-loop; other site 85962001695 H-loop/switch region; other site 85962001696 The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; Region: BAR; cl12013 85962001697 Smr domain; Region: Smr; pfam01713 85962001698 UDP-N-acetylmuramate--alanine ligase; Region: murC; TIGR01082 85962001699 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 85962001700 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 85962001701 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 85962001702 succinyldiaminopimelate transaminase; Region: DapC_gpp; TIGR03538 85962001703 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 85962001704 pyridoxal 5'-phosphate binding site [chemical binding]; other site 85962001705 homodimer interface [polypeptide binding]; other site 85962001706 catalytic residue [active] 85962001707 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 85962001708 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase; Region: ispG_gcpE; TIGR00612 85962001709 Tetrahydrodipicolinate N-succinyltransferase N-terminal; Region: THDPS_N; pfam14790 85962001710 Tetrahydrodipicolinate N-succinyltransferase [Amino acid transport and metabolism]; Region: DapD; COG2171 85962001711 Tetrahydrodipicolinate N-succinyltransferase middle; Region: THDPS_M; pfam14789 85962001712 Putative 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate (THDP) N-succinyltransferase (THP succinyltransferase), C-terminal left-handed parallel alpha-helix (LbH) domain: This group is composed of mostly uncharacterized proteins containing an N-terminal...; Region: LbH_THP_succinylT_putative; cd04649 85962001713 putative trimer interface [polypeptide binding]; other site 85962001714 putative CoA binding site [chemical binding]; other site 85962001715 Uncharacterized conserved protein [Function unknown]; Region: COG1479 85962001716 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 85962001717 Putative NADPH-quinone reductase (modulator of drug activity B) [General function prediction only]; Region: MdaB; COG2249 85962001718 hydrogenase (NiFe) small subunit (hydA); Region: hydA; TIGR00391 85962001719 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 85962001720 NiFe/NiFeSe hydrogenase small subunit C-terminal; Region: NiFe_hyd_SSU_C; pfam14720 85962001721 Ni,Fe-hydrogenase I large subunit [Energy production and conversion]; Region: HyaB; COG0374 85962001722 Ni/Fe-hydrogenase, b-type cytochrome subunit; Region: CytB-hydogenase; TIGR02125 85962001723 Endopeptidases belonging to membrane-bound hydrogenases group. These hydrogenases transfer electrons from H2 to a cytochrome that is bound to a membrane-located complex coupling electron transfer to transmembrane proton translocation. Endopeptidase HybD...; Region: H2MP_MemB-H2up; cd06062 85962001724 putative substrate-binding site; other site 85962001725 nickel binding site [ion binding]; other site 85962001726 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962001727 ExsB is a transcription regulator related protein. It is a subfamily of a Adenosine nucleotide binding superfamily of proteins. This protein family is represented by a single member in nearly every completed large (> 1000 genes) prokaryotic genome. In...; Region: ExsB; cd01995 85962001728 Ligand Binding Site [chemical binding]; other site 85962001729 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 85962001730 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 85962001731 active site 85962001732 NTP binding site [chemical binding]; other site 85962001733 metal binding triad [ion binding]; metal-binding site 85962001734 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 85962001735 NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase; Region: NAD_binding_11; pfam14833 85962001736 NAD(P)H:FMN oxidoreductase family. This domain catalyzes the reduction of flavin, nitrocompound, quinones and azo compounds using NADH or NADPH as an electron donor. The enzyme is a homodimer, and each monomer binds a FMN as co-factor. This family...; Region: NfsB_like_nitroreductase; cd02149 85962001737 dimer interface [polypeptide binding]; other site 85962001738 FMN binding site [chemical binding]; other site 85962001739 glutamylglutaminyl-tRNA synthetase; Provisional; Region: PRK12410 85962001740 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 85962001741 active site 85962001742 nucleotide binding site [chemical binding]; other site 85962001743 HIGH motif; other site 85962001744 KMSKS motif; other site 85962001745 Predicted integral membrane protein [Function unknown]; Region: COG0762 85962001746 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 85962001747 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 85962001748 N-acetyl-D-glucosamine binding site [chemical binding]; other site 85962001749 catalytic residue [active] 85962001750 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 85962001751 active site 85962001752 tetramer interface; other site 85962001753 sensor protein RstB; Provisional; Region: PRK10604 85962001754 EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase); Region: EPSP_synthase; pfam00275 85962001755 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 85962001756 hinge; other site 85962001757 active site 85962001758 aspartate ammonia-lyase; Provisional; Region: aspA; PRK12273 85962001759 Aspartase; Region: Aspartase; cd01357 85962001760 active sites [active] 85962001761 tetramer interface [polypeptide binding]; other site 85962001762 Uracil-DNA glycosylases (UDG) and related enzymes; Region: UDG_like; cl00483 85962001763 ligand binding site [chemical binding]; other site 85962001764 active site 85962001765 Glycosyltransferase family 10 (fucosyltransferase); Region: Glyco_transf_10; pfam00852 85962001766 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 85962001767 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 85962001768 motif II; other site 85962001769 nonheme-containing ferritins; Region: Nonheme_Ferritin; cd01055 85962001770 Ferritin-like domain; Region: Ferritin; pfam00210 85962001771 ferroxidase diiron center [ion binding]; other site 85962001772 hypothetical protein; Provisional; Region: PRK08444 85962001773 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 85962001774 FeS/SAM binding site; other site 85962001775 Outer membrane protein/protective antigen OMA87 [Cell envelope biogenesis, outer membrane]; Region: COG4775 85962001776 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 85962001777 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 85962001778 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 85962001779 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 85962001780 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 85962001781 Surface antigen; Region: Bac_surface_Ag; pfam01103 85962001782 hypothetical protein; Provisional; Region: PRK08445 85962001783 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 85962001784 FeS/SAM binding site; other site 85962001785 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 85962001786 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 85962001787 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 85962001788 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 85962001789 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 85962001790 GatB domain; Region: GatB_Yqey; smart00845 85962001791 SurA N-terminal domain; Region: SurA_N; pfam09312 85962001792 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]; Region: COG2956 85962001793 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]; Region: COG1439 85962001794 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 85962001795 RNA/DNA hybrid binding site [nucleotide binding]; other site 85962001796 active site 85962001797 ribonuclease III; Reviewed; Region: rnc; PRK00102 85962001798 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 85962001799 dimerization interface [polypeptide binding]; other site 85962001800 active site 85962001801 metal binding site [ion binding]; metal-binding site 85962001802 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 85962001803 dsRNA binding site [nucleotide binding]; other site 85962001804 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 85962001805 Tetramer interface [polypeptide binding]; other site 85962001806 active site 85962001807 FMN-binding site [chemical binding]; other site 85962001808 Protein of unknown function (DUF2603); Region: DUF2603; pfam10788 85962001809 oxygen-independent coproporphyrinogen III oxidase; Region: hemN; TIGR00538 85962001810 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 85962001811 FeS/SAM binding site; other site 85962001812 HemN C-terminal domain; Region: HemN_C; pfam06969 85962001813 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 85962001814 4Fe-4S dicluster domain; Region: Fer4_8; pfam13183 85962001815 Cysteine-rich domain; Region: CCG; pfam02754 85962001816 Cysteine-rich domain; Region: CCG; pfam02754 85962001817 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cl00309 85962001818 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962001819 aspartate aminotransferase; Provisional; Region: PRK05764 85962001820 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 85962001821 pyridoxal 5'-phosphate binding site [chemical binding]; other site 85962001822 homodimer interface [polypeptide binding]; other site 85962001823 catalytic residue [active] 85962001824 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 85962001825 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 85962001826 active site 85962001827 DNA binding site [nucleotide binding] 85962001828 Int/Topo IB signature motif; other site 85962001829 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 85962001830 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 85962001831 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 85962001832 DNA binding site [nucleotide binding] 85962001833 active site 85962001834 Predicted permeases [General function prediction only]; Region: COG0730 85962001835 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK08447 85962001836 ATP cone domain; Region: ATP-cone; pfam03477 85962001837 Class I ribonucleotide reductase; Region: RNR_I; cd01679 85962001838 active site 85962001839 dimer interface [polypeptide binding]; other site 85962001840 catalytic residues [active] 85962001841 effector binding site; other site 85962001842 R2 peptide binding site; other site 85962001843 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK14359 85962001844 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 85962001845 Substrate binding site; other site 85962001846 Mg++ binding site; other site 85962001847 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 85962001848 active site 85962001849 substrate binding site [chemical binding]; other site 85962001850 CoA binding site [chemical binding]; other site 85962001851 Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]; Region: FecA; COG4772 85962001852 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 85962001853 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 85962001854 ferrous iron transporter FeoB; Region: feoB; TIGR00437 85962001855 G1 box; other site 85962001856 GTP/Mg2+ binding site [chemical binding]; other site 85962001857 Switch I region; other site 85962001858 G2 box; other site 85962001859 G3 box; other site 85962001860 Switch II region; other site 85962001861 G4 box; other site 85962001862 G5 box; other site 85962001863 Nucleoside recognition; Region: Gate; pfam07670 85962001864 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 85962001865 Nucleoside recognition; Region: Gate; pfam07670 85962001866 putative acyltransferase; Provisional; Region: PRK05790 85962001867 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 85962001868 dimer interface [polypeptide binding]; other site 85962001869 active site 85962001870 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 85962001871 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 85962001872 Short chain fatty acid transporter; Region: SCFA_trans; pfam02667 85962001873 N-methylhydantoinase A/acetone carboxylase, beta subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuA; COG0145 85962001874 Hydantoinase/oxoprolinase N-terminal region; Region: Hydant_A_N; pfam05378 85962001875 Hydantoinase/oxoprolinase; Region: Hydantoinase_A; pfam01968 85962001876 Hydantoinase B/oxoprolinase; Region: Hydantoinase_B; cl19816 85962001877 Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcxC; COG4647 85962001878 Integral membrane diacylglycerol kinase; Region: DAGK_IM; cd14264 85962001879 putative active site [active] 85962001880 trimer interface [polypeptide binding]; other site 85962001881 putative active site [active] 85962001882 Zn binding site [ion binding]; other site 85962001883 DNA gyrase subunit A; Validated; Region: PRK05560 85962001884 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 85962001885 CAP-like domain; other site 85962001886 active site 85962001887 primary dimer interface [polypeptide binding]; other site 85962001888 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 85962001889 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 85962001890 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 85962001891 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 85962001892 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 85962001893 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 85962001894 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 85962001895 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 85962001896 active site 85962001897 phosphorylation site [posttranslational modification] 85962001898 intermolecular recognition site; other site 85962001899 dimerization interface [polypeptide binding]; other site 85962001900 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 85962001901 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 85962001902 Walker A motif; other site 85962001903 ATP binding site [chemical binding]; other site 85962001904 Walker B motif; other site 85962001905 arginine finger; other site 85962001906 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 85962001907 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 85962001908 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 85962001909 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 85962001910 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962001911 16S rRNA (cytosine(1402)-N(4))-methyltransferase; Region: TIGR00006 85962001912 Uncharacterized conserved protein [Function unknown]; Region: COG1912 85962001913 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962001914 Competence protein ComGF [Intracellular trafficking and secretion]; Region: ComGF; COG4940 85962001915 Predicted hydrolases of HD superfamily [General function prediction only]; Region: COG1896 85962001916 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 85962001917 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 85962001918 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 85962001919 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 85962001920 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 85962001921 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 85962001922 Walker A/P-loop; other site 85962001923 ATP binding site [chemical binding]; other site 85962001924 Q-loop/lid; other site 85962001925 ABC transporter signature motif; other site 85962001926 Walker B; other site 85962001927 D-loop; other site 85962001928 H-loop/switch region; other site 85962001929 tRNA threonylcarbamoyl adenosine modification protein YjeE; Region: T6A_YjeE; TIGR00150 85962001930 DNA polymerase III subunits gamma and tau; Validated; Region: PRK08451 85962001931 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 85962001932 Walker A motif; other site 85962001933 ATP binding site [chemical binding]; other site 85962001934 Walker B motif; other site 85962001935 arginine finger; other site 85962001936 Lysine efflux permease [General function prediction only]; Region: COG1279 85962001937 Protein of unknown function (DUF1104); Region: DUF1104; pfam06518 85962001938 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962001939 Type II (periplasmic) bacterial L-asparaginase; Region: L-asparaginase_II; cd08964 85962001940 active site 85962001941 homotetramer interface [polypeptide binding]; other site 85962001942 homodimer interface [polypeptide binding]; other site 85962001943 anaerobic C4-dicarboxylate transporter; Reviewed; Region: PRK09412 85962001944 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962001945 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 85962001946 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 85962001947 FMN binding site [chemical binding]; other site 85962001948 active site 85962001949 catalytic residues [active] 85962001950 substrate binding site [chemical binding]; other site 85962001951 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 85962001952 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 85962001953 Ligand Binding Site [chemical binding]; other site 85962001954 DRE-TIM metallolyase superfamily; Region: DRE_TIM_metallolyase; cl18962 85962001955 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 85962001956 G1 box; other site 85962001957 GTP/Mg2+ binding site [chemical binding]; other site 85962001958 G2 box; other site 85962001959 Switch I region; other site 85962001960 G3 box; other site 85962001961 Switch II region; other site 85962001962 G4 box; other site 85962001963 chromosome segregation protein SMC, primarily archaeal type; Region: SMC_prok_A; TIGR02169 85962001964 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 85962001965 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 85962001966 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 85962001967 FeS/SAM binding site; other site 85962001968 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 85962001969 active site 85962001970 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]; Region: COG0075 85962001971 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 85962001972 catalytic residue [active] 85962001973 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 85962001974 tetramer interfaces [polypeptide binding]; other site 85962001975 binuclear metal-binding site [ion binding]; other site 85962001976 D-alanyl-alanine synthetase A; Reviewed; Region: ddl; PRK01966 85962001977 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 85962001978 ATP-grasp domain; Region: ATP-grasp_4; cl17255 85962001979 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 85962001980 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 85962001981 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 85962001982 FHIT (fragile histidine family): FHIT proteins, related to the HIT family carry a motif HxHxH/Qxx (x, is a hydrophobic amino acid), On the basis of sequence, substrate specificity, structure, evolution and mechanism, HIT proteins are classified into...; Region: FHIT; cd01275 85962001983 nucleotide binding site/active site [active] 85962001984 HIT family signature motif; other site 85962001985 catalytic residue [active] 85962001986 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 85962001987 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 85962001988 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 85962001989 active site 85962001990 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 85962001991 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 85962001992 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 85962001993 RNA binding surface [nucleotide binding]; other site 85962001994 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 85962001995 active site 85962001996 Fibronectin type 3 domain-containing protein [General function prediction only]; Region: COG3401 85962001997 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 85962001998 Interdomain contacts; other site 85962001999 Cytokine receptor motif; other site 85962002000 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 85962002001 Interdomain contacts; other site 85962002002 Cytokine receptor motif; other site 85962002003 tRNA (guanine-N(7)-)-methyltransferase; Provisional; Region: PRK14121 85962002004 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 85962002005 S-adenosylmethionine binding site [chemical binding]; other site 85962002006 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 85962002007 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 85962002008 Walker A/P-loop; other site 85962002009 ATP binding site [chemical binding]; other site 85962002010 Q-loop/lid; other site 85962002011 ABC transporter signature motif; other site 85962002012 Walker B; other site 85962002013 D-loop; other site 85962002014 H-loop/switch region; other site 85962002015 Cell division protein [Cell division and chromosome partitioning]; Region: FtsX; COG2177 85962002016 Uncharacterized protein conserved in bacteria (DUF2317); Region: DUF2317; cl19511 85962002017 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 85962002018 Peptidase family M23; Region: