-- dump date 20140619_112530 -- class Genbank::misc_feature -- table misc_feature_note -- id note 985080000001 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 985080000002 putative RNA binding site [nucleotide binding]; other site 985080000003 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 985080000004 homopentamer interface [polypeptide binding]; other site 985080000005 active site 985080000006 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 985080000007 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 985080000008 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 985080000009 active site clefts [active] 985080000010 zinc binding site [ion binding]; other site 985080000011 dimer interface [polypeptide binding]; other site 985080000012 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 985080000013 active site 985080000014 dimer interface [polypeptide binding]; other site 985080000015 pantoate--beta-alanine ligase; Region: panC; TIGR00018 985080000016 Pantoate-beta-alanine ligase; Region: PanC; cd00560 985080000017 active site 985080000018 ATP-binding site [chemical binding]; other site 985080000019 pantoate-binding site; other site 985080000020 HXXH motif; other site 985080000021 potential frameshift: common BLAST hit: gi|383749069|ref|YP_005424172.1| outer membrane protein HopZ 985080000022 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 985080000023 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 985080000024 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 985080000025 ring oligomerisation interface [polypeptide binding]; other site 985080000026 ATP/Mg binding site [chemical binding]; other site 985080000027 stacking interactions; other site 985080000028 hinge regions; other site 985080000029 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 985080000030 oligomerisation interface [polypeptide binding]; other site 985080000031 mobile loop; other site 985080000032 roof hairpin; other site 985080000033 DNA primase, catalytic core; Region: dnaG; TIGR01391 985080000034 CHC2 zinc finger; Region: zf-CHC2; pfam01807 985080000035 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 985080000036 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 985080000037 active site 985080000038 metal binding site [ion binding]; metal-binding site 985080000039 interdomain interaction site; other site 985080000040 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 985080000041 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 985080000042 Ligand Binding Site [chemical binding]; other site 985080000043 TrbC/VIRB2 family; Region: TrbC; cl01583 985080000044 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 985080000045 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 985080000046 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 985080000047 Walker A motif; other site 985080000048 ATP binding site [chemical binding]; other site 985080000049 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 985080000050 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3014 985080000051 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 985080000052 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 985080000053 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 985080000054 active site 985080000055 phosphorylation site [posttranslational modification] 985080000056 intermolecular recognition site; other site 985080000057 dimerization interface [polypeptide binding]; other site 985080000058 carboxynorspermidine decarboxylase; Region: nspC; TIGR01047 985080000059 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Carboxynorspermidine Decarboxylase; Region: PLPDE_III_CANSDC; cd06829 985080000060 dimer interface [polypeptide binding]; other site 985080000061 active site 985080000062 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 985080000063 catalytic residues [active] 985080000064 substrate binding site [chemical binding]; other site 985080000065 lipid A 1-phosphatase; Reviewed; Region: PRK09597 985080000066 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 985080000067 active site 985080000068 lipid A phosphoethanolamine transferase; Reviewed; Region: PRK09598 985080000069 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 985080000070 Sulfatase; Region: Sulfatase; pfam00884 985080000071 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 985080000072 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 985080000073 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 985080000074 dimer interface [polypeptide binding]; other site 985080000075 active site 985080000076 citrylCoA binding site [chemical binding]; other site 985080000077 NADH binding [chemical binding]; other site 985080000078 cationic pore residues; other site 985080000079 oxalacetate/citrate binding site [chemical binding]; other site 985080000080 coenzyme A binding site [chemical binding]; other site 985080000081 catalytic triad [active] 985080000082 isocitrate dehydrogenase; Validated; Region: PRK07362 985080000083 isocitrate dehydrogenase; Reviewed; Region: PRK07006 985080000084 Protein of unknown function (DUF1523); Region: DUF1523; pfam07509 985080000085 Dethiobiotin synthetase [Coenzyme metabolism]; Region: BioD; COG0132 985080000086 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 985080000087 Ligand Binding Site [chemical binding]; other site 985080000088 Uncharacterized conserved protein [Function unknown]; Region: COG2127 985080000089 ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]; Region: clpA; COG0542 985080000090 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 985080000091 Walker A motif; other site 985080000092 ATP binding site [chemical binding]; other site 985080000093 Walker B motif; other site 985080000094 arginine finger; other site 985080000095 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 985080000096 Walker A motif; other site 985080000097 ATP binding site [chemical binding]; other site 985080000098 Walker B motif; other site 985080000099 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 985080000100 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 985080000101 tetramerization interface [polypeptide binding]; other site 985080000102 active site 985080000103 hypothetical protein; Provisional; Region: PRK03762 985080000104 PDZ domain; Region: PDZ_2; pfam13180 985080000105 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 985080000106 Type IV secretory pathway, TrbL components [Intracellular trafficking and secretion]; Region: TrbL; COG3846 985080000107 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 985080000108 Type IV secretory pathway, VirB9 components [Intracellular trafficking and secretion]; Region: VirB9; COG3504 985080000109 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 985080000110 VirB7 interaction site; other site 985080000111 Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion]; Region: VirB10; COG2948 985080000112 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 985080000113 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 985080000114 Substrate binding site; other site 985080000115 Cupin domain; Region: Cupin_2; cl17218 985080000116 GDP-mannose 4,6-dehydratase; Region: gmd; TIGR01472 985080000117 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 985080000118 NADP-binding site; other site 985080000119 homotetramer interface [polypeptide binding]; other site 985080000120 substrate binding site [chemical binding]; other site 985080000121 homodimer interface [polypeptide binding]; other site 985080000122 active site 985080000123 GDP-fucose synthetase, extended (e) SDRs; Region: GDP_FS_SDR_e; cd05239 985080000124 GDP-4-keto-6-deoxymannose-3, 5-epimerase-4-reductase; Region: PLN02725 985080000125 NADP binding site [chemical binding]; other site 985080000126 active site 985080000127 putative substrate binding site [chemical binding]; other site 985080000128 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 985080000129 dimerization interface [polypeptide binding]; other site 985080000130 hydrogenase expression/formation protein HypE; Region: hypE; TIGR02124 985080000131 ATP binding site [chemical binding]; other site 985080000132 Acylphosphatase; Region: Acylphosphatase; pfam00708 985080000133 [NiFe] hydrogenase maturation protein HypF; Region: hypF; TIGR00143 985080000134 HypF finger; Region: zf-HYPF; pfam07503 985080000135 HypF finger; Region: zf-HYPF; pfam07503 985080000136 Telomere recombination; Region: Sua5_yciO_yrdC; pfam01300 985080000137 Peptidylarginine deiminase and related enzymes [Amino acid transport and metabolism]; Region: COG2957 985080000138 Porphyromonas-type peptidyl-arginine deiminase; Region: PAD_porph; pfam04371 985080000139 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 985080000140 DNA methylase; Region: N6_N4_Mtase; pfam01555 985080000141 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 985080000142 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 985080000143 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 985080000144 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 985080000145 cofactor binding site; other site 985080000146 DNA binding site [nucleotide binding] 985080000147 substrate interaction site [chemical binding]; other site 985080000148 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0827 985080000149 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 985080000150 S-adenosylmethionine binding site [chemical binding]; other site 985080000151 Eco57I restriction-modification methylase; Region: Eco57I; pfam07669 985080000152 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 985080000153 Na(+)/proline cotransporter PutP and related proteins; solute binding domain; Region: SLC5sbd_PutP; cd11475 985080000154 Na binding site [ion binding]; other site 985080000155 Proline dehydrogenase; Region: Pro_dh; pfam01619 985080000156 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 985080000157 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 985080000158 Glutamate binding site [chemical binding]; other site 985080000159 NAD binding site [chemical binding]; other site 985080000160 catalytic residues [active] 985080000161 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed; Region: PRK09603 985080000162 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 985080000163 A nuclease of the HNH/ENDO VII superfamily with conserved WHH; Region: WHH; pfam14414 985080000164 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; pfam09346 985080000165 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 985080000166 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 985080000167 Urease accessory protein UreH [Posttranslational modification, protein turnover, chaperones]; Region: UreH; COG0829 985080000168 