Peptidase_M23; pfam01551 85962002019 flagellar protein FlaG; Provisional; Region: PRK08452 85962002020 flagellar capping protein; Validated; Region: fliD; PRK08453 85962002021 Flagellar hook-associated protein 2 N-terminus; Region: FliD_N; pfam02465 85962002022 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 85962002023 flagellar biosynthetic protein FliS; Region: fliS; TIGR00208 85962002024 Family of activating enzymes (E1) of ubiquitin-like proteins related to the E.coli hypothetical protein ygdL. The common reaction mechanism catalyzed by E1-like enzymes begins with a nucleophilic attack of the C-terminal carboxylate of the ubiquitin-like...; Region: YgdL_like; cd00755 85962002025 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 85962002026 putative ATP binding site [chemical binding]; other site 85962002027 putative substrate interface [chemical binding]; other site 85962002028 N-carbamoylputrescine amidohydrolase (CPA) (class 11 nitrilases); Region: CPA; cd07573 85962002029 putative active site; other site 85962002030 catalytic triad [active] 85962002031 putative dimer interface [polypeptide binding]; other site 85962002032 Predicted permease [General function prediction only]; Region: COG2056 85962002033 Na+-H+ antiporter family; Region: Na_H_antiport_2; pfam13726 85962002034 Na+/H+ antiporter family; Region: Na_H_antiporter; pfam03553 85962002035 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Thermotoga marina NorM; Region: MATE_NorM_like; cd13137 85962002036 putative efflux protein, MATE family; Region: matE; TIGR00797 85962002037 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that...; Region: KH-I; cd00105 85962002038 nucleic acid binding region [nucleotide binding]; other site 85962002039 G-X-X-G motif; other site 85962002040 Predicted HD superfamily hydrolase [General function prediction only]; Region: COG1418 85962002041 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 85962002042 Zn2+ binding site [ion binding]; other site 85962002043 Mg2+ binding site [ion binding]; other site 85962002044 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212 85962002045 signal recognition particle-docking protein FtsY; Region: ftsY; TIGR00064 85962002046 SRP54-type protein, GTPase domain; Region: SRP54; pfam00448 85962002047 Predicted Fe-S-cluster oxidoreductase [General function prediction only]; Region: COG0727 85962002048 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 85962002049 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 85962002050 FeS/SAM binding site; other site 85962002051 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 85962002052 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 85962002053 GTP binding site; other site 85962002054 flagellar biosynthetic protein FlhB; Region: flhB; TIGR00328 85962002055 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 85962002056 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 85962002057 active site 85962002058 metal binding site [ion binding]; metal-binding site 85962002059 Nitronate monooxygenase; Region: NMO; pfam03060 85962002060 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase...; Region: NPD_like; cd04730 85962002061 FMN binding site [chemical binding]; other site 85962002062 substrate binding site [chemical binding]; other site 85962002063 putative catalytic residue [active] 85962002064 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 85962002065 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 85962002066 active site 85962002067 HIGH motif; other site 85962002068 dimer interface [polypeptide binding]; other site 85962002069 KMSKS motif; other site 85962002070 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 85962002071 RNA binding surface [nucleotide binding]; other site 85962002072 (p)ppGpp synthetase, RelA/SpoT family; Region: spoT_relA; TIGR00691 85962002073 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 85962002074 Zn2+ binding site [ion binding]; other site 85962002075 Mg2+ binding site [ion binding]; other site 85962002076 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 85962002077 synthetase active site [active] 85962002078 NTP binding site [chemical binding]; other site 85962002079 metal binding site [ion binding]; metal-binding site 85962002080 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 85962002081 DNA-directed RNA polymerase, subunit K/omega [Transcription]; Region: RpoZ; COG1758 85962002082 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 85962002083 putative nucleotide binding site [chemical binding]; other site 85962002084 uridine monophosphate binding site [chemical binding]; other site 85962002085 homohexameric interface [polypeptide binding]; other site 85962002086 Predicted periplasmic solute-binding protein [General function prediction only]; Region: COG1427 85962002087 aconitate hydratase 2; Region: acnB; TIGR00117 85962002088 Aconitate B N-terminal domain; Region: Aconitase_B_N; pfam11791 85962002089 Aconitase B swivel domain. Aconitate hydratase B is involved in energy metabolism as part of the TCA cycle. It catalyses the formation of cis-aconitate from citrate. This is the aconitase swivel domain, which undergoes swivelling conformational change in...; Region: AcnB_Swivel; cd01576 85962002090 substrate binding site [chemical binding]; other site 85962002091 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 85962002092 substrate binding site [chemical binding]; other site 85962002093 ligand binding site [chemical binding]; other site 85962002094 FOG: Transposase [DNA replication, recombination, and repair]; Region: COG5659 85962002095 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 85962002096 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 85962002097 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 85962002098 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 85962002099 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 85962002100 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 85962002101 nucleotide binding region [chemical binding]; other site 85962002102 ATP-binding site [chemical binding]; other site 85962002103 SecA Wing and Scaffold domain; Region: SecA_SW; pfam07516 85962002104 SEC-C motif; Region: SEC-C; cl19389 85962002105 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 85962002106 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 85962002107 FtsX-like permease family; Region: FtsX; pfam02687 85962002108 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 85962002109 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 85962002110 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 85962002111 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 85962002112 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 85962002113 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 85962002114 metal-binding site [ion binding] 85962002115 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 85962002116 Soluble P-type ATPase [General function prediction only]; Region: COG4087 85962002117 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 85962002118 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 85962002119 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 85962002120 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 85962002121 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 85962002122 active site 85962002123 catalytic residues [active] 85962002124 metal binding site [ion binding]; metal-binding site 85962002125 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 85962002126 oligomer interface [polypeptide binding]; other site 85962002127 active site residues [active] 85962002128 trigger factor; Provisional; Region: tig; PRK01490 85962002129 Bacterial trigger factor protein (TF); Region: Trigger_N; pfam05697 85962002130 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 85962002131 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 85962002132 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962002133 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 85962002134 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 85962002135 trimer interface [polypeptide binding]; other site 85962002136 dimer interface [polypeptide binding]; other site 85962002137 putative active site [active] 85962002138 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 85962002139 MPT binding site; other site 85962002140 trimer interface [polypeptide binding]; other site 85962002141 MoaE family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor for a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoaE; cd00756 85962002142 MoaE homodimer interface [polypeptide binding]; other site 85962002143 MoaD interaction [polypeptide binding]; other site 85962002144 active site residues [active] 85962002145 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 85962002146 MoaE interaction surface [polypeptide binding]; other site 85962002147 MoeB interaction surface [polypeptide binding]; other site 85962002148 thiocarboxylated glycine; other site 85962002149 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 85962002150 dimerization interface [polypeptide binding]; other site 85962002151 active site 85962002152 Domain of unknown function (DUF3943); Region: DUF3943; pfam13084 85962002153 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional; Region: PRK09314 85962002154 3,4-dihydroxy-2-butanone 4-phosphate synthase [Coenzyme metabolism]; Region: RibB; COG0108 85962002155 GTP cyclohydrolase II [Coenzyme metabolism]; Region: RibA; COG0807 85962002156 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of...; Region: Glyco_transf_25; cd06532 85962002157 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG1451 85962002158 Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]; Region: FecA; COG4772 85962002159 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 85962002160 holo-[acyl-carrier-protein] synthase; Region: acpS; TIGR00516 85962002161 flagellar basal body-associated protein FliL; Reviewed; Region: fliL; PRK08455 85962002162 RNA methyltransferase, RsmD family; Region: TIGR00095 85962002163 Uncharacterized conserved protein [Function unknown]; Region: COG1565 85962002164 Putative S-adenosyl-L-methionine-dependent methyltransferase; Region: Methyltransf_28; pfam02636 85962002165 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 85962002166 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 2 [Coenzyme metabolism]; Region: ThiF; COG0476 85962002167 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 85962002168 ATP binding site [chemical binding]; other site 85962002169 substrate interface [chemical binding]; other site 85962002170 flagellar motor protein MotA; Validated; Region: PRK08456 85962002171 flagellar motor protein MotB; Reviewed; Region: motB; PRK08457 85962002172 Membrane MotB of proton-channel complex MotA/MotB; Region: MotB_plug; pfam13677 85962002173 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 85962002174 ligand binding site [chemical binding]; other site 85962002175 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 85962002176 dimer interface [polypeptide binding]; other site 85962002177 conserved gate region; other site 85962002178 putative PBP binding loops; other site 85962002179 ABC-ATPase subunit interface; other site 85962002180 Periplasmic glycine betaine/choline-binding (lipo)protein of an ABC-type transport system (osmoprotectant binding protein) [Cell envelope biogenesis, outer membrane]; Region: OpuBC; COG1732 85962002181 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 85962002182 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 85962002183 Walker A/P-loop; other site 85962002184 ATP binding site [chemical binding]; other site 85962002185 Q-loop/lid; other site 85962002186 ABC transporter signature motif; other site 85962002187 Walker B; other site 85962002188 D-loop; other site 85962002189 H-loop/switch region; other site 85962002190 excinuclease ABC, C subunit; Region: uvrC; TIGR00194 85962002191 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 85962002192 GIY-YIG motif/motif A; other site 85962002193 active site 85962002194 catalytic site [active] 85962002195 putative DNA binding site [nucleotide binding]; other site 85962002196 metal binding site [ion binding]; metal-binding site 85962002197 UvrB/uvrC motif; Region: UVR; pfam02151 85962002198 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 85962002199 homoserine dehydrogenase; Provisional; Region: PRK06349 85962002200 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 85962002201 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 85962002202 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 85962002203 Predicted endonuclease distantly related to archaeal Holliday junction resolvase [DNA replication, recombination, and repair]; Region: COG0792 85962002204 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 85962002205 catalytic residues [active] 85962002206 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 85962002207 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl19134 85962002208 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 85962002209 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of...; Region: Glyco_transf_25; cd06532 85962002210 RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins; Region: RRM_HP0827_like; cd12399 85962002211 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 85962002212 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 85962002213 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 85962002214 active site 85962002215 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 85962002216 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit; Region: gatA; TIGR00132 85962002217 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 85962002218 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 85962002219 CoA-binding site [chemical binding]; other site 85962002220 ATP-binding [chemical binding]; other site 85962002221 spermidine synthase; Provisional; Region: speE; PRK00536 85962002222 GTP-binding protein Der; Reviewed; Region: PRK00093 85962002223 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 85962002224 G1 box; other site 85962002225 GTP/Mg2+ binding site [chemical binding]; other site 85962002226 Switch I region; other site 85962002227 G2 box; other site 85962002228 Switch II region; other site 85962002229 G3 box; other site 85962002230 G4 box; other site 85962002231 G5 box; other site 85962002232 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 85962002233 G1 box; other site 85962002234 GTP/Mg2+ binding site [chemical binding]; other site 85962002235 Switch I region; other site 85962002236 G2 box; other site 85962002237 G3 box; other site 85962002238 Switch II region; other site 85962002239 G4 box; other site 85962002240 G5 box; other site 85962002241 KH-domain-like of EngA bacterial GTPase enzymes, C-terminal; Region: KH_dom-like; pfam14714 85962002242 histone-like DNA-binding protein HU; Region: HU; cd13831 85962002243 dimer interface [polypeptide binding]; other site 85962002244 DNA binding site [nucleotide binding] 85962002245 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3018 85962002246 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3018 85962002247 Long-chain fatty acid transport protein [Lipid metabolism]; Region: FadL; COG2067 85962002248 UDP-N-acetylglucosamine 4,6-dehydratase; Region: PseB; TIGR03589 85962002249 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 85962002250 NAD(P) binding site [chemical binding]; other site 85962002251 homodimer interface [polypeptide binding]; other site 85962002252 substrate binding site [chemical binding]; other site 85962002253 active site 85962002254 phosphopantothenoylcysteine decarboxylase / phosphopantothenate--cysteine ligase; Region: coaBC_dfp; TIGR00521 85962002255 Flavoprotein; Region: Flavoprotein; cl19190 85962002256 DNA / pantothenate metabolizm flavoprotein; Region: DFP; pfam04127 85962002257 Thiamine monophosphate synthase (TMP synthase)/TenI. TMP synthase catalyzes an important step in the thiamine biosynthesis pathway, the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5-; Region: TMP_TenI; cd00564 85962002258 thiamine phosphate binding site [chemical binding]; other site 85962002259 active site 85962002260 pyrophosphate binding site [ion binding]; other site 85962002261 4-amino-5-hydroxymethyl-2-methyl-pyrimidine phosphate kinase (HMPP-kinase) catalyzes two consecutive phosphorylation steps in the thiamine phosphate biosynthesis pathway, leading to the synthesis of vitamin B1. The first step is the phosphorylation of...; Region: HMPP_kinase; cd01169 85962002262 dimer interface [polypeptide binding]; other site 85962002263 substrate binding site [chemical binding]; other site 85962002264 ATP binding site [chemical binding]; other site 85962002265 4-methyl-5-beta-hydroxyethylthiazole (Thz) kinase catalyzes the phosphorylation of the hydroxylgroup of Thz. A reaction that allows cells to recycle Thz into the thiamine biosynthesis pathway, as an alternative to its synthesis from cysteine, tyrosine...; Region: THZ_kinase; cd01170 85962002266 substrate binding site [chemical binding]; other site 85962002267 multimerization interface [polypeptide binding]; other site 85962002268 ATP binding site [chemical binding]; other site 85962002269 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 85962002270 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 85962002271 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 85962002272 ATP binding site [chemical binding]; other site 85962002273 putative Mg++ binding site [ion binding]; other site 85962002274 Type I restriction and modification enzyme - subunit R C terminal; Region: EcoR124_C; pfam12008 85962002275 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 85962002276 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 85962002277 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 85962002278 type I restriction system adenine methylase (hsdM); Region: hsdM; TIGR00497 85962002279 HsdM N-terminal domain; Region: HsdM_N; pfam12161 85962002280 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 85962002281 S-adenosylmethionine binding site [chemical binding]; other site 85962002282 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 85962002283 PAP2_like_2 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_2; cd03392 85962002284 active site 85962002285 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2958 85962002286 HB1, ASXL, restriction endonuclease HTH domain; Region: HARE-HTH; cl01319 85962002287 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 85962002288 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 85962002289 AAA domain; Region: AAA_17; pfam13207 85962002290 ABC transporter; Region: ABC_tran_2; pfam12848 85962002291 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 85962002292 guanosine 5'-monophosphate oxidoreductase; Provisional; Region: PRK05458 85962002293 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 85962002294 active site 85962002295 Predicted membrane protein involved in D-alanine export [Cell envelope biogenesis, outer membrane]; Region: DltB; COG1696 85962002296 Phosphoheptose isomerase is a member of the SIS (Sugar ISomerase) superfamily. Phosphoheptose isomerase catalyzes the isomerization of sedoheptulose 7-phosphate into D-glycero-D-mannoheptose 7-phosphate. This is the first step of the biosynthesis of...; Region: SIS_GmhA; cd05006 85962002297 dimer interface [polypeptide binding]; other site 85962002298 active site 85962002299 ADP-heptose synthase, bifunctional sugar kinase/adenylyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaE; COG2870 85962002300 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 85962002301 putative ribose interaction site [chemical binding]; other site 85962002302 putative ADP binding site [chemical binding]; other site 85962002303 rfaE bifunctional protein, domain II; Region: rfaE_dom_II; TIGR02199 85962002304 active site 85962002305 nucleotide binding site [chemical binding]; other site 85962002306 HIGH motif; other site 85962002307 KMSKS motif; other site 85962002308 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 85962002309 ADP-L-glycero-D-manno-heptose-6-epimerase; Region: heptose_epim; TIGR02197 85962002310 NAD(P) binding site [chemical binding]; other site 85962002311 active site 85962002312 D,D-heptose 1,7-bisphosphate phosphatase; Region: GmhB_yaeD; TIGR00213 85962002313 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 85962002314 active site 85962002315 motif I; other site 85962002316 motif II; other site 85962002317 Uncharacterized conserved protein [Function unknown]; Region: COG2836 85962002318 pantothenate kinase; Reviewed; Region: PRK13333 85962002319 PQQ-like domain; Region: PQQ_2; pfam13360 85962002320 Plasminogen-binding protein pgbA C-terminal; Region: PGBA_C; pfam15437 85962002321 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 85962002322 trimer interface [polypeptide binding]; other site 85962002323 active site 85962002324 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 85962002325 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 85962002326 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 85962002327 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 85962002328 lipid-A-disaccharide synthase; Region: lpxB; TIGR00215 85962002329 hydrogenase nickel incorporation protein; Provisional; Region: hypA; PRK00564 85962002330 flagellar hook protein FlgE; Validated; Region: flgE; PRK08425 85962002331 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 85962002332 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 85962002333 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 85962002334 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 85962002335 CDP-diacylglycerol pyrophosphatase, bacterial type; Region: cdh; TIGR00672 85962002336 alkylphosphonate utilization operon protein PhnA; Region: phnA; TIGR00686 85962002337 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; pfam08274 85962002338 PhnA protein; Region: PhnA; pfam03831 85962002339 ferrous iron transport protein B; Reviewed; Region: feoB; PRK09554 85962002340 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 85962002341 Clade 3 of the heme-binding enzyme catalase; Region: catalase_clade_3; cd08156 85962002342 tetramer interface [polypeptide binding]; other site 85962002343 heme binding pocket [chemical binding]; other site 85962002344 NADPH binding site [chemical binding]; other site 85962002345 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 85962002346 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 85962002347 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 85962002348 active site 85962002349 putative DNA-binding cleft [nucleotide binding]; other site 85962002350 dimer interface [polypeptide binding]; other site 85962002351 Uncharacterized conserved protein [Function unknown]; Region: COG1432 85962002352 Uncharacterized conserved protein [Function unknown]; Region: COG1432 85962002353 LabA_like proteins; Region: LabA_like; cd06167 85962002354 putative metal binding site [ion binding]; other site 85962002355 chromosome segregation protein SMC, primarily archaeal type; Region: SMC_prok_A; TIGR02169 85962002356 Holliday junction DNA helicase, RuvA subunit; Region: ruvA; TIGR00084 85962002357 RuvA N terminal domain; Region: RuvA_N; pfam01330 85962002358 Helix-hairpin-helix domain; Region: HHH_5; pfam14520 85962002359 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 85962002360 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 85962002361 MviN-like protein; Region: MVIN; pfam03023 85962002362 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 85962002363 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 85962002364 active site 85962002365 HIGH motif; other site 85962002366 KMSKS motif; other site 85962002367 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 85962002368 tRNA binding surface [nucleotide binding]; other site 85962002369 anticodon binding site; other site 85962002370 Vacuolating cyotoxin; Region: VacA; pfam02691 85962002371 Autotransporter beta-domain; Region: Autotransporter; pfam03797 85962002372 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 85962002373 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 85962002374 Walker A/P-loop; other site 85962002375 ATP binding site [chemical binding]; other site 85962002376 Q-loop/lid; other site 85962002377 ABC transporter signature motif; other site 85962002378 Walker B; other site 85962002379 D-loop; other site 85962002380 H-loop/switch region; other site 85962002381 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 85962002382 ABC-ATPase subunit interface; other site 85962002383 dimer interface [polypeptide binding]; other site 85962002384 putative PBP binding regions; other site 85962002385 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 85962002386 short chain dehydrogenase; Provisional; Region: PRK06914 85962002387 NADP binding site [chemical binding]; other site 85962002388 active site 85962002389 steroid binding site; other site 85962002390 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 85962002391 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3041 85962002392 inosine 5-monophosphate dehydrogenase; Validated; Region: PRK06843 85962002393 addiction module toxin component, YafQ family; Region: TIGR00053 85962002394 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962002395 hydrogenase expression/formation protein HypD; Region: hypD; TIGR00075 85962002396 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypC; COG0298 85962002397 hydrogenase accessory protein HypB; Region: hypB; TIGR00073 85962002398 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 85962002399 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 85962002400 acetate kinase A/propionate kinase 2; Reviewed; Region: PRK00180 85962002401 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 85962002402 flagellar basal body rod modification protein; Reviewed; Region: flgD; PRK05842 85962002403 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 85962002404 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 85962002405 flagellar hook protein FlgE; Validated; Region: flgE; PRK05841 85962002406 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 85962002407 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 85962002408 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0827 85962002409 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 85962002410 S-adenosylmethionine binding site [chemical binding]; other site 85962002411 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 85962002412 Part of AAA domain; Region: AAA_19; pfam13245 85962002413 UvrD-like helicase C-terminal domain; Region: UvrD_C_2; pfam13538 85962002414 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962002415 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962002416 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 85962002417 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 85962002418 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 85962002419 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 85962002420 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 85962002421 ATP-grasp domain; Region: ATP-grasp_4; cl17255 85962002422 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; smart01096 85962002423 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 85962002424 ATP-grasp domain; Region: ATP-grasp_4; cl17255 85962002425 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 85962002426 IMP binding site; other site 85962002427 dimer interface [polypeptide binding]; other site 85962002428 interdomain contacts; other site 85962002429 partial ornithine binding site; other site 85962002430 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 85962002431 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; pfam00044 85962002432 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 85962002433 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 85962002434 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 85962002435 The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature; Region: BAR; cl12013 85962002436 Outer membrane protein (OmpH-like); Region: OmpH; pfam03938 85962002437 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 85962002438 PPE-repeat proteins [Cell motility and secretion]; Region: COG5651 85962002439 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 85962002440 Autotransporter beta-domain; Region: Autotransporter; pfam03797 85962002441 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962002442 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cd00491 85962002443 active site 1 [active] 85962002444 dimer interface [polypeptide binding]; other site 85962002445 hexamer interface [polypeptide binding]; other site 85962002446 active site 2 [active] 85962002447 recombination protein RecR; Region: recR; TIGR00615 85962002448 RecR protein; Region: RecR; pfam02132 85962002449 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 85962002450 putative active site [active] 85962002451 putative metal-binding site [ion binding]; other site 85962002452 tetramer interface [polypeptide binding]; other site 85962002453 Pseudouridine synthase, similar to Escherichia coli TruD; Region: PseudoU_synth_EcTruD; cd02575 85962002454 Permutation of conserved domain; other site 85962002455 active site 85962002456 heat shock protein HtpX; Provisional; Region: PRK02870 85962002457 GTP cyclohydrolase I; Region: folE; TIGR00063 85962002458 active site 85962002459 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 85962002460 substrate binding pocket [chemical binding]; other site 85962002461 chain length determination region; other site 85962002462 substrate-Mg2+ binding site; other site 85962002463 catalytic residues [active] 85962002464 aspartate-rich region 1; other site 85962002465 active site lid residues [active] 85962002466 aspartate-rich region 2; other site 85962002467 5'/3'-nucleotidase SurE; Region: surE; TIGR00087 85962002468 6-pyruvoyl-tetrahydropterin synthase [Coenzyme metabolism]; Region: COG0720 85962002469 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 85962002470 4Fe-4S single cluster domain; Region: Fer4_14; pfam13394 85962002471 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 85962002472 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 85962002473 Coenzyme A binding pocket [chemical binding]; other site 85962002474 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 85962002475 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 85962002476 putative substrate translocation pore; other site 85962002477 Uncharacterized conserved protein [Function unknown]; Region: COG1479 85962002478 Protein of unknown function DUF262; Region: DUF262; pfam03235 85962002479 ABC-type amino acid transport system, permease component [Amino acid transport and metabolism]; Region: HisM; COG0765 85962002480 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 85962002481 dimer interface [polypeptide binding]; other site 85962002482 conserved gate region; other site 85962002483 putative PBP binding loops; other site 85962002484 ABC-ATPase subunit interface; other site 85962002485 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 85962002486 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 85962002487 substrate binding pocket [chemical binding]; other site 85962002488 membrane-bound complex binding site; other site 85962002489 hinge residues; other site 85962002490 alanine racemase; Region: alr; TIGR00492 85962002491 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 85962002492 active site 85962002493 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 85962002494 dimer interface [polypeptide binding]; other site 85962002495 substrate binding site [chemical binding]; other site 85962002496 catalytic residues [active] 85962002497 amino acid carrier protein; Region: agcS; TIGR00835 85962002498 FAD dependent oxidoreductase; Region: DAO; pfam01266 85962002499 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl19134 85962002500 YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no...; Region: YjgF_YER057c_UK114_family; cd00448 85962002501 homotrimer interaction site [polypeptide binding]; other site 85962002502 putative active site [active] 85962002503 TRL-like protein family; Region: TRL; pfam13146 85962002504 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 85962002505 Na+/H+ antiporter family; Region: Na_H_antiporter; pfam03553 85962002506 DRE-TIM metallolyase superfamily; Region: DRE_TIM_metallolyase; cl18962 85962002507 Uncharacterized conserved protein [Function unknown]; Region: COG1576 85962002508 acetyl-CoA carboxylase, carboxyl transferase, beta subunit; Region: accD; TIGR00515 85962002509 putative recombination protein RecO; Provisional; Region: PRK13908 85962002510 competence/damage-inducible protein CinA C-terminal domain; Region: cinA_cterm; TIGR00199 85962002511 NAD(P)H:FMN oxidoreductase family. This domain catalyzes the reduction of flavin, nitrocompound, quinones and azo compounds using NADH or NADPH as an electron donor. The enzyme is a homodimer, and each monomer binds a FMN as co-factor. This family...; Region: NfsB_like_nitroreductase; cd02149 85962002512 dimer interface [polypeptide binding]; other site 85962002513 FMN binding site [chemical binding]; other site 85962002514 prolipoprotein diacylglyceryl transferase; Region: lgt; TIGR00544 85962002515 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 85962002516 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 85962002517 active site 85962002518 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 85962002519 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 85962002520 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 85962002521 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]; Region: COG1579 85962002522 Putative zinc ribbon domain; Region: DUF164; pfam02591 85962002523 dinuclear metal center protein, YbgI/SA1388 family; Region: YbgI_SA1388; TIGR00486 85962002524 Class II Glycyl-tRNA synthetase (GlyRS) alpha subunit core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes and in arabidopsis. It is responsible for the...; Region: GlyRS_alpha_core; cd00733 85962002525 dimer interface [polypeptide binding]; other site 85962002526 motif 1; other site 85962002527 active site 85962002528 motif 2; other site 85962002529 motif 3; other site 85962002530 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 85962002531 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 85962002532 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 85962002533 acyl carrier protein; Provisional; Region: acpP; PRK00982 85962002534 Predicted GTPases (dynamin-related) [General function prediction only]; Region: COG0699 85962002535 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 85962002536 G1 box; other site 85962002537 GTP/Mg2+ binding site [chemical binding]; other site 85962002538 G2 box; other site 85962002539 Switch I region; other site 85962002540 G3 box; other site 85962002541 Switch II region; other site 85962002542 G4 box; other site 85962002543 G5 box; other site 85962002544 Mnd1 family; Region: Mnd1; pfam03962 85962002545 Circularly permuted YlqF-related GTPases; Region: YlqF_related_GTPase; cl17249 85962002546 GTP/Mg2+ binding site [chemical binding]; other site 85962002547 G5 box; other site 85962002548 Predicted GTPases (dynamin-related) [General function prediction only]; Region: COG0699 85962002549 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 85962002550 G1 box; other site 85962002551 G1 box; other site 85962002552 GTP/Mg2+ binding site [chemical binding]; other site 85962002553 G2 box; other site 85962002554 Switch I region; other site 85962002555 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 85962002556 G3 box; other site 85962002557 Switch II region; other site 85962002558 G4 box; other site 85962002559 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 85962002560 G1 box; other site 85962002561 GTP/Mg2+ binding site [chemical binding]; other site 85962002562 Predicted GTPases (dynamin-related) [General function prediction only]; Region: COG0699 85962002563 G2 box; other site 85962002564 Switch I region; other site 85962002565 G3 box; other site 85962002566 Switch II region; other site 85962002567 G4 box; other site 85962002568 Uncharacterized virulence-associated protein D [Function unknown]; Region: VapD; COG3309 85962002569 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 85962002570 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 85962002571 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 85962002572 PRC-barrel domain; Region: PRC; pfam05239 85962002573 Biotin-lipoyl like; Region: Biotin_lipoyl_2; cl19169 85962002574 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 85962002575 Outer membrane efflux protein; Region: OEP; pfam02321 85962002576 glycyl-tRNA synthetase, tetrameric type, beta subunit; Region: glyS; TIGR00211 85962002577 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl17215 85962002578 2,3-bisphosphoglycerate-independent phosphoglycerate mutase; Region: pgm_bpd_ind; TIGR01307 85962002579 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C subunit; Region: gatC; TIGR00135 85962002580 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase [Coenzyme metabolism]; Region: BioA; COG0161 85962002581 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 85962002582 inhibitor-cofactor binding pocket; inhibition site 85962002583 pyridoxal 5'-phosphate binding site [chemical binding]; other site 85962002584 catalytic residue [active] 85962002585 SurA N-terminal domain; Region: SurA_N_3; cl07813 85962002586 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 85962002587 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 85962002588 cell division protein FtsA; Region: ftsA; TIGR01174 85962002589 Cell division protein FtsA; Region: FtsA; smart00842 85962002590 Cell division protein FtsA; Region: FtsA; pfam14450 85962002591 cell division protein FtsZ; Validated; Region: PRK09330 85962002592 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 85962002593 nucleotide binding site [chemical binding]; other site 85962002594 SulA interaction site; other site 85962002595 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 85962002596 active site 85962002597 Exonuclease VII, large subunit [DNA replication, recombination, and repair]; Region: XseA; COG1570 85962002598 Mechanosensitive ion channel; Region: MS_channel; pfam00924 85962002599 Domain of unknown function (DUF1887); Region: DUF1887; pfam09002 85962002600 Type IV secretory pathway, VirD2 components (relaxase) [Intracellular trafficking and secretion]; Region: VirD2; COG3843 85962002601 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG1943 85962002602 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 85962002603 Helix-turn-helix domain; Region: HTH_OrfB_IS605; pfam12323 85962002604 Probable transposase; Region: OrfB_IS605; pfam01385 85962002605 Putative transposase DNA-binding domain; Region: OrfB_Zn_ribbon; pfam07282 85962002606 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 85962002607 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 85962002608 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 85962002609 active site 85962002610 catalytic residues [active] 85962002611 DNA binding site [nucleotide binding] 85962002612 Int/Topo IB signature motif; other site 85962002613 Type IV secretory pathway, VirD2 components (relaxase) [Intracellular trafficking and secretion]; Region: VirD2; COG3843 85962002614 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 85962002615 Helix-turn-helix domain; Region: HTH_OrfB_IS605; pfam12323 85962002616 Probable transposase; Region: OrfB_IS605; pfam01385 85962002617 Putative transposase DNA-binding domain; Region: OrfB_Zn_ribbon; pfam07282 85962002618 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG1943 85962002619 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 85962002620 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 85962002621 P-loop; other site 85962002622 Magnesium ion binding site [ion binding]; other site 85962002623 Type IV secretory pathway, VirD4 components [Intracellular trafficking and secretion]; Region: VirD4; COG3505 85962002624 TraM recognition site of TraD and TraG; Region: TraG-D_C; pfam12696 85962002625 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG1943 85962002626 Polyphosphate kinase [Inorganic ion transport and metabolism]; Region: Ppk; COG0855 85962002627 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 85962002628 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 85962002629 Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C1_like; cd09165 85962002630 putative domain interface [polypeptide binding]; other site 85962002631 putative active site [active] 85962002632 catalytic site [active] 85962002633 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 85962002634 putative domain interface [polypeptide binding]; other site 85962002635 putative active site [active] 85962002636 catalytic site [active] 85962002637 dihydroorotate dehydrogenase, subfamily 2; Region: pyrD_sub2; TIGR01036 85962002638 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 85962002639 quinone interaction residues [chemical binding]; other site 85962002640 active site 85962002641 catalytic residues [active] 85962002642 FMN binding site [chemical binding]; other site 85962002643 substrate binding site [chemical binding]; other site 85962002644 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 85962002645 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 85962002646 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 85962002647 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 85962002648 dimer interface [polypeptide binding]; other site 85962002649 active site 85962002650 catalytic residue [active] 85962002651 7-alpha-hydroxysteroid dehydrogenase; Provisional; Region: PRK08416 85962002652 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK08063 