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cd00882 985080000169 G1 box; other site 985080000170 GTP/Mg2+ binding site [chemical binding]; other site 985080000171 G2 box; other site 985080000172 Switch I region; other site 985080000173 G3 box; other site 985080000174 Switch II region; other site 985080000175 G4 box; other site 985080000176 G5 box; other site 985080000177 potential frameshift: common BLAST hit: gi|15611135|ref|NP_222786.1| urease accessory protein 985080000178 UreF; Region: UreF; pfam01730 985080000179 UreF; Region: UreF; pfam01730 985080000180 urease accessory protein UreE; Provisional; Region: ureE; PRK13261 985080000181 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 985080000182 dimer interface [polypeptide binding]; other site 985080000183 catalytic residues [active] 985080000184 AmiS/UreI family transporter; Region: AmiS_UreI; pfam02293 985080000185 urease subunit beta; Provisional; Region: ureB; PRK13985 985080000186 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 985080000187 subunit interactions [polypeptide binding]; other site 985080000188 active site 985080000189 flap region; other site 985080000190 urease subunit alpha; Provisional; Region: PRK13986 985080000191 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 985080000192 alpha-gamma subunit interface [polypeptide binding]; other site 985080000193 beta-gamma subunit interface [polypeptide binding]; other site 985080000194 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 985080000195 gamma-beta subunit interface [polypeptide binding]; other site 985080000196 alpha-beta subunit interface [polypeptide binding]; other site 985080000197 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 985080000198 phosphoglucosamine mutase; Provisional; Region: glmM; PRK14324 985080000199 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 985080000200 active site 985080000201 substrate binding site [chemical binding]; other site 985080000202 metal binding site [ion binding]; metal-binding site 985080000203 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 985080000204 peptide chain release factor 1; Validated; Region: prfA; PRK00591 985080000205 This domain is found in peptide chain release factors; Region: PCRF; smart00937 985080000206 RF-1 domain; Region: RF-1; pfam00472 985080000207 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 985080000208 potential frameshift: common BLAST hit: gi|15611146|ref|NP_222797.1| methyl-accepting chemotaxis protein (MCP) 985080000209 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 985080000210 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 985080000211 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 985080000212 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 985080000213 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 985080000214 23S rRNA interface [nucleotide binding]; other site 985080000215 L3 interface [polypeptide binding]; other site 985080000216 Predicted dehydrogenase [General function prediction only]; Region: COG0579 985080000217 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl17341 985080000218 NLPC_P60 stabilising domain, N term; Region: N_NLPC_P60; pfam12912 985080000219 SH3 domain of the SH3b1 type; Region: SH3_6; pfam12913 985080000220 SH3 domain of SH3b2 type; Region: SH3_7; pfam12914 985080000221 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 985080000222 NlpC/P60 family; Region: NLPC_P60; pfam00877 985080000223 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 985080000224 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 985080000225 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 985080000226 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 985080000227 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 985080000228 DNA binding residues [nucleotide binding] 985080000229 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Validated; Region: PRK05584 985080000230 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Region: MTA/SAH-Nsdase; TIGR01704 985080000231 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 985080000232 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 985080000233 Protein of unknown function (DUF511); Region: DUF511; pfam04373 985080000234 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 985080000235 DNA methylase; Region: N6_N4_Mtase; pfam01555 985080000236 Alpha-1,2-fucosyltransferase; Region: Fut1_Fut2_like; cd11301 985080000237 Glycosyl transferase family 11; Region: Glyco_transf_11; pfam01531 985080000238 GDP-Fucose binding site [chemical binding]; other site 985080000239 2-hydroxyacid dehydrogenase; Provisional; Region: PRK08410 985080000240 Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; Region: FDH_GDH_like; cl17240 985080000241 NAD binding site [chemical binding]; other site 985080000242 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 985080000243 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 985080000244 pyridoxal 5'-phosphate binding site [chemical binding]; other site 985080000245 catalytic residue [active] 985080000246 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 985080000247 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 985080000248 dimer interface [polypeptide binding]; other site 985080000249 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 985080000250 Ligand Binding Site [chemical binding]; other site 985080000251 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 985080000252 putative glycosyl transferase; Provisional; Region: PRK10063 985080000253 WfgS and WfeV are involved in O-antigen biosynthesis; Region: GT_2_WfgS_like; cd06433 985080000254 metal-binding site 985080000255 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 985080000256 HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain; Region: HAMP; smart00304 985080000257 dimerization interface [polypeptide binding]; other site 985080000258 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 985080000259 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 985080000260 dimer interface [polypeptide binding]; other site 985080000261 putative CheW interface [polypeptide binding]; other site 985080000262 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases [Nucleotide transport and metabolism]; Region: UshA; COG0737 985080000263 Escherichia coli CpdB and related proteins, N-terminal metallophosphatase domain; Region: MPP_CpdB_N; cd07410 985080000264 active site 985080000265 metal binding site [ion binding]; metal-binding site 985080000266 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 985080000267 S-ribosylhomocysteinase; Provisional; Region: PRK02260 985080000268 cystathionine gamma-synthase/cystathionine beta-lyase; Validated; Region: PRK06176 985080000269 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 985080000270 homodimer interface [polypeptide binding]; other site 985080000271 substrate-cofactor binding pocket; other site 985080000272 pyridoxal 5'-phosphate binding site [chemical binding]; other site 985080000273 catalytic residue [active] 985080000274 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 985080000275 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 985080000276 dimer interface [polypeptide binding]; other site 985080000277 pyridoxal 5'-phosphate binding site [chemical binding]; other site 985080000278 catalytic residue [active] 985080000279 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 985080000280 Nucleotide-binding domain of human HSPA9 and similar proteins; Region: HSPA9-Ssq1-like_NBD; cd10234 985080000281 nucleotide binding site [chemical binding]; other site 985080000282 NEF interaction site [polypeptide binding]; other site 985080000283 SBD interface [polypeptide binding]; other site 985080000284 Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: GrpE; COG0576 985080000285 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 985080000286 dimer interface [polypeptide binding]; other site 985080000287 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 985080000288 heat-inducible transcription repressor; Provisional; Region: PRK03911 985080000289 hypothetical protein; Provisional; Region: PRK05834 985080000290 Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II); Region: Aldolase_II; cl00214 985080000291 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2604 985080000292 flagellin B; Provisional; Region: PRK13588 985080000293 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 985080000294 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 985080000295 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 985080000296 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 985080000297 DNA topoisomerase I; Validated; Region: PRK05582 985080000298 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 985080000299 active site 985080000300 interdomain interaction site; other site 985080000301 putative metal-binding site [ion binding]; other site 985080000302 nucleotide binding site [chemical binding]; other site 985080000303 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 985080000304 domain I; other site 985080000305 DNA binding groove [nucleotide binding] 985080000306 phosphate binding site [ion binding]; other site 985080000307 domain II; other site 985080000308 domain III; other site 985080000309 nucleotide binding site [chemical binding]; other site 985080000310 catalytic site [active] 985080000311 domain IV; other site 985080000312 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 985080000313 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 985080000314 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 985080000315 Fe-S oxidoreductases [Energy production and conversion]; Region: COG0731 985080000316 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 985080000317 FeS/SAM binding site; other site 985080000318 Helicobacter pylori protein of unknown function (DUF874); Region: DUF874; pfam05917 985080000319 phosphoenolpyruvate synthase; Validated; Region: PRK06464 985080000320 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 985080000321 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 985080000322 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 985080000323 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK12305 985080000324 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; pfam07973 985080000325 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 985080000326 active site 985080000327 dimer interface [polypeptide binding]; other site 985080000328 motif 1; other site 985080000329 motif 2; other site 985080000330 motif 3; other site 985080000331 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 985080000332 anticodon binding site; other site 985080000333 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 