85962002653 NAD(P) binding site [chemical binding]; other site 85962002654 active site 85962002655 CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase; Region: pgsA; TIGR00560 85962002656 Amino acid transporters [Amino acid transport and metabolism]; Region: LysP; COG0833 85962002657 Transmembrane amino acid transporter protein; Region: Aa_trans; cl17468 85962002658 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 85962002659 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 85962002660 PDZ domain of trypsin-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 85962002661 protein binding site [polypeptide binding]; other site 85962002662 PDZ domain of trypsin-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 85962002663 protein binding site [polypeptide binding]; other site 85962002664 bifunctional 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase/2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase protein; Provisional; Region: ispDF; PRK09382 85962002665 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 85962002666 substrate binding site; other site 85962002667 dimer interface; other site 85962002668 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 85962002669 homotrimer interaction site [polypeptide binding]; other site 85962002670 zinc binding site [ion binding]; other site 85962002671 CDP-binding sites; other site 85962002672 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 85962002673 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 85962002674 active site 85962002675 dimerization interface [polypeptide binding]; other site 85962002676 5'-3' exonuclease; Provisional; Region: PRK14976 85962002677 PIN (PilT N terminus) domain: Superfamily; Region: PIN_SF; cl14812 85962002678 putative active site [active] 85962002679 Helix-hairpin-helix class 2 (Pol1 family) motifs; Region: HhH2; smart00279 85962002680 DNA binding site [nucleotide binding] 85962002681 metal binding site [ion binding]; metal-binding site 85962002682 chaperone protein DnaJ; Region: DnaJ_bact; TIGR02349 85962002683 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 85962002684 HSP70 interaction site [polypeptide binding]; other site 85962002685 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 85962002686 substrate binding site [polypeptide binding]; other site 85962002687 dimer interface [polypeptide binding]; other site 85962002688 Helix-Turn-Helix DNA binding domain of the HspR transcription regulator; Region: HTH_HspR; cd04766 85962002689 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 85962002690 DNA binding residues [nucleotide binding] 85962002691 putative dimer interface [polypeptide binding]; other site 85962002692 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]; Region: MGS1; COG2256 85962002693 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 85962002694 Walker A motif; other site 85962002695 ATP binding site [chemical binding]; other site 85962002696 Walker B motif; other site 85962002697 arginine finger; other site 85962002698 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 85962002699 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 85962002700 metal binding site 2 [ion binding]; metal-binding site 85962002701 putative DNA binding helix; other site 85962002702 metal binding site 1 [ion binding]; metal-binding site 85962002703 dimer interface [polypeptide binding]; other site 85962002704 structural Zn2+ binding site [ion binding]; other site 85962002705 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4731 85962002706 Beta-galactosidase, beta subunit [Carbohydrate transport and metabolism]; Region: EbgC; COG2731 85962002707 flagellar motor switch protein FliY; Validated; Region: PRK08432 85962002708 flagellar motor switch protein FliN; Region: fliN; TIGR02480 85962002709 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 85962002710 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 85962002711 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 85962002712 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 85962002713 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 85962002714 DNA binding residues [nucleotide binding] 85962002715 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 85962002716 FleN is a member of the Fer4_NifH superfamily. It shares the common function as an ATPase, with the ATP-binding domain at the N-terminus. In Pseudomonas aeruginosa, FleN gene is involved in regulating the number of flagella and chemotactic motility by...; Region: FleN-like; cd02038 85962002717 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 85962002718 P-loop; other site 85962002719 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK05703 85962002720 SRP54-type protein, GTPase domain; Region: SRP54; pfam00448 85962002721 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK). Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and amino acids as well as formyl-tRNA. Mammalian cells are able to utilize pre-formed folates after...; Region: HPPK; cd00483 85962002722 catalytic center binding site [active] 85962002723 ATP binding site [chemical binding]; other site 85962002724 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 85962002725 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 85962002726 Similar to Prolidase and Aminopeptidase P. The members of this subfamily presumably catalyse hydrolysis of Xaa-Pro dipeptides and/or release of any N-terminal amino acid, including proline, that is linked with proline; Region: APP-like; cd01092 85962002727 active site 85962002728 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 85962002729 trimer interface [polypeptide binding]; other site 85962002730 active site 85962002731 dimer interface [polypeptide binding]; other site 85962002732 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 85962002733 O-Antigen ligase; Region: Wzy_C; pfam04932 85962002734 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 85962002735 16S/18S rRNA binding site [nucleotide binding]; other site 85962002736 S13e-L30e interaction site [polypeptide binding]; other site 85962002737 25S rRNA binding site [nucleotide binding]; other site 85962002738 flagellar biosynthesis protein FlhA; Region: FlhA; TIGR01398 85962002739 Predicted phosphohydrolase (DHH superfamily) [General function prediction only]; Region: COG2404 85962002740 DHH family; Region: DHH; pfam01368 85962002741 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 85962002742 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 85962002743 active site 85962002744 intermolecular recognition site; other site 85962002745 dimerization interface [polypeptide binding]; other site 85962002746 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 85962002747 DNA binding site [nucleotide binding] 85962002748 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 85962002749 Predicted phosphohydrolases [General function prediction only]; Region: Icc; COG1409 85962002750 putative active site [active] 85962002751 putative metal binding site [ion binding]; other site 85962002752 acetyl-CoA synthetase; Provisional; Region: PRK00174 85962002753 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 85962002754 active site 85962002755 CoA binding site [chemical binding]; other site 85962002756 acyl-activating enzyme (AAE) consensus motif; other site 85962002757 AMP binding site [chemical binding]; other site 85962002758 acetate binding site [chemical binding]; other site 85962002759 Sm and related proteins; Region: Sm_like; cl00259 85962002760 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 85962002761 putative oligomer interface [polypeptide binding]; other site 85962002762 putative RNA binding site [nucleotide binding]; other site 85962002763 ribosome-binding factor A; Region: rbfA; TIGR00082 85962002764 translation initiation factor IF-2; Region: IF-2; TIGR00487 85962002765 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 85962002766 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 85962002767 G1 box; other site 85962002768 putative GEF interaction site [polypeptide binding]; other site 85962002769 GTP/Mg2+ binding site [chemical binding]; other site 85962002770 Switch I region; other site 85962002771 G2 box; other site 85962002772 G3 box; other site 85962002773 Switch II region; other site 85962002774 G4 box; other site 85962002775 G5 box; other site 85962002776 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 85962002777 Translation-initiation factor 2; Region: IF-2; pfam11987 85962002778 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 85962002779 Predicted nucleic-acid-binding protein implicated in transcription termination [Transcription]; Region: COG2740 85962002780 putative RNA binding cleft [nucleotide binding]; other site 85962002781 homoserine kinase; Region: thrB; TIGR00191 85962002782 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 85962002783 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214 85962002784 UDP-3-0-acyl N-acetylglucosamine deacetylase; Region: lpxC; TIGR00325 85962002785 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 85962002786 septum formation inhibitor; Reviewed; Region: minC; PRK00556 85962002787 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 85962002788 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 85962002789 Peptidase family M23; Region: Peptidase_M23; pfam01551 85962002790 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962002791 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962002792 Ketopantoate hydroxymethyltransferase (KPHMT) is the first enzyme in the pantothenate biosynthesis pathway. Ketopantoate hydroxymethyltransferase (KPHMT) catalyzes the first committed step in the biosynthesis of pantothenate (vitamin B5), which is a...; Region: KPHMT-like; cd06557 85962002793 oligomerization interface [polypeptide binding]; other site 85962002794 active site 85962002795 metal binding site [ion binding]; metal-binding site 85962002796 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 85962002797 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 85962002798 Walker A motif; other site 85962002799 ATP binding site [chemical binding]; other site 85962002800 Walker B motif; other site 85962002801 arginine finger; other site 85962002802 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 85962002803 sec-independent translocase; Provisional; Region: PRK04098 85962002804 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 85962002805 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 85962002806 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 85962002807 S-adenosylmethionine binding site [chemical binding]; other site 85962002808 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962002809 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 85962002810 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 85962002811 active site 85962002812 phosphorylation site [posttranslational modification] 85962002813 intermolecular recognition site; other site 85962002814 dimerization interface [polypeptide binding]; other site 85962002815 ribosomal protein L11 methyltransferase; Region: prmA; TIGR00406 85962002816 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 85962002817 S-adenosylmethionine binding site [chemical binding]; other site 85962002818 FtsH Extracellular; Region: FtsH_ext; pfam06480 85962002819 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 85962002820 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 85962002821 Walker A motif; other site 85962002822 ATP binding site [chemical binding]; other site 85962002823 Walker B motif; other site 85962002824 arginine finger; other site 85962002825 Peptidase family M41; Region: Peptidase_M41; pfam01434 85962002826 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 85962002827 CDP-diacylglycerol--serine O-phosphatidyltransferase; Region: pssA; TIGR00473 85962002828 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 85962002829 metal-binding site [ion binding] 85962002830 fungal transcription factor regulatory middle homology region; Region: fungal_TF_MHR; cd12148 85962002831 copper-(or silver)-translocating P-type ATPase; Region: ATPase-IB1_Cu; TIGR01511 85962002832 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 85962002833 Soluble P-type ATPase [General function prediction only]; Region: COG4087 85962002834 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 85962002835 metal-binding site [ion binding] 85962002836 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cl11393 85962002837 active site 85962002838 Zn binding site [ion binding]; other site 85962002839 High-affinity nickel permease [Inorganic ion transport and metabolism]; Region: HoxN; COG3376 85962002840 Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from...; Region: TOPRIM; cd00188 85962002841 active site 85962002842 metal binding site [ion binding]; metal-binding site 85962002843 Predicted ATPases [General function prediction only]; Region: COG1106 85962002844 AAA domain; Region: AAA_23; pfam13476 85962002845 Walker A/P-loop; other site 85962002846 ATP binding site [chemical binding]; other site 85962002847 AAA domain; Region: AAA_21; pfam13304 85962002848 Predicted endonuclease distantly related to archaeal Holliday junction resolvase and Mrr-like restriction enzymes [Defense mechanisms]; Region: COG1787 85962002849 Restriction endonuclease; Region: Mrr_cat; pfam04471 85962002850 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 85962002851 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 85962002852 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 85962002853 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 85962002854 Walker A/P-loop; other site 85962002855 ATP binding site [chemical binding]; other site 85962002856 Q-loop/lid; other site 85962002857 ABC transporter signature motif; other site 85962002858 Walker B; other site 85962002859 D-loop; other site 85962002860 H-loop/switch region; other site 85962002861 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 85962002862 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 85962002863 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 85962002864 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 85962002865 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 85962002866 hemolysin TlyA family protein; Region: tly; TIGR00478 85962002867 RNA binding surface [nucleotide binding]; other site 85962002868 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 85962002869 S-adenosylmethionine binding site [chemical binding]; other site 85962002870 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 85962002871 riboflavin kinase/FMN adenylyltransferase; Region: ribF; TIGR00083 85962002872 active site 85962002873 Riboflavin kinase; Region: Flavokinase; smart00904 85962002874 transketolase, bacterial and yeast; Region: tktlase_bact; TIGR00232 85962002875 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 85962002876 TPP-binding site [chemical binding]; other site 85962002877 dimer interface [polypeptide binding]; other site 85962002878 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 85962002879 PYR/PP interface [polypeptide binding]; other site 85962002880 dimer interface [polypeptide binding]; other site 85962002881 TPP binding site [chemical binding]; other site 85962002882 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 85962002883 Inactivated superfamily I helicase [DNA replication, recombination, and repair]; Region: COG3893 85962002884 RecB family exonuclease [DNA replication, recombination, and repair]; Region: COG2887 85962002885 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 85962002886 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 85962002887 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 85962002888 alpha-ketoglutarate transporter; Provisional; Region: PRK10406 85962002889 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 85962002890 putative substrate translocation pore; other site 85962002891 Flagellar basal body rod protein [Cell motility and secretion]; Region: FlgG; COG4786 85962002892 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 85962002893 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 85962002894 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 85962002895 Helix-turn-helix domain; Region: HTH_OrfB_IS605; pfam12323 85962002896 Probable transposase; Region: OrfB_IS605; pfam01385 85962002897 Putative transposase DNA-binding domain; Region: OrfB_Zn_ribbon; pfam07282 85962002898 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG1943 85962002899 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 85962002900 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 85962002901 binding surface 85962002902 TPR motif; other site 85962002903 Sel1-like repeats; Region: SEL1; smart00671 85962002904 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 85962002905 TPR motif; other site 85962002906 binding surface 85962002907 Entner-Doudoroff aldolase; Region: eda; TIGR01182 85962002908 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 85962002909 active site 85962002910 intersubunit interface [polypeptide binding]; other site 85962002911 catalytic residue [active] 85962002912 6-phosphogluconate dehydratase; Region: edd; TIGR01196 85962002913 Glucose-6-phosphate 1-dehydrogenase [Carbohydrate transport and metabolism]; Region: Zwf; COG0364 85962002914 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 85962002915 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 85962002916 6PGL: 6-Phosphogluconolactonase (6PGL) subfamily; 6PGL catalyzes the second step of the oxidative phase of the pentose phosphate pathway, the hydrolyzation of 6-phosphoglucono-1,5-lactone (delta form) to 6-phosphogluconate. 6PGL is thought to guard...; Region: 6PGL; cd01400 85962002917 putative active site [active] 85962002918 glucokinase, proteobacterial type; Region: glk; TIGR00749 85962002919 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 85962002920 nucleotide binding site [chemical binding]; other site 85962002921 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 85962002922 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD1; cd05283 85962002923 putative NAD(P) binding site [chemical binding]; other site 85962002924 putative substrate binding site [chemical binding]; other site 85962002925 catalytic Zn binding site [ion binding]; other site 85962002926 structural Zn binding site [ion binding]; other site 85962002927 dimer interface [polypeptide binding]; other site 85962002928 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 85962002929 Glycosyl transferase family 8; Region: Glyco_transf_8; pfam01501 85962002930 active site 85962002931 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962002932 pyruvate flavodoxin oxidoreductase subunit gamma; Validated; Region: PRK05844 85962002933 pyruvate flavodoxin oxidoreductase subunit delta; Reviewed; Region: porD; PRK09625 85962002934 4Fe-4S binding domain; Region: Fer4; pfam00037 85962002935 pyruvate flavodoxin oxidoreductase subunit alpha; Reviewed; Region: porA; PRK09622 85962002936 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 85962002937 dimer interface [polypeptide binding]; other site 85962002938 PYR/PP interface [polypeptide binding]; other site 85962002939 TPP binding site [chemical binding]; other site 85962002940 substrate binding site [chemical binding]; other site 85962002941 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 85962002942 pyruvate ferredoxin oxidoreductase subunit beta; Provisional; Region: PRK11865 85962002943 Thiamine pyrophosphate (TPP family), PFOR porB-like subfamily, TPP-binding module; composed of proteins similar to the beta subunit (porB) of the Helicobacter pylori four-subunit pyruvate ferredoxin oxidoreductase (PFOR), which are also found in archaea...; Region: TPP_PFOR_porB_like; cd03376 85962002944 TPP-binding site [chemical binding]; other site 85962002945 putative dimer interface [polypeptide binding]; other site 85962002946 adenylosuccinate lyase; Provisional; Region: PRK08470 85962002947 Adenylsuccinate lyase (ASL)_subgroup 1; Region: Adenylsuccinate_lyase_1; cd01360 85962002948 tetramer interface [polypeptide binding]; other site 85962002949 active site 85962002950 Adenylosuccinate lyase C-terminus; Region: ADSL_C; smart00998 85962002951 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962002952 excinuclease ABC subunit B; Provisional; Region: PRK05298 85962002953 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 85962002954 ATP binding site [chemical binding]; other site 85962002955 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 85962002956 putative Mg++ binding site [ion binding]; other site 85962002957 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 85962002958 nucleotide binding region [chemical binding]; other site 85962002959 ATP-binding site [chemical binding]; other site 85962002960 Ultra-violet resistance protein B; Region: UvrB; pfam12344 85962002961 UvrB/uvrC motif; Region: UVR; pfam02151 85962002962 F0F1 ATP synthase subunit B; Provisional; Region: PRK14471; cl17192 85962002963 Protein of unknown function (DUF3519); Region: DUF3519; pfam12033 85962002964 Protein of unknown function (DUF3519); Region: DUF3519; pfam12033 85962002965 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 85962002966 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 85962002967 binding surface 85962002968 TPR motif; other site 85962002969 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 85962002970 binding surface 85962002971 TPR motif; other site 85962002972 gamma-glutamyltranspeptidase; Region: g_glut_trans; TIGR00066 85962002973 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK08471 85962002974 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 85962002975 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 85962002976 cofactor binding site; other site 85962002977 DNA binding site [nucleotide binding] 85962002978 substrate interaction site [chemical binding]; other site 85962002979 Anti-sigma-28 factor, FlgM; Region: FlgM; pfam04316 85962002980 FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]; Region: SlpA; COG1047 85962002981 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl19519 85962002982 phage lysis regulatory protein, LysB family; Region: phage_LysB; TIGR03495 85962002983 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 85962002984 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 85962002985 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 85962002986 ligand binding site [chemical binding]; other site 85962002987 translocation protein TolB; Provisional; Region: tolB; PRK04043 85962002988 TolB amino-terminal domain; Region: TolB_N; pfam04052 85962002989 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 85962002990 TolR protein; Region: tolR; TIGR02801 85962002991 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; pfam01618 85962002992 ATP synthase, F1 epsilon subunit (delta in mitochondria); Region: ATP_synt_epsi; TIGR01216 85962002993 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 85962002994 gamma subunit interface [polypeptide binding]; other site 85962002995 epsilon subunit interface [polypeptide binding]; other site 85962002996 LBP interface [polypeptide binding]; other site 85962002997 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 85962002998 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 85962002999 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 85962003000 alpha subunit interaction interface [polypeptide binding]; other site 85962003001 Walker A motif; other site 85962003002 ATP binding site [chemical binding]; other site 85962003003 Walker B motif; other site 85962003004 inhibitor binding site; inhibition site 85962003005 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 85962003006 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 85962003007 core domain interface [polypeptide binding]; other site 85962003008 delta subunit interface [polypeptide binding]; other site 85962003009 epsilon subunit interface [polypeptide binding]; other site 85962003010 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 85962003011 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 85962003012 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 85962003013 beta subunit interaction interface [polypeptide binding]; other site 85962003014 Walker A motif; other site 85962003015 ATP binding site [chemical binding]; other site 85962003016 Walker B motif; other site 85962003017 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 85962003018 F0F1 ATP synthase subunit delta; Provisional; Region: PRK13431 85962003019 F0F1 ATP synthase subunit B; Validated; Region: PRK08475 85962003020 F0F1 ATP synthase subunit B; Provisional; Region: PRK14471; cl17192 85962003021 F0F1 ATP synthase subunit B'; Validated; Region: PRK08476 85962003022 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 85962003023 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 85962003024 ParB-like nuclease domain; Region: ParB; smart00470 85962003025 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 85962003026 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 85962003027 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 85962003028 P-loop; other site 85962003029 Magnesium ion binding site [ion binding]; other site 85962003030 biotin--protein ligase; Provisional; Region: PRK08477 85962003031 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 85962003032 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 85962003033 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 85962003034 putative active site [active] 85962003035 substrate binding site [chemical binding]; other site 85962003036 putative cosubstrate binding site; other site 85962003037 catalytic site [active] 85962003038 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 85962003039 substrate binding site [chemical binding]; other site 85962003040 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4694 85962003041 Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunits; Region: iSH2_PI3K_IA_R; cl17108 85962003042 heterodimer interface [polypeptide binding]; other site 85962003043 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 85962003044 Walker B; other site 85962003045 D-loop; other site 85962003046 H-loop/switch region; other site 85962003047 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4487 85962003048 Lambda phage tail tape-measure protein (Tape_meas_lam_C); Region: Tape_meas_lam_C; cl19901 85962003049 Protein of unknown function (DUF342); Region: DUF342; cl19219 85962003050 Uncharacterized protein conserved in bacteria (DUF2130); Region: DUF2130; pfam09903 85962003051 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 85962003052 tRNA (guanine-N1)-methyltransferase; Region: trmD; TIGR00088 85962003053 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK14593 85962003054 RimM N-terminal domain; Region: RimM; pfam01782 85962003055 PRC-barrel domain; Region: PRC; pfam05239 85962003056 KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional...; Region: KH-II; cd02409 85962003057 G-X-X-G motif; other site 85962003058 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 85962003059 signal recognition particle protein; Provisional; Region: PRK10867 85962003060 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 85962003061 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 85962003062 P loop; other site 85962003063 GTP binding site [chemical binding]; other site 85962003064 Signal peptide binding domain; Region: SRP_SPB; pfam02978 85962003065 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 85962003066 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 85962003067 active site 85962003068 HIGH motif; other site 85962003069 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 85962003070 KMSKS motif; other site 85962003071 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 85962003072 tRNA binding surface [nucleotide binding]; other site 85962003073 anticodon binding site; other site 85962003074 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 85962003075 flagellar assembly protein FliW; Provisional; Region: PRK13283 85962003076 undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase; Region: murG; TIGR01133 85962003077 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 85962003078 homodimer interface [polypeptide binding]; other site 85962003079 active site 85962003080 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962003081 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962003082 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 85962003083 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; pfam03807 85962003084 Pyrroline-5-carboxylate reductase dimerization; Region: P5CR_dimer; pfam14748 85962003085 Protein involved in cell division [Cell division and chromosome partitioning]; Region: Fic; COG2184 85962003086 metal-binding heat shock protein; Provisional; Region: PRK00016 85962003087 flavodoxin FldA; Validated; Region: PRK09267 85962003088 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 85962003089 Uncharacterized protein, possibly involved in nitrogen fixation [Inorganic ion transport and metabolism]; Region: FixS; COG3197 85962003090 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 85962003091 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl19134 85962003092 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 85962003093 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 85962003094 putative substrate translocation pore; other site 85962003095 Major Facilitator Superfamily; Region: MFS_1; pfam07690 85962003096 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 85962003097 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 85962003098 active site 85962003099 dimer interface [polypeptide binding]; other site 85962003100 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 85962003101 dimer interface [polypeptide binding]; other site 85962003102 active site 85962003103 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 85962003104 carbon starvation protein A; Provisional; Region: PRK15015 85962003105 Carbon starvation protein CstA; Region: CstA; pfam02554 85962003106 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 85962003107 ABC-type amino acid transport system, permease component [Amino acid transport and metabolism]; Region: HisM; COG0765 85962003108 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 85962003109 dimer interface [polypeptide binding]; other site 85962003110 conserved gate region; other site 85962003111 putative PBP binding loops; other site 85962003112 ABC-ATPase subunit interface; other site 85962003113 ABC-type amino acid transport system, permease component [Amino acid transport and metabolism]; Region: HisM; COG0765 85962003114 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 85962003115 dimer interface [polypeptide binding]; other site 85962003116 conserved gate region; other site 85962003117 putative PBP binding loops; other site 85962003118 ABC-ATPase subunit interface; other site 85962003119 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 85962003120 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 85962003121 Walker A/P-loop; other site 85962003122 ATP binding site [chemical binding]; other site 85962003123 Q-loop/lid; other site 85962003124 ABC transporter signature motif; other site 85962003125 Walker B; other site 85962003126 D-loop; other site 85962003127 H-loop/switch region; other site 85962003128 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 85962003129 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 85962003130 substrate binding pocket [chemical binding]; other site 85962003131 membrane-bound complex binding site; other site 85962003132 hinge residues; other site 85962003133 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 85962003134 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 85962003135 putative substrate translocation pore; other site 85962003136 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 85962003137 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962003138 purine-nucleoside phosphorylase, family 1 (deoD); Region: deoD; TIGR00107 85962003139 phosphopentomutase; Provisional; Region: PRK05362 85962003140 Nucleoside permease [Nucleotide transport and metabolism]; Region: NupC; COG1972 85962003141 Na+ dependent nucleoside transporter N-terminus; Region: Nucleos_tra2_N; pfam01773 85962003142 Nucleoside recognition; Region: Gate; pfam07670 85962003143 Na+ dependent nucleoside transporter C-terminus; Region: Nucleos_tra2_C; pfam07662 85962003144 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 85962003145 Major Facilitator Superfamily; Region: MFS_1; pfam07690 85962003146 putative substrate translocation pore; other site 85962003147 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 85962003148 This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This subfamily; Region: Alpha_ANH_like_II; cd01993 85962003149 Ligand Binding Site [chemical binding]; other site 85962003150 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 85962003151 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 85962003152 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA; Region: MATE_MepA_like; cd13143 85962003153 putative arabinose transporter; Provisional; Region: PRK03545 85962003154 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 85962003155 putative substrate translocation pore; other site 85962003156 Carbonic anhydrase alpha, prokaryotic-like subfamily. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon...; Region: alpha_CA_prokaryotic_like; cd03124 85962003157 active site 85962003158 zinc binding site [ion binding]; other site 85962003159 Helicobacter pylori protein of unknown function (DUF874); Region: DUF874; pfam05917 85962003160 aspartate-semialdehyde dehydrogenase (peptidoglycan organisms); Region: asd_B; TIGR01296 85962003161 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; pfam01118 85962003162 Semialdehyde dehydrogenase, dimerization domain; Region: Semialdhyde_dhC; pfam02774 85962003163 Histidyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: HisS; COG0124 85962003164 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 85962003165 dimer interface [polypeptide binding]; other site 85962003166 motif 1; other site 85962003167 active site 85962003168 motif 2; other site 85962003169 motif 3; other site 85962003170 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 85962003171 anticodon binding site; other site 85962003172 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 85962003173 putative active site [active] 85962003174 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 85962003175 voltage-dependent potassium channel beta subunit, animal; Region: Kv_beta; TIGR01293 85962003176 active site 85962003177 catalytic tetrad [active] 85962003178 elongation factor G; Reviewed; Region: PRK00007 85962003179 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 85962003180 G1 box; other site 85962003181 putative GEF interaction site [polypeptide binding]; other site 85962003182 GTP/Mg2+ binding site [chemical binding]; other site 85962003183 Switch I region; other site 85962003184 G2 box; other site 85962003185 G3 box; other site 85962003186 Switch II region; other site 85962003187 G4 box; other site 85962003188 G5 box; other site 85962003189 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 85962003190 Elongation Factor G, domain II; Region: EFG_II; pfam14492 85962003191 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 85962003192 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 85962003193 30S ribosomal protein S7; Validated; Region: PRK05302 85962003194 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 85962003195 S17 interaction site [polypeptide binding]; other site 85962003196 S8 interaction site; other site 85962003197 16S rRNA interaction site [nucleotide binding]; other site 85962003198 streptomycin interaction site [chemical binding]; other site 85962003199 23S rRNA interaction site [nucleotide binding]; other site 85962003200 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 85962003201 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed; Region: PRK09603 85962003202 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 85962003203 RPB12 interaction site [polypeptide binding]; other site 85962003204 RPB1 interaction site [polypeptide binding]; other site 85962003205 RNA polymerase beta subunit external 1 domain; Region: RNA_pol_Rpb2_45; pfam10385 85962003206 RPB10 interaction site [polypeptide binding]; other site 85962003207 RPB11 interaction site [polypeptide binding]; other site 85962003208 RPB3 interaction site [polypeptide binding]; other site 85962003209 Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; Region: RNAP_beta'_N; cd01609 85962003210 beta and beta' interface [polypeptide binding]; other site 85962003211 beta' and sigma factor interface [polypeptide binding]; other site 85962003212 Zn-binding [ion binding]; other site 85962003213 active site region [active] 85962003214 catalytic site [active] 85962003215 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 85962003216 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 85962003217 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 85962003218 DNA binding site [nucleotide binding] 85962003219 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 85962003220 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 85962003221 core dimer interface [polypeptide binding]; other site 85962003222 peripheral dimer interface [polypeptide binding]; other site 85962003223 L10 interface [polypeptide binding]; other site 85962003224 L11 interface [polypeptide binding]; other site 85962003225 putative EF-Tu interaction site [polypeptide binding]; other site 85962003226 putative EF-G interaction site [polypeptide binding]; other site 85962003227 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 85962003228 23S rRNA interface [nucleotide binding]; other site 85962003229 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 85962003230 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 85962003231 mRNA/rRNA interface [nucleotide binding]; other site 85962003232 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 85962003233 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 85962003234 23S rRNA interface [nucleotide binding]; other site 85962003235 L7/L12 interface [polypeptide binding]; other site 85962003236 putative thiostrepton binding site; other site 85962003237 L25 interface [polypeptide binding]; other site 85962003238 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 85962003239 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 85962003240 putative homodimer interface [polypeptide binding]; other site 85962003241 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 85962003242 heterodimer interface [polypeptide binding]; other site 85962003243 homodimer interface [polypeptide binding]; other site 85962003244 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK07597 85962003245 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 85962003246 elongation factor Tu; Reviewed; Region: PRK00049 85962003247 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 85962003248 G1 box; other site 85962003249 GEF interaction site [polypeptide binding]; other site 85962003250 GTP/Mg2+ binding site [chemical binding]; other site 85962003251 Switch I region; other site 85962003252 G2 box; other site 85962003253 G3 box; other site 85962003254 Switch II region; other site 85962003255 G4 box; other site 85962003256 G5 box; other site 85962003257 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 85962003258 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 85962003259 Antibiotic Binding Site [chemical binding]; other site 85962003260 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 85962003261 ATP-binding cassette domain of multidrug resistance protein-like transporters; Region: ABCC_MRP_Like; cd03228 85962003262 Walker A/P-loop; other site 85962003263 ATP binding site [chemical binding]; other site 85962003264 Q-loop/lid; other site 85962003265 ABC transporter signature motif; other site 85962003266 Walker B; other site 85962003267 D-loop; other site 85962003268 H-loop/switch region; other site 85962003269 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 85962003270 haloacid dehalogenase-like hydrolase; Region: HAD; cl19137 85962003271 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG3392 85962003272 serine O-acetyltransferase; Region: cysE; TIGR01172 85962003273 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 85962003274 trimer interface [polypeptide binding]; other site 85962003275 active site 85962003276 substrate binding site [chemical binding]; other site 85962003277 CoA binding site [chemical binding]; other site 85962003278 F0F1 ATP synthase subunit C; Validated; Region: PRK08482 85962003279 RNase PH-like 3'-5' exoribonucleases; Region: RNase_PH; cl03114 85962003280 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 85962003281 oligomer interface [polypeptide binding]; other site 85962003282 RNA binding site [nucleotide binding]; other site 85962003283 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 85962003284 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 85962003285 RNase E interface [polypeptide binding]; other site 85962003286 trimer interface [polypeptide binding]; other site 85962003287 active site 85962003288 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 85962003289 putative nucleic acid binding region [nucleotide binding]; other site 85962003290 G-X-X-G motif; other site 85962003291 Ribosomal protein S1-like RNA-binding domain; Region: S1; smart00316 85962003292 RNA binding site [nucleotide binding]; other site 85962003293 Predicted phosphoribosyltransferases [General function prediction only]; Region: COG1926 85962003294 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 85962003295 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 85962003296 Organic solvent tolerance protein; Region: OstA_C; pfam04453 85962003297 Predicted membrane protein/domain [Function unknown]; Region: COG1714 85962003298 phosphoribosylamine--glycine ligase; Region: purD; TIGR00877 85962003299 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 85962003300 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 85962003301 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 85962003302 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 85962003303 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 85962003304 Walker A/P-loop; other site 85962003305 ATP binding site [chemical binding]; other site 85962003306 Q-loop/lid; other site 85962003307 ABC transporter signature motif; other site 85962003308 Walker B; other site 85962003309 D-loop; other site 85962003310 H-loop/switch region; other site 85962003311 Cis (Z)-Isoprenyl Diphosphate Synthases; Region: Cis_IPPS; cd00475 85962003312 active site 85962003313 dimer interface [polypeptide binding]; other site 85962003314 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 85962003315 FAD binding domain; Region: FAD_binding_4; pfam01565 85962003316 FAD linked oxidases, C-terminal domain; Region: FAD-oxidase_C; pfam02913 85962003317 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 85962003318 4Fe-4S dicluster domain; Region: Fer4_8; pfam13183 85962003319 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 85962003320 active site residue [active] 85962003321 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 85962003322 active site 85962003323 camphor resistance protein CrcB; Provisional; Region: PRK14204 85962003324 coproporphyrinogen III oxidase; Provisional; Region: PRK08446 85962003325 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 85962003326 FeS/SAM binding site; other site 85962003327 HemN C-terminal domain; Region: HemN_C; pfam06969 85962003328 Cytochrome c553 [Energy production and conversion]; Region: COG2863 85962003329 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 85962003330 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 85962003331 putative active site [active] 85962003332 Ap4A binding site [chemical binding]; other site 85962003333 nudix motif; other site 85962003334 putative metal binding site [ion binding]; other site 85962003335 aspartate kinase; Reviewed; Region: PRK06635 85962003336 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 85962003337 putative nucleotide binding site [chemical binding]; other site 85962003338 putative catalytic residues [active] 85962003339 putative Mg ion binding site [ion binding]; other site 85962003340 putative aspartate binding site [chemical binding]; other site 85962003341 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 85962003342 putative allosteric regulatory site; other site 85962003343 ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related domains; Region: ACT_AK-LysC-DapG-like_2; cd04923 85962003344 DNA replication regulator; Region: HobA; pfam12163 85962003345 DNA polymerase III subunit delta'; Validated; Region: PRK08485 85962003346 Dihydropteroate synthase and related enzymes [Coenzyme metabolism]; Region: FolP; COG0294 85962003347 DHPS subgroup of Pterin binding enzymes. DHPS (dihydropteroate synthase), a functional homodimer, catalyzes the condensation of p-aminobenzoic acid (pABA) in the de novo biosynthesis of folate, which is an essential cofactor in both nucleic acid and...; Region: DHPS; cd00739 85962003348 substrate binding pocket [chemical binding]; other site 85962003349 dimer interface [polypeptide binding]; other site 85962003350 inhibitor binding site; inhibition site 85962003351 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 85962003352 EamA-like transporter family; Region: EamA; pfam00892 85962003353 EamA-like transporter family; Region: EamA; cl17759 85962003354 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl19158 85962003355 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2952 85962003356 Carbamoylphosphate synthase small subunit [Amino acid transport and metabolism / Nucleotide transport and metabolism]; Region: CarA; COG0505 85962003357 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; pfam00988 85962003358 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 85962003359 catalytic site [active] 85962003360 subunit interface [polypeptide binding]; other site 85962003361 aliphatic amidases (class 2 nitrilases); Region: aliphatic_amidase; cd07565 85962003362 multimer interface [polypeptide binding]; other site 85962003363 active site 85962003364 catalytic triad [active] 85962003365 dimer interface [polypeptide binding]; other site 85962003366 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 85962003367 active site 85962003368 dimer interface [polypeptide binding]; other site 85962003369 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 85962003370 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 85962003371 motif 1; other site 85962003372 active site 85962003373 motif 2; other site 85962003374 motif 3; other site 85962003375 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 85962003376 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2841 85962003377 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962003378 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 85962003379 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 85962003380 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 85962003381 dimer interface [polypeptide binding]; other site 85962003382 ssDNA binding site [nucleotide binding]; other site 85962003383 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between...; Region: TroA-like; cl00262 85962003384 tetramer (dimer of dimers) interface [polypeptide binding]; other site 85962003385 intersubunit interface [polypeptide binding]; other site 85962003386 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 85962003387 DNA polymerase III subunit delta; Validated; Region: PRK08487 85962003388 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; cl19912 85962003389 Exoribonuclease R [Transcription]; Region: VacB; COG0557 85962003390 RNB domain; Region: RNB; pfam00773 85962003391 shikimate 5-dehydrogenase; Region: aroE; TIGR00507 85962003392 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 85962003393 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 85962003394 shikimate binding site; other site 85962003395 NAD(P) binding site [chemical binding]; other site 85962003396 Bacterial SH3 domain homologues; Region: SH3b; smart00287 85962003397 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4174 85962003398 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 85962003399 dimer interface [polypeptide binding]; other site 85962003400 conserved gate region; other site 85962003401 putative PBP binding loops; other site 85962003402 ABC-ATPase subunit interface; other site 85962003403 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 85962003404 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 85962003405 tryptophanyl-tRNA synthetase; Reviewed; Region: PRK00927 85962003406 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 85962003407 active site 85962003408 HIGH motif; other site 85962003409 dimer interface [polypeptide binding]; other site 85962003410 KMSKS motif; other site 85962003411 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 85962003412 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 85962003413 S-adenosylmethionine binding site [chemical binding]; other site 85962003414 Preprotein translocase subunit SecG [Intracellular trafficking and secretion]; Region: SecG; COG1314 85962003415 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 85962003416 hinge region; other site 85962003417 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 85962003418 active site 85962003419 RDD family; Region: RDD; pfam06271 85962003420 SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+; Region: SIR2; cl00195 85962003421 NADH dehydrogenase subunit A; Validated; Region: PRK08489 85962003422 NADH dehydrogenase subunit B; Validated; Region: PRK06411 85962003423 NADH dehydrogenase subunit C; Provisional; Region: PRK08491 85962003424 NADH dehydrogenase I, D subunit; Region: NuoD; TIGR01962 85962003425 Ni,Fe-hydrogenase III large subunit [Energy production and conversion]; Region: HycE; COG3261 85962003426 NADH dehydrogenase subunit G; Validated; Region: PRK08493 85962003427 NADH dehydrogenase subunit G; Validated; Region: PRK08493 85962003428 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 85962003429 catalytic loop [active] 85962003430 iron binding site [ion binding]; other site 85962003431 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 85962003432 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 85962003433 molybdopterin cofactor binding site; other site 85962003434 Domain of unknown function (DUF4350); Region: DUF4350; pfam14258 85962003435 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 85962003436 NADH-quinone oxidoreductase, chain I; Region: NuoI; TIGR01971 85962003437 4Fe-4S double cluster binding domain; Region: Fer4_16; pfam13484 85962003438 4Fe-4S dicluster domain; Region: Fer4_8; pfam13183 85962003439 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 85962003440 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 85962003441 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 85962003442 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 85962003443 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 85962003444 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 85962003445 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 85962003446 proton-translocating NADH-quinone oxidoreductase, chain N; Region: NDH_I_N; TIGR01770 85962003447 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 85962003448 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 85962003449 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 85962003450 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 85962003451 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 85962003452 active site 85962003453 substrate binding site [chemical binding]; other site 85962003454 metal binding site [ion binding]; metal-binding site 85962003455 Ttryptophan synthase (TRPS) alpha subunit (TSA). TPRS is a bifunctional tetrameric enzyme (2 alpha and 2 beta subunits) that catalyzes the last two steps of L-tryptophan biosynthesis. Alpha and beta subunit catalyze two distinct reactions which are both...; Region: Tryptophan_synthase_alpha; cd04724 85962003456 substrate binding site [chemical binding]; other site 85962003457 active site 85962003458 catalytic residues [active] 85962003459 heterodimer interface [polypeptide binding]; other site 85962003460 Tryptophan synthase-beta: Trptophan synthase is a bifunctional enzyme that catalyses the last two steps in the biosynthesis of L-tryptophan via its alpha and beta reactions. In the alpha reaction, indole 3-glycerol phosphate is cleaved reversibly to...; Region: Trp-synth_B; cd06446 85962003461 pyridoxal 5'-phosphate binding site [chemical binding]; other site 85962003462 catalytic residue [active] 85962003463 bifunctional indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase; Provisional; Region: PRK09427 85962003464 Indole-3-glycerol phosphate synthase (IGPS); an enzyme in the tryptophan biosynthetic pathway, catalyzing the ring closure reaction of 1-(o-carboxyphenylamino)-1-deoxyribulose-5-phosphate (CdRP) to indole-3-glycerol phosphate (IGP), accompanied by the...; Region: IGPS; cd00331 85962003465 active site 85962003466 ribulose/triose binding site [chemical binding]; other site 85962003467 phosphate binding site [ion binding]; other site 85962003468 substrate (anthranilate) binding pocket [chemical binding]; other site 85962003469 product (indole) binding pocket [chemical binding]; other site 85962003470 Phosphoribosylanthranilate isomerase (PRAI) catalyzes the fourth step of the tryptophan biosynthesis, the conversion of N-(5'- phosphoribosyl)-anthranilate (PRA) to 1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate (CdRP). Most PRAIs are...; Region: PRAI; cd00405 85962003471 active site 85962003472 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 85962003473 anthranilate phosphoribosyltransferase; Region: trpD; TIGR01245 85962003474 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 85962003475 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 85962003476 Glutamine amidotransferase class-I; Region: GATase; pfam00117 85962003477 glutamine binding [chemical binding]; other site 85962003478 catalytic triad [active] 85962003479 anthranilate synthase component I, proteobacterial subset; Region: trpE_proteo; TIGR00565 85962003480 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 85962003481 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 85962003482 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 85962003483 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 85962003484 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 85962003485 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 85962003486 active site 85962003487 motif I; other site 85962003488 motif II; other site 85962003489 Uncharacterized conserved protein [Function unknown]; Region: COG2353 85962003490 thiaminase II; Region: salvage_TenA; TIGR04306 85962003491 Nicotinamide mononucleotide transporter [Coenzyme metabolism]; Region: PnuC; COG3201 85962003492 Thiamine pyrophosphokinase [Coenzyme metabolism]; Region: THI80; COG1564 85962003493 Thiamine pyrophosphokinase; Region: TPK; cd07995 85962003494 active site 85962003495 dimerization interface [polypeptide binding]; other site 85962003496 thiamine binding site [chemical binding]; other site 85962003497 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 85962003498 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 85962003499 alphaNTD homodimer interface [polypeptide binding]; other site 85962003500 DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type; Region: rpoA; TIGR02027 85962003501 alphaNTD - beta interaction site [polypeptide binding]; other site 85962003502 alphaNTD - beta' interaction site [polypeptide binding]; other site 85962003503 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 85962003504 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 85962003505 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 85962003506 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 85962003507 RNA binding surface [nucleotide binding]; other site 85962003508 30S ribosomal protein S11; Validated; Region: PRK05309 85962003509 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 85962003510 50S ribosomal protein L36; Reviewed; Region: rpmJ; PRK00465 85962003511 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 85962003512 rRNA binding site [nucleotide binding]; other site 85962003513 predicted 30S ribosome binding site; other site 85962003514 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 85962003515 active site 85962003516 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 85962003517 SecY translocase; Region: SecY; pfam00344 85962003518 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 85962003519 ribosomal protein S5, bacterial/organelle type; Region: rpsE_bact; TIGR01021 85962003520 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 85962003521 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 85962003522 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 85962003523 23S rRNA interface [nucleotide binding]; other site 85962003524 L21e interface [polypeptide binding]; other site 85962003525 5S rRNA interface [nucleotide binding]; other site 85962003526 L27 interface [polypeptide binding]; other site 85962003527 L5 interface [polypeptide binding]; other site 85962003528 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 85962003529 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 85962003530 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 85962003531 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08061 85962003532 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 85962003533 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 85962003534 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 85962003535 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 85962003536 RNA binding site [nucleotide binding]; other site 85962003537 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 85962003538 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 85962003539 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 85962003540 putative translocon interaction site; other site 85962003541 23S rRNA interface [nucleotide binding]; other site 85962003542 signal recognition particle (SRP54) interaction site; other site 85962003543 L23 interface [polypeptide binding]; other site 85962003544 trigger factor interaction site; other site 85962003545 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 85962003546 23S rRNA interface [nucleotide binding]; other site 85962003547 5S rRNA interface [nucleotide binding]; other site 85962003548 putative antibiotic binding site [chemical binding]; other site 85962003549 L25 interface [polypeptide binding]; other site 85962003550 L27 interface [polypeptide binding]; other site 85962003551 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 85962003552 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 85962003553 G-X-X-G motif; other site 85962003554 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 85962003555 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 85962003556 putative translocon binding site; other site 85962003557 protein-rRNA interface [nucleotide binding]; other site 85962003558 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 85962003559 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 85962003560 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 85962003561 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 85962003562 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 85962003563 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 85962003564 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 85962003565 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 85962003566 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 85962003567 AAA domain; Region: AAA_14; pfam13173 85962003568 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 85962003569 Bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 85962003570 RNA/DNA hybrid binding site [nucleotide binding]; other site 85962003571 active site 85962003572 fumarate hydratase, class II; Region: fumC_II; TIGR00979 85962003573 Class II fumarases; Region: Fumarase_classII; cd01362 85962003574 active site 85962003575 tetramer interface [polypeptide binding]; other site 85962003576 YtkA-like; Region: YtkA; pfam13115 85962003577 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 85962003578 Biotin-lipoyl like; Region: Biotin_lipoyl_2; cl19169 85962003579 Outer membrane efflux protein; Region: OEP; pfam02321 85962003580 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 85962003581 HlyD family secretion protein; Region: HlyD_3; pfam13437 85962003582 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 85962003583 MMPL family; Region: MMPL; cl14618 85962003584 Predicted branched-chain amino acid permeases (azaleucine resistance) [Amino acid transport and metabolism]; Region: AzlD; COG1687 85962003585 4-azaleucine resistance probable transporter AzlC; Region: azlC; TIGR00346 85962003586 chaperone protein DnaJ; Provisional; Region: PRK14288 85962003587 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 85962003588 HSP70 interaction site [polypeptide binding]; other site 85962003589 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 85962003590 substrate binding site [polypeptide binding]; other site 85962003591 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 85962003592 Zn binding sites [ion binding]; other site 85962003593 dimer interface [polypeptide binding]; other site 85962003594 Synaptonemal complex protein 1 (SCP-1); Region: SCP-1; pfam05483 85962003595 Uncharacterized conserved protein [Function unknown]; Region: COG1432 85962003596 LabA_like proteins; Region: LabA_like; cd06167 85962003597 putative metal binding site [ion binding]; other site 85962003598 tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase; Region: trmU; TIGR00420 85962003599 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 85962003600 Ligand Binding Site [chemical binding]; other site 85962003601 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 85962003602 HSP70 interaction site [polypeptide binding]; other site 85962003603 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 85962003604 active site 85962003605 (T/H)XGH motif; other site 85962003606 nickel responsive regulator; Provisional; Region: PRK00630 85962003607 Ribbon-helix-helix protein, copG family; Region: RHH_1; pfam01402 85962003608 NikR C terminal nickel binding domain; Region: NikR_C; pfam08753 85962003609 tonB-system energizer ExbB, group 2; Region: exbB2; TIGR02805 85962003610 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 