985080000334 translation initiation factor IF-3; Region: infC; TIGR00168 985080000335 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 985080000336 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 985080000337 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 985080000338 23S rRNA binding site [nucleotide binding]; other site 985080000339 L21 binding site [polypeptide binding]; other site 985080000340 L13 binding site [polypeptide binding]; other site 985080000341 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 985080000342 Protein of unknown function (DUF1104); Region: DUF1104; pfam06518 985080000343 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 985080000344 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 985080000345 Serine dehydratase alpha chain; Region: SDH_alpha; pfam03313 985080000346 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 985080000347 serine transporter; Region: stp; TIGR00814 985080000348 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase [Amino acid transport and metabolism]; Region: AroG; COG3200 985080000349 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 985080000350 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 985080000351 catalytic triad [active] 985080000352 Uncharacterized conserved protein [Function unknown]; Region: COG1556 985080000353 iron-sulfur cluster-binding protein; Region: TIGR00273 985080000354 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 985080000355 Domain of unknown function (DUF3390); Region: DUF3390; pfam11870 985080000356 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 985080000357 Cysteine-rich domain; Region: CCG; pfam02754 985080000358 Cysteine-rich domain; Region: CCG; pfam02754 985080000359 L-lactate transport; Region: lctP; TIGR00795 985080000360 L-lactate permease [Energy production and conversion]; Region: LldP; COG1620 985080000361 L-lactate permease [Energy production and conversion]; Region: LldP; COG1620 985080000362 L-lactate transport; Region: lctP; TIGR00795 985080000363 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 985080000364 DNA glycosylase MutY; Provisional; Region: PRK13910 985080000365 minor groove reading motif; other site 985080000366 helix-hairpin-helix signature motif; other site 985080000367 substrate binding pocket [chemical binding]; other site 985080000368 active site 985080000369 DNA glycosylase (MutY in bacteria and hMYH in humans) is responsible for repairing misread A*oxoG residues to C*G by removing the inappropriately paired adenine base from the DNA backbone. It belongs to the Nudix hydrolase superfamily and is important...; Region: DNA_Glycosylase_C; cd03431 985080000370 DNA binding and oxoG recognition site [nucleotide binding] 985080000371 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 985080000372 Sodium:sulfate symporter transmembrane region; Region: Na_sulph_symp; pfam00939 985080000373 transmembrane helices; other site 985080000374 Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is...; Region: Heme_Cu_Oxidase_I; cl00275 985080000375 Low-spin heme binding site [chemical binding]; other site 985080000376 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 985080000377 D-pathway; other site 985080000378 Putative water exit pathway; other site 985080000379 Binuclear center (active site) [active] 985080000380 K-pathway; other site 985080000381 Putative proton exit pathway; other site 985080000382 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 985080000383 cytochrome c oxidase, cbb3-type, subunit II; Region: ccoO; TIGR00781 985080000384 cytochrome c oxidase, cbb3-type, CcoQ subunit, epsilon-Proteobacterial; Region: cbb3_Q_epsi; TIGR02736 985080000385 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 985080000386 Cytochrome c; Region: Cytochrom_C; pfam00034 985080000387 Cytochrome c; Region: Cytochrom_C; pfam00034 985080000388 Family of unknown function (DUF4006); Region: DUF4006; pfam13179 985080000389 Predicted periplasmic solute-binding protein [General function prediction only]; Region: COG2107 985080000390 recombinase A; Provisional; Region: recA; PRK09354 985080000391 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 985080000392 hexamer interface [polypeptide binding]; other site 985080000393 Walker A motif; other site 985080000394 ATP binding site [chemical binding]; other site 985080000395 Walker B motif; other site 985080000396 enolase; Provisional; Region: eno; PRK00077 985080000397 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 985080000398 dimer interface [polypeptide binding]; other site 985080000399 metal binding site [ion binding]; metal-binding site 985080000400 substrate binding pocket [chemical binding]; other site 985080000401 AMIN domain; Region: AMIN; pfam11741 985080000402 Shikimate kinase [Amino acid transport and metabolism]; Region: AroK; COG0703 985080000403 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 985080000404 ADP binding site [chemical binding]; other site 985080000405 magnesium binding site [ion binding]; other site 985080000406 putative shikimate binding site; other site 985080000407 Cache domain; Region: Cache_1; pfam02743 985080000408 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 985080000409 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 985080000410 Ligand binding site; other site 985080000411 metal-binding site 985080000412 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 985080000413 Sel1-like repeats; Region: SEL1; smart00671 985080000414 Sel1-like repeats; Region: SEL1; smart00671 985080000415 Sel1-like repeats; Region: SEL1; smart00671 985080000416 Sel1 repeat; Region: Sel1; cl02723 985080000417 Sel1-like repeats; Region: SEL1; smart00671 985080000418 Sel1-like repeats; Region: SEL1; smart00671 985080000419 hypothetical protein; Provisional; Region: PRK12378 985080000420 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 985080000421 dimer interface [polypeptide binding]; other site 985080000422 active site 985080000423 Schiff base residues; other site 985080000424 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 985080000425 HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain; Region: HAMP; smart00304 985080000426 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 985080000427 dimer interface [polypeptide binding]; other site 985080000428 phosphorylation site [posttranslational modification] 985080000429 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 985080000430 ATP binding site [chemical binding]; other site 985080000431 Mg2+ binding site [ion binding]; other site 985080000432 G-X-G motif; other site 985080000433 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 985080000434 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 985080000435 active site 985080000436 phosphorylation site [posttranslational modification] 985080000437 intermolecular recognition site; other site 985080000438 dimerization interface [polypeptide binding]; other site 985080000439 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 985080000440 DNA binding site [nucleotide binding] 985080000441 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 985080000442 Peptidase family U32; Region: Peptidase_U32; pfam01136 985080000443 peptide chain release factor 2; Region: prfB; TIGR00020 985080000444 This domain is found in peptide chain release factors; Region: PCRF; smart00937 985080000445 RF-1 domain; Region: RF-1; pfam00472 985080000446 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 985080000447 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 985080000448 dimer interface [polypeptide binding]; other site 985080000449 putative functional site; other site 985080000450 putative MPT binding site; other site 985080000451 Flagellar biosynthesis pathway, component FliR [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FliR; COG1684 985080000452 Etoposide-induced protein 2.4 (EI24); Region: EI24; pfam07264 985080000453 Parvulin-like peptidyl-prolyl isomerase [Posttranslational modification, protein turnover, chaperones]; Region: SurA; COG0760 985080000454 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 985080000455 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 985080000456 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 985080000457 intersubunit interface [polypeptide binding]; other site 985080000458 active site 985080000459 zinc binding site [ion binding]; other site 985080000460 Na+ binding site [ion binding]; other site 985080000461 elongation factor P; Validated; Region: PRK00529 985080000462 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 985080000463 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 985080000464 RNA binding site [nucleotide binding]; other site 985080000465 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 985080000466 RNA binding site [nucleotide binding]; other site 985080000467 pseudaminic acid synthase; Region: PseI; TIGR03586 985080000468 NeuB family; Region: NeuB; pfam03102 985080000469 C-terminal SAF domain of sialic acid synthetase; Region: SAF_NeuB_like; cd11615 985080000470 NeuB binding interface [polypeptide binding]; other site 985080000471 putative substrate binding site [chemical binding]; other site 985080000472 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 985080000473 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 985080000474 Walker A/P-loop; other site 985080000475 ATP binding site [chemical binding]; other site 985080000476 Q-loop/lid; other site 985080000477 ABC transporter signature motif; other site 985080000478 Walker B; other site 985080000479 D-loop; other site 985080000480 H-loop/switch region; other site 985080000481 apolipoprotein N-acyltransferase; Reviewed; Region: PRK12291 985080000482 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cl11424 985080000483 active site 985080000484 catalytic triad [active] 985080000485 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 985080000486 Colicin V production protein; Region: Colicin_V; pfam02674 985080000487 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 985080000488 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 985080000489 dimer interface [polypeptide binding]; other site 985080000490 putative anticodon binding site; other site 985080000491 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 985080000492 motif 1; other site 985080000493 active site 985080000494 motif 2; other site 985080000495 motif 3; other site 985080000496 serine hydroxymethyltransferase; Reviewed; Region: PRK13034 985080000497 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 985080000498 dimer interface [polypeptide binding]; other site 985080000499 active site 985080000500 glycine-pyridoxal phosphate binding site [chemical binding]; other site 985080000501 folate