85962003611 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 85962003612 TonB family C-terminal domain; Region: tonB_Cterm; TIGR01352 85962003613 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962003614 Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]; Region: TerC; COG0861 85962003615 CorA-like Mg2+ transporter protein; Region: CorA; pfam01544 85962003616 Mg2+ transporter Helicobacter pylori CorA-like subgroup; Region: HpCorA-like; cd12836 85962003617 Cl binding site [ion binding]; other site 85962003618 oligomer interface [polypeptide binding]; other site 85962003619 phosphoglycerate kinase; Provisional; Region: pgk; PRK00073 85962003620 substrate binding site [chemical binding]; other site 85962003621 hinge regions; other site 85962003622 ADP binding site [chemical binding]; other site 85962003623 catalytic site [active] 85962003624 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; pfam00044 85962003625 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 85962003626 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 85962003627 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 85962003628 ligand binding site [chemical binding]; other site 85962003629 active site 85962003630 UGI interface [polypeptide binding]; other site 85962003631 catalytic site [active] 85962003632 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 85962003633 putative acyl-acceptor binding pocket; other site 85962003634 Bacterial SH3 domain; Region: SH3_3; pfam08239 85962003635 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 85962003636 C-terminal peptidase (prc); Region: prc; TIGR00225 85962003637 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 85962003638 protein binding site [polypeptide binding]; other site 85962003639 Catalytic dyad [active] 85962003640 DNA methylase; Region: N6_N4_Mtase; pfam01555 85962003641 nicotinate-nucleotide pyrophosphorylase; Provisional; Region: PRK05848 85962003642 Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase), also called nicotinate-nucleotide pyrophosphorylase, is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid (QA) with...; Region: QPRTase; cd01572 85962003643 dimerization interface [polypeptide binding]; other site 85962003644 active site 85962003645 quinolinate synthetase complex, A subunit; Region: nadA; TIGR00550 85962003646 phosphatidylserine decarboxylase; Provisional; Region: PRK03934 85962003647 phosphodiesterase; Provisional; Region: PRK12704 85962003648 4-Hydroxybenzoate polyprenyltransferase; Region: PT_UbiA_COQ2; cd13959 85962003649 putative active site [active] 85962003650 Predicted membrane metal-binding protein [General function prediction only]; Region: ComEC; COG0658 85962003651 Competence protein; Region: Competence; pfam03772 85962003652 replicative DNA helicase; Provisional; Region: PRK08506 85962003653 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 85962003654 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 85962003655 Walker A motif; other site 85962003656 ATP binding site [chemical binding]; other site 85962003657 Walker B motif; other site 85962003658 DNA binding loops [nucleotide binding] 85962003659 yjeF N-terminal region; Region: yjeF_nterm; TIGR00197 85962003660 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 85962003661 putative substrate binding site [chemical binding]; other site 85962003662 putative ATP binding site [chemical binding]; other site 85962003663 heavy metal sensor kinase; Region: cztS_silS_copS; TIGR01386 85962003664 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 85962003665 dimer interface [polypeptide binding]; other site 85962003666 phosphorylation site [posttranslational modification] 85962003667 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 85962003668 ATP binding site [chemical binding]; other site 85962003669 Mg2+ binding site [ion binding]; other site 85962003670 G-X-G motif; other site 85962003671 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 85962003672 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 85962003673 active site 85962003674 phosphorylation site [posttranslational modification] 85962003675 intermolecular recognition site; other site 85962003676 dimerization interface [polypeptide binding]; other site 85962003677 Transcriptional regulatory protein, C terminal; Region: Trans_reg_C; smart00862 85962003678 DNA binding site [nucleotide binding] 85962003679 DNA methylase; Region: N6_N4_Mtase; pfam01555 85962003680 DNA methylase; Region: N6_N4_Mtase; pfam01555 85962003681 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 85962003682 DNA methylase; Region: N6_N4_Mtase; pfam01555 85962003683 DEAD-like helicases superfamily; Region: DEXDc; smart00487 85962003684 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 85962003685 ATP binding site [chemical binding]; other site 85962003686 putative Mg++ binding site [ion binding]; other site 85962003687 Cell shape-determining protein [Cell envelope biogenesis, outer membrane]; Region: MreC; COG1792 85962003688 rod shape-determining protein MreB; Provisional; Region: PRK13927 85962003689 MreB and similar proteins; Region: MreB_like; cd10225 85962003690 nucleotide binding site [chemical binding]; other site 85962003691 Mg binding site [ion binding]; other site 85962003692 putative protofilament interaction site [polypeptide binding]; other site 85962003693 RodZ interaction site [polypeptide binding]; other site 85962003694 endopeptidase Clp ATP-binding regulatory subunit (clpX); Region: clpX; TIGR00382 85962003695 ClpX C4-type zinc finger; Region: zf-C4_ClpX; smart00994 85962003696 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 85962003697 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 85962003698 Walker A motif; other site 85962003699 ATP binding site [chemical binding]; other site 85962003700 Walker B motif; other site 85962003701 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 85962003702 Acyl-[acyl carrier protein]; Region: LpxA; COG1043 85962003703 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 85962003704 active site 85962003705 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 85962003706 flagellar assembly protein FliW; Provisional; Region: PRK13282 85962003707 DNA uptake lipoprotein [General function prediction only]; Region: ComL; COG4105 85962003708 ATP-dependent protease La (LON) domain; Region: LON; pfam02190 85962003709 ATP-dependent protease La; Region: lon; TIGR00763 85962003710 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 85962003711 Walker A motif; other site 85962003712 ATP binding site [chemical binding]; other site 85962003713 Walker B motif; other site 85962003714 arginine finger; other site 85962003715 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 85962003716 prephenate dehydrogenase; Validated; Region: PRK08507 85962003717 Prephenate dehydrogenase; Region: PDH; pfam02153 85962003718 DNA/RNA endonuclease G, NUC1 [Nucleotide transport and metabolism]; Region: NUC1; COG1864 85962003719 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 85962003720 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 85962003721 Fructose-1,6-bisphosphatase [Carbohydrate transport and metabolism]; Region: Fbp; COG0158 85962003722 active site 85962003723 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 85962003724 substrate binding site [chemical binding]; other site 85962003725 hexamer interface [polypeptide binding]; other site 85962003726 metal binding site [ion binding]; metal-binding site 85962003727 DNA polymerase III subunit epsilon; Provisional; Region: PRK08517 85962003728 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 85962003729 active site 85962003730 catalytic site [active] 85962003731 substrate binding site [chemical binding]; other site 85962003732 electron transport complex protein RnfC; Provisional; Region: PRK05035 85962003733 Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]; Region: COG1293 85962003734 Domain of unknown function (DUF814); Region: DUF814; pfam05670 85962003735 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 85962003736 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 85962003737 Walker A/P-loop; other site 85962003738 ATP binding site [chemical binding]; other site 85962003739 Q-loop/lid; other site 85962003740 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 85962003741 Q-loop/lid; other site 85962003742 ABC transporter signature motif; other site 85962003743 Walker B; other site 85962003744 D-loop; other site 85962003745 H-loop/switch region; other site 85962003746 NAD kinase [Coenzyme metabolism]; Region: nadF; COG0061 85962003747 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962003748 Uncharacterized conserved protein [Function unknown]; Region: COG1479 85962003749 Uncharacterized conserved protein [Function unknown]; Region: COG1479 85962003750 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 85962003751 Alanine dehydrogenase NAD-binding and catalytic domains; Region: L-AlaDH; cd05305 85962003752 hexamer interface [polypeptide binding]; other site 85962003753 ligand binding site [chemical binding]; other site 85962003754 putative active site [active] 85962003755 NAD(P) binding site [chemical binding]; other site 85962003756 Arginase family; Region: Arginase; cd09989 85962003757 active site 85962003758 Mn binding site [ion binding]; other site 85962003759 oligomer interface [polypeptide binding]; other site 85962003760 Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]; Region: FecA; COG4772 85962003761 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 85962003762 Protein of unknown function DUF45; Region: DUF45; pfam01863 85962003763 type I site-specific deoxyribonuclease, HsdR family; Region: hsdR; TIGR00348 85962003764 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 85962003765 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 85962003766 ATP binding site [chemical binding]; other site 85962003767 putative Mg++ binding site [ion binding]; other site 85962003768 HsdM N-terminal domain; Region: HsdM_N; pfam12161 85962003769 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 85962003770 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 85962003771 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 85962003772 biotin synthase; Provisional; Region: PRK08508 85962003773 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 85962003774 FeS/SAM binding site; other site 85962003775 Biotin and Thiamin Synthesis associated domain; Region: BATS; pfam06968 85962003776 YihY family inner membrane protein; Region: yihY_not_rbn; TIGR00765 85962003777 Uncharacterized conserved protein [Function unknown]; Region: COG1479 85962003778 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 85962003779 Single-stranded DNA-specific exonuclease [DNA replication, recombination, and repair]; Region: RecJ; COG0608 85962003780 DHH family; Region: DHH; pfam01368 85962003781 Uncharacterized protein with a von Willebrand factor type A (vWA) domain [General function prediction only]; Region: COG4867 85962003782 7-cyano-7-deazaguanine reductase; Region: QueF-II; TIGR03139 85962003783 Uncharacterized homolog of plant Iojap protein [Function unknown]; Region: COG0799 85962003784 AAA domain; Region: AAA_17; cl19128 85962003785 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 85962003786 A4GalT_like proteins catalyze the addition of galactose or glucose residues to the lipooligosaccharide (LOS) or lipopolysaccharide (LPS) of the bacterial cell surface; Region: GT8_A4GalT_like; cd04194 85962003787 Ligand binding site; other site 85962003788 metal-binding site 85962003789 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 85962003790 TMEM141 protein family; Region: TMEM141; pfam15110 85962003791 Sulfatase; Region: Sulfatase; pfam00884 85962003792 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13904 85962003793 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 85962003794 flagellar biosynthesis protein FliQ; Validated; Region: fliQ; PRK05700 85962003795 flagellum-specific ATP synthase; Validated; Region: fliI; PRK08472 85962003796 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 85962003797 Walker A motif/ATP binding site; other site 85962003798 Walker B motif; other site 85962003799 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 85962003800 ATP binding site [chemical binding]; other site 85962003801 Walker A motif; other site 85962003802 hexamer interface [polypeptide binding]; other site 85962003803 Walker B motif; other site 85962003804 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 85962003805 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 85962003806 active site 85962003807 HIGH motif; other site 85962003808 KMSKS motif; other site 85962003809 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 85962003810 tRNA binding surface [nucleotide binding]; other site 85962003811 anticodon binding site; other site 85962003812 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 85962003813 RNA binding surface [nucleotide binding]; other site 85962003814 23S rRNA m2A2503 methyltransferase; Region: TIGR00048 85962003815 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 85962003816 FeS/SAM binding site; other site 85962003817 KpsF/GutQ family protein; Region: kpsF; TIGR00393 85962003818 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 85962003819 putative active site [active] 85962003820 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 85962003821 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 85962003822 Metallo-beta-lactamase superfamily; Region: Lactamase_B; pfam00753 85962003823 RNA-metabolizing metallo-beta-lactamase; Region: RMMBL; pfam07521 85962003824 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 85962003825 S-adenosylmethionine binding site [chemical binding]; other site 85962003826 formyltetrahydrofolate deformylase; Region: PurU; TIGR00655 85962003827 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 85962003828 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 85962003829 putative active site [active] 85962003830 putative substrate binding site [chemical binding]; other site 85962003831 putative cosubstrate binding site; other site 85962003832 catalytic site [active] 85962003833 Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: SppA; COG0616 85962003834 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 85962003835 tandem repeat interface [polypeptide binding]; other site 85962003836 oligomer interface [polypeptide binding]; other site 85962003837 active site residues [active] 85962003838 TIR domain; Region: TIR_2; cl17458 85962003839 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 85962003840 active site 85962003841 carbon storage regulator; Provisional; Region: PRK00568 85962003842 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: PRK04181 85962003843 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 85962003844 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 85962003845 SmpB-tmRNA interface; other site 85962003846 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; pfam01618 85962003847 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 85962003848 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 85962003849 ribonuclease P protein component, eubacterial; Region: rnpA; TIGR00188 85962003850 hypothetical protein; Provisional; Region: PRK14374 85962003851 membrane protein insertase; Provisional; Region: PRK01318 85962003852 YidC periplasmic domain; Region: YidC_periplas; pfam14849 85962003853 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 85962003854 Predicted RNA-binding protein [General function prediction only]; Region: Jag; COG1847 85962003855 Jag N-terminus; Region: Jag_N; pfam14804 85962003856 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 85962003857 tRNA modification GTPase TrmE; Region: mnmE_trmE_thdF; TIGR00450 85962003858 Circularly permuted YlqF-related GTPases; Region: YlqF_related_GTPase; cl17249 85962003859 GTP/Mg2+ binding site [chemical binding]; other site 85962003860 G4 box; other site 85962003861 G5 box; other site 85962003862 trmE is a tRNA modification GTPase; Region: trmE; cd04164 85962003863 G1 box; other site 85962003864 G1 box; other site 85962003865 GTP/Mg2+ binding site [chemical binding]; other site 85962003866 Switch I region; other site 85962003867 Switch I region; other site 85962003868 G2 box; other site 85962003869 G2 box; other site 85962003870 Switch II region; other site 85962003871 G3 box; other site 85962003872 G3 box; other site 85962003873 Switch II region; other site 85962003874 G4 box; other site 85962003875 G5 box; other site 85962003876 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 85962003877 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962003878 LPP20 lipoprotein; Region: LPP20; pfam02169 85962003879 LPP20 lipoprotein; Region: LPP20; pfam02169 85962003880 Collagen-binding surface adhesin SpaP (antigen I/II family) [General function prediction only]; Region: FlgN; COG3417 85962003881 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 85962003882 catalytic residues [active] 85962003883 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 85962003884 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 85962003885 RNA binding surface [nucleotide binding]; other site 85962003886 pseudouridine synthase; Region: TIGR00093 85962003887 active site 85962003888 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE3; Region: PHP_PolIIIA_DnaE3; cd12113 85962003889 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 85962003890 active site 85962003891 PHP Thumb interface [polypeptide binding]; other site 85962003892 metal binding site [ion binding]; metal-binding site 85962003893 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 85962003894 Helix-hairpin-helix motif; Region: HHH_6; pfam14579 85962003895 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 85962003896 generic binding surface I; other site 85962003897 generic binding surface II; other site 85962003898 Cytochrome c peroxidase [Inorganic ion transport and metabolism]; Region: MauG; COG1858 85962003899 Di-haem cytochrome c peroxidase; Region: CCP_MauG; pfam03150 85962003900 Heat shock protein [Posttranslational modification, protein turnover, chaperones]; Region: HslJ; COG3187 85962003901 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 85962003902 mce related protein; Region: MCE; pfam02470 85962003903 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 85962003904 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 85962003905 Walker A/P-loop; other site 85962003906 ATP binding site [chemical binding]; other site 85962003907 Q-loop/lid; other site 85962003908 ABC transporter signature motif; other site 85962003909 Walker B; other site 85962003910 D-loop; other site 85962003911 H-loop/switch region; other site 85962003912 conserved hypothetical integral membrane protein; Region: TIGR00056 85962003913 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962003914 branched-chain amino acid aminotransferase; Provisional; Region: PRK13357 85962003915 BCAT_beta_family: Branched-chain aminotransferase catalyses the transamination of the branched-chain amino acids leusine, isoleucine and valine to their respective alpha-keto acids, alpha-ketoisocaproate, alpha-keto-beta-methylvalerate and...; Region: BCAT_beta_family; cd01557 85962003916 homodimer interface [polypeptide binding]; other site 85962003917 substrate-cofactor binding pocket; other site 85962003918 catalytic residue [active] 85962003919 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962003920 DNA polymerase I; Region: pola; TIGR00593 85962003921 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 85962003922 active site 85962003923 metal binding site 1 [ion binding]; metal-binding site 85962003924 putative 5' ssDNA interaction site; other site 85962003925 metal binding site 3; metal-binding site 85962003926 metal binding site 2 [ion binding]; metal-binding site 85962003927 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 85962003928 putative DNA binding site [nucleotide binding]; other site 85962003929 putative metal binding site [ion binding]; other site 85962003930 3'-5' exonuclease; Region: 35EXOc; smart00474 85962003931 active site 85962003932 substrate binding site [chemical binding]; other site 85962003933 catalytic site [active] 85962003934 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 85962003935 active site 85962003936 DNA binding site [nucleotide binding] 85962003937 catalytic site [active] 85962003938 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 85962003939 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 85962003940 This model contains proteins with the VRR-NUC domain; Region: VRR_NUC; smart00990 85962003941 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 85962003942 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 85962003943 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 85962003944 active site 85962003945 thymidylate kinase; Validated; Region: tmk; PRK00698 85962003946 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 