binding site [chemical binding]; other site 985080000502 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 985080000503 nucleotide binding site [chemical binding]; other site 985080000504 Eukaryotic and archaeal DNA primase small subunit; Region: DNA_primase_S; pfam01896 985080000505 Sporulation related domain; Region: SPOR; cl10051 985080000506 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 985080000507 Protein of unknown function DUF262; Region: DUF262; pfam03235 985080000508 Uncharacterized conserved protein [Function unknown]; Region: COG1479 985080000509 Uncharacterized protein family, UPF0114; Region: UPF0114; cl01078 985080000510 Phosphatidylserine/phosphatidylglycerophosphate/car diolipin synthases and related enzymes [Lipid metabolism]; Region: Cls; COG1502 985080000511 Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_1; cd09111 985080000512 putative active site [active] 985080000513 catalytic site [active] 985080000514 Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_2; cd09113 985080000515 putative active site [active] 985080000516 catalytic site [active] 985080000517 fumarate reductase iron-sulfur subunit; Provisional; Region: frdB; PRK13552 985080000518 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 985080000519 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 985080000520 fumarate reductase flavoprotein subunit; Provisional; Region: PRK08626 985080000521 L-aspartate oxidase; Provisional; Region: PRK06175 985080000522 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 985080000523 fumarate reductase cytochrome b-556 subunit; Provisional; Region: PRK13553 985080000524 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 985080000525 Iron-sulfur protein interface; other site 985080000526 proximal heme binding site [chemical binding]; other site 985080000527 distal heme binding site [chemical binding]; other site 985080000528 dimer interface [polypeptide binding]; other site 985080000529 triosephosphate isomerase; Provisional; Region: PRK14567 985080000530 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 985080000531 substrate binding site [chemical binding]; other site 985080000532 dimer interface [polypeptide binding]; other site 985080000533 catalytic triad [active] 985080000534 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK08415 985080000535 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 985080000536 NAD binding site [chemical binding]; other site 985080000537 homotetramer interface [polypeptide binding]; other site 985080000538 homodimer interface [polypeptide binding]; other site 985080000539 substrate binding site [chemical binding]; other site 985080000540 active site 985080000541 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Region: lipid_A_lpxD; TIGR01853 985080000542 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 985080000543 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 985080000544 trimer interface [polypeptide binding]; other site 985080000545 active site 985080000546 UDP-GlcNAc binding site [chemical binding]; other site 985080000547 lipid binding site [chemical binding]; lipid-binding site 985080000548 S-adenosylmethionine synthetase; Validated; Region: PRK05250 985080000549 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 985080000550 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 985080000551 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 985080000552 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 985080000553 active site 985080000554 multimer interface [polypeptide binding]; other site 985080000555 Uncharacterized ACR, COG1399; Region: DUF177; cl00616 985080000556 Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]; Region: RpmF; COG0333 985080000557 fatty acid/phospholipid synthesis protein PlsX; Region: plsX; TIGR00182 985080000558 3-oxoacyl-(acyl-carrier-protein) synthase III; Region: fabH; TIGR00747 985080000559 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 985080000560 dimer interface [polypeptide binding]; other site 985080000561 active site 985080000562 CoA binding pocket [chemical binding]; other site 985080000563 AAA ATPase domain; Region: AAA_15; pfam13175 985080000564 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cd00267 985080000565 Walker B; other site 985080000566 D-loop; other site 985080000567 H-loop/switch region; other site 985080000568 antiporter inner membrane protein; Provisional; Region: PRK11670 985080000569 Domain of unknown function DUF59; Region: DUF59; pfam01883 985080000570 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 985080000571 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 985080000572 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 985080000573 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 985080000574 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 985080000575 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 985080000576 heat shock protein 90; Provisional; Region: PRK05218 985080000577 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 985080000578 ATP binding site [chemical binding]; other site 985080000579 Mg2+ binding site [ion binding]; other site 985080000580 G-X-G motif; other site 985080000581 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 985080000582 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 985080000583 binding surface 985080000584 TPR motif; other