85962003947 TMP-binding site; other site 85962003948 ATP-binding site [chemical binding]; other site 85962003949 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 85962003950 active site 85962003951 (T/H)XGH motif; other site 85962003952 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Provisional; Region: PRK06029 85962003953 flagellar basal body P-ring biosynthesis protein FlgA; Reviewed; Region: flgA; PRK08515 85962003954 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 85962003955 Part of AAA domain; Region: AAA_19; pfam13245 85962003956 AAA domain; Region: AAA_14; pfam13173 85962003957 UvrD-like helicase C-terminal domain; Region: UvrD_C_2; pfam13538 85962003958 TPR repeat; Region: TPR_11; pfam13414 85962003959 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 85962003960 TPR motif; other site 85962003961 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 85962003962 binding surface 85962003963 TPR motif; other site 85962003964 seryl-tRNA synthetase; Provisional; Region: PRK05431 85962003965 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 85962003966 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 85962003967 dimer interface [polypeptide binding]; other site 85962003968 active site 85962003969 motif 1; other site 85962003970 motif 2; other site 85962003971 motif 3; other site 85962003972 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cd07197 85962003973 active site 85962003974 catalytic triad [active] 85962003975 dimer interface [polypeptide binding]; other site 85962003976 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK14065 85962003977 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 85962003978 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 85962003979 S-adenosylmethionine binding site [chemical binding]; other site 85962003980 TIGR00701 family protein; Region: TIGR00701 85962003981 uncharacterized protein, YigZ family; Region: IMPACT_YIGZ; TIGR00257 85962003982 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 85962003983 YhgE/Pip N-terminal domain; Region: pip_yhgE_Nterm; cl19580 85962003984 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 85962003985 ABC-2 type transporter; Region: ABC2_membrane; cl17235 85962003986 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 85962003987 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 85962003988 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 85962003989 HlyD family secretion protein; Region: HlyD_3; pfam13437 85962003990 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 85962003991 Outer membrane efflux protein; Region: OEP; pfam02321 85962003992 Outer membrane efflux protein; Region: OEP; pfam02321 85962003993 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 85962003994 Domain of unknown function DUF21; Region: DUF21; pfam01595 85962003995 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 85962003996 Transporter associated domain; Region: CorC_HlyC; smart01091 85962003997 Phosphate transporter family; Region: PHO4; pfam01384 85962003998 NifU-like domain; Region: NifU; pfam01106 85962003999 UDP-N-acetylmuramyl-tripeptide synthetase; Region: murE; TIGR01085 85962004000 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 85962004001 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 85962004002 Transaldolase-like proteins from plants and bacteria; Region: Transaldolase_like; cd00955 85962004003 putative active site [active] 85962004004 catalytic residue [active] 85962004005 ribosomal protein L25, Ctc-form; Region: ctc_TL5; TIGR00731 85962004006 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 85962004007 5S rRNA interface [nucleotide binding]; other site 85962004008 CTC domain interface [polypeptide binding]; other site 85962004009 L16 interface [polypeptide binding]; other site 85962004010 Ribosomal protein TL5, C-terminal domain; Region: Ribosomal_TL5_C; pfam14693 85962004011 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 85962004012 putative active site [active] 85962004013 catalytic residue [active] 85962004014 Predicted permeases [General function prediction only]; Region: COG0795 85962004015 Catalytic domain of type II restriction endonucleases BfiI and NgoFVII, and uncharacterized proteins with a DEAD domain; Region: PLDc_Bfil_DEXD_like; cd09117 85962004016 PLD-like domain; Region: PLDc_2; pfam13091 85962004017 homodimer interface [polypeptide binding]; other site 85962004018 putative active site [active] 85962004019 catalytic site [active] 85962004020 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962004021 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3399 85962004022 Putative metal-binding domain of cation transport ATPase; Region: ATPase-cat_bd; pfam12156 85962004023 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 85962004024 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 85962004025 metal-binding site [ion binding] 85962004026 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 85962004027 haloacid dehalogenase-like hydrolase; Region: HAD; pfam12710 85962004028 Soluble P-type ATPase [General function prediction only]; Region: COG4087 85962004029 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 85962004030 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 85962004031 S-adenosylmethionine binding site [chemical binding]; other site 85962004032 Riboflavin-specific deaminase. Riboflavin biosynthesis protein RibD (Diaminohydroxyphosphoribosylaminopyrimidine deaminase) catalyzes the deamination of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate, which is an intermediate step in the...; Region: Riboflavin_deaminase-reductase; cd01284 85962004033 catalytic motif [active] 85962004034 Zn binding site [ion binding]; other site 85962004035 Pyrimidine reductase, riboflavin biosynthesis [Coenzyme metabolism]; Region: RibD; COG1985 85962004036 sodium--glutamate symport carrier (gltS); Region: gltS; TIGR00210 85962004037 Saccharopine dehydrogenase and related proteins [Amino acid transport and metabolism]; Region: LYS9; COG1748 85962004038 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 85962004039 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 85962004040 4Fe-4S binding domain; Region: Fer4_5; pfam12801 85962004041 4Fe-4S dicluster domain; Region: Fer4_18; pfam13746 85962004042 IG-like fold at C-terminal of FixG, putative oxidoreductase; Region: FixG_C; pfam11614 85962004043 acyl-phosphate glycerol 3-phosphate acyltransferase; Region: TIGR00023 85962004044 FolB domain; Region: folB_dom; TIGR00526 85962004045 active site 85962004046 TonB-dependent heme/hemoglobin receptor family protein; Region: TonB-hemin; TIGR01785 85962004047 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 85962004048 selenocysteine synthase; Provisional; Region: PRK04311 85962004049 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; cl18945 85962004050 transcription elongation factor NusA; Provisional; Region: nusA; PRK12328 85962004051 NusA N-terminal domain; Region: NusA_N; pfam08529 85962004052 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 85962004053 RNA binding site [nucleotide binding]; other site 85962004054 NusA-like KH domain; Region: KH_5; pfam13184 85962004055 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 85962004056 G-X-X-G motif; other site 85962004057 Type II restriction enzyme, methylase subunits [Defense mechanisms]; Region: COG1002 85962004058 Eco57I restriction-modification methylase; Region: Eco57I; pfam07669 85962004059 Restriction endonuclease [Defense mechanisms]; Region: COG3587 85962004060 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 85962004061 ATP binding site [chemical binding]; other site 85962004062 putative Mg++ binding site [ion binding]; other site 85962004063 ATP-dependent DNA helicase RecG; Region: recG; TIGR00643 85962004064 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 85962004065 ssDNA binding site; other site 85962004066 generic binding surface II; other site 85962004067 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 85962004068 ATP binding site [chemical binding]; other site 85962004069 putative Mg++ binding site [ion binding]; other site 85962004070 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 85962004071 nucleotide binding region [chemical binding]; other site 85962004072 ATP-binding site [chemical binding]; other site 85962004073 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85962004074 Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Ape1-like_AP-endo; cd09087 85962004075 active site 85962004076 putative catalytic site [active] 85962004077 DNA binding site [nucleotide binding] 85962004078 putative phosphate binding site [ion binding]; other site 85962004079 metal binding site A [ion binding]; metal-binding site 85962004080 AP binding site [nucleotide binding]; other site 85962004081 metal binding site B [ion binding]; metal-binding site 85962004082 SLAIN motif-containing family; Region: SLAIN; pfam15301 85962004083 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 85962004084 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 85962004085 Walker A motif; other site 85962004086 ATP binding site [chemical binding]; other site 85962004087 Walker B motif; other site 85962004088 arginine finger; other site 85962004089 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 85962004090 DnaA box-binding interface [nucleotide binding]; other site 85962004091 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 85962004092 Protein of unknown function (DUF2443); Region: DUF2443; pfam10398 85962004093 glucosamine--fructose-6-phosphate aminotransferase (isomerizing); Region: glmS; TIGR01135 85962004094 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 85962004095 glutaminase active site [active] 85962004096 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 85962004097 dimer interface [polypeptide binding]; other site 85962004098 active site 85962004099 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 85962004100 dimer interface [polypeptide binding]; other site 85962004101 active site 85962004102 Predicted alternative thymidylate synthase [Nucleotide transport and metabolism]; Region: THY1; COG1351 85962004103 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 85962004104 Helix-turn-helix domain; Region: HTH_OrfB_IS605; pfam12323 85962004105 Probable transposase; Region: OrfB_IS605; pfam01385 85962004106 Putative transposase DNA-binding domain; Region: OrfB_Zn_ribbon; pfam07282 85962004107 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG1943 85962004108 Cytochrome c1 [Energy production and conversion]; Region: CYT1; COG2857 85962004109 Cytochrome c; Region: Cytochrom_C; pfam00034 85962004110 Cytochrome c; Region: Cytochrom_C; cl11414 85962004111 Cytochrome b subunit of the bc complex [Energy production and conversion]; Region: QcrB; COG1290 85962004112 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 85962004113 intrachain domain interface; other site 85962004114 interchain domain interface [polypeptide binding]; other site 85962004115 heme bH binding site [chemical binding]; other site 85962004116 Qi binding site; other site 85962004117 heme bL binding site [chemical binding]; other site 85962004118 Qo binding site; other site 85962004119 interchain domain interface [polypeptide binding]; other site 85962004120 intrachain domain interface; other site 85962004121 Qi binding site; other site 85962004122 Cytochrome b(C-terminal)/b6/petD; Region: Cytochrom_B_C; pfam00032 85962004123 Qo binding site; other site 85962004124 Rieske Fe-S protein [Energy production and conversion]; Region: QcrA; COG0723 85962004125 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 85962004126 [2Fe-2S] cluster binding site [ion binding]; other site 85962004127 transcription-repair coupling factor (mfd); Region: mfd; TIGR00580 85962004128 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 85962004129 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 85962004130 ATP binding site [chemical binding]; other site 85962004131 putative Mg++ binding site [ion binding]; other site 85962004132 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 85962004133 nucleotide binding region [chemical binding]; other site 85962004134 ATP-binding site [chemical binding]; other site 85962004135 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 85962004136 Integral membrane protein CcmA involved in cell shape determination [Cell envelope biogenesis, outer membrane]; Region: CcmA; COG1664 85962004137 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 85962004138 Peptidase family M23; Region: Peptidase_M23; pfam01551 85962004139 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 85962004140 Peptidase family M23; Region: Peptidase_M23; pfam01551 85962004141 folylpolyglutamate synthase/dihydrofolate synthase; Region: folC; TIGR01499 85962004142 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 85962004143 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 85962004144 Lipopolysaccharide-assembly; Region: LptE; pfam04390 85962004145 leucyl-tRNA synthetase, eubacterial and mitochondrial family; Region: leuS_bact; TIGR00396 85962004146 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 85962004147 active site 85962004148 HIGH motif; other site 85962004149 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 85962004150 KMSKS motif; other site 85962004151 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 85962004152 tRNA binding surface [nucleotide binding]; other site 85962004153 anticodon binding site; other site 85962004154 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 85962004155 protein-export membrane protein SecF; Region: 3a0501s07; TIGR00966 85962004156 Protein export membrane protein; Region: SecD_SecF; pfam02355 85962004157 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 85962004158 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 85962004159 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 85962004160 pH-dependent sodium/proton antiporter; Provisional; Region: nhaA; PRK14856 85962004161 Part of AAA domain; Region: AAA_19; pfam13245 85962004162 putative recombination protein RecB; Provisional; Region: PRK13909 85962004163 Protein of unknown function (DUF342); Region: DUF342; cl19219 85962004164 UvrD-like helicase C-terminal domain; Region: UvrD_C_2; cl19402 85962004165 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 85962004166 rRNA interaction site [nucleotide binding]; other site 85962004167 S8 interaction site; other site 85962004168 putative laminin-1 binding site; other site 85962004169 translation elongation factor Ts; Region: tsf; TIGR00116 85962004170 UBA/TS-N domain; Region: UBA; pfam00627 85962004171 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 85962004172 Penicillin-binding Protein dimerization domain; Region: PBP_dimer; pfam03717 85962004173 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 85962004174 flagellar hook-basal body protein FliE; Reviewed; Region: fliE; PRK03907 85962004175 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 85962004176 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 85962004177 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 85962004178 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK05680 85962004179 flagellar basal body rod protein FlgB; Provisional; Region: flgB; cl19173 85962004180 Cell cycle protein; Region: FTSW_RODA_SPOVE; pfam01098 85962004181 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 85962004182 Periplasmic binding protein TroA_d. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a...; Region: TroA_d; cd01141 85962004183 putative ligand binding site [chemical binding]; other site 85962004184 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 85962004185 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between...; Region: TroA-like; cl00262 85962004186 intersubunit interface [polypeptide binding]; other site 85962004187 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 85962004188 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 85962004189 dimer interface [polypeptide binding]; other site 85962004190 decamer (pentamer of dimers) interface [polypeptide binding]; other site 85962004191 catalytic triad [active] 85962004192 peroxidatic and resolving cysteines [active] 85962004193 ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]; Region: NlpA; COG1464 85962004194 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 85962004195 Penicillin-binding Protein dimerization domain; Region: PBP_dimer; pfam03717 85962004196 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 85962004197 Predicted GTPase [General function prediction only]; Region: COG0218 85962004198 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 85962004199 G1 box; other site 85962004200 GTP/Mg2+ binding site [chemical binding]; other site 85962004201 Switch I region; other site 85962004202 G2 box; other site 85962004203 G3 box; other site 85962004204 Switch II region; other site 85962004205 G4 box; other site 85962004206 G5 box; other site 85962004207 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1934 85962004208 OstA-like protein; Region: OstA; pfam03968 85962004209 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 85962004210 active site 85962004211 motif I; other site 85962004212 motif II; other site 85962004213 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 85962004214 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 85962004215 Sporulation related domain; Region: SPOR; pfam05036 85962004216 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 85962004217 N-acetyl-D-glucosamine binding site [chemical binding]; other site 85962004218 catalytic residue [active] 85962004219 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 85962004220 Predicted metal-dependent hydrolases with the TIM-barrel fold [General function prediction only]; Region: COG1099 85962004221 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 85962004222 active site 85962004223 riboflavin synthase, alpha subunit; Region: ribE; TIGR00187 85962004224 Lumazine binding domain; Region: Lum_binding; pfam00677 85962004225 Lumazine binding domain; Region: Lum_binding; pfam00677 85962004226 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 85962004227 DL-methionine transporter ATP-binding subunit; Provisional; Region: metN; PRK11153 85962004228 ATP-binding cassette domain of methionine transporter; Region: ABC_MetN_methionine_transporter; cd03258 85962004229 Walker A/P-loop; other site 85962004230 ATP binding site [chemical binding]; other site 85962004231 Q-loop/lid; other site 85962004232 ABC transporter signature motif; other site 85962004233 Walker B; other site 85962004234 D-loop; other site 85962004235 H-loop/switch region; other site 85962004236 NIL domain; Region: NIL; pfam09383 85962004237 ABC-type metal ion transport system, permease component [Inorganic ion transport and metabolism]; Region: AbcD; COG2011 85962004238 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 85962004239 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 85962004240 active site 85962004241 anthranilate phosphoribosyltransferase; Region: PLN02641 85962004242 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 85962004243 PAP2_like_5 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_5; cd03394 85962004244 active site 85962004245 This subfamily is composed of uncharacterized bacterial glycosyltransferases in the MraY-like family. This family contains both eukaryotic and prokaryotic UDP-D-N-acetylhexosamine:polyprenol phosphate D-N-acetylhexosamine-1-phosphate transferases, which...; Region: GT_MraY_like; cd06912 85962004246 Mg++ binding site [ion binding]; other site 85962004247 putative catalytic motif [active] 85962004248 Pyridoxine 5'-phosphate (PNP) synthase domain; pyridoxal 5'-phosphate is the active form of vitamin B6 that acts as an essential, ubiquitous coenzyme in amino acid metabolism. In bacteria, formation of pyridoxine 5'-phosphate is a step in...; Region: PNPsynthase; cd00003 85962004249 active site 85962004250 hydrophilic channel; other site 85962004251 dimerization interface [polypeptide binding]; other site 85962004252 catalytic residues [active] 85962004253 active site lid [active] 85962004254 4-hydroxythreonine-4-phosphate dehydrogenase; Provisional; Region: pdxA; PRK03946 85962004255 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 85962004256 metallohydrolase, glycoprotease/Kae1 family; Region: gcp_kae1; TIGR00329 85962004257 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 85962004258 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 85962004259 flagellar basal body rod protein FlgB; Provisional; Region: flgB; cl19173 85962004260 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 85962004261 hypothetical protein; Provisional; Region: PRK10236 85962004262 Domain of unknown function (DUF3944); Region: DUF3944; pfam13099 85962004263 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4735 85962004264 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4735 85962004265 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4735