site 985080000585 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 985080000586 TPR motif; other site 985080000587 binding surface 985080000588 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 985080000589 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 985080000590 metal binding site [ion binding]; metal-binding site 985080000591 dimer interface [polypeptide binding]; other site 985080000592 glucose-inhibited division protein A; Region: gidA; TIGR00136 985080000593 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 985080000594 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 985080000595 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 985080000596 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 985080000597 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 985080000598 transmembrane helices; other site 985080000599 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 985080000600 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 985080000601 1-deoxy-D-xylulose 5-phosphate reductoisomerase [Lipid metabolism]; Region: Dxr; COG0743 985080000602 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 985080000603 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 985080000604 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 985080000605 Beta-1,4-N-acetylgalactosaminyltransferase (CgtA); Region: CgtA; pfam06306 985080000606 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 985080000607 substrate binding site [chemical binding]; other site 985080000608 Helix-turn-helix domain; Region: HTH_28; pfam13518 985080000609 cysteine desulfurase, NifS family, epsilon proteobacteria type; Region: nifS_epsilon; TIGR03403 985080000610 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 985080000611 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 985080000612 catalytic residue [active] 985080000613 Fe-S cluster assembly protein NifU; Region: NifU_proper; TIGR02000 985080000614 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 985080000615 trimerization site [polypeptide binding]; other site 985080000616 active site 985080000617 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 985080000618 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 985080000619 Ribbon-helix-helix protein, copG family; Region: RHH_1; pfam01402 985080000620 DNA repair protein RadA; Region: sms; TIGR00416 985080000621 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 985080000622 Walker A motif/ATP binding site; other site 985080000623 ATP binding site [chemical binding]; other site 985080000624 Walker B motif; other site 985080000625 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 985080000626 Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: MsrA; COG0225 985080000627 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: COG0229 985080000628 SelR domain; Region: SelR; pfam01641 985080000629 Predicted permeases [General function prediction only]; Region: COG0730 985080000630 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 985080000631 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 985080000632 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 985080000633 Sulfate transporter family; Region: Sulfate_transp; pfam00916 985080000634 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 985080000635 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 985080000636 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 985080000637 Ligand binding site; other site 985080000638 oligomer interface; other site 985080000639 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 985080000640 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 985080000641 hypothetical protein; Provisional; Region: PRK04081 985080000642 Glutathionylspermidine synthase [Amino acid transport and metabolism]; Region: Gsp; COG0754 985080000643 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3295 985080000644 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 985080000645 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 985080000646 binding surface 985080000647 TPR motif; other site 985080000648 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 985080000649 binding surface 985080000650 TPR motif; other site 985080000651 Sel1-like repeats; Region: SEL1; smart00671 985080000652 Sel1-like repeats; Region: SEL1; smart00671 985080000653 Cytochrome c; Region: Cytochrom_C; cl11414 985080000654 Porphobilinogen deaminase [Coenzyme metabolism]; Region: HemC; COG0181 985080000655 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 985080000656 domain interfaces; other site 985080000657 active site 985080000658 prolyl-tRNA synthetase; Provisional; Region: PRK09194 985080000659 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 985080000660 dimer interface [polypeptide binding]; other site 985080000661 motif 1; other site 985080000662 active site 985080000663 motif 2; other site 985080000664 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 985080000665 putative deacylase active site [active] 985080000666 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 985080000667 active site 985080000668 motif 3; other site 985080000669 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 985080000670 anticodon binding site; other site 985080000671 glutamyl-tRNA reductase; Region: hemA; TIGR01035 985080000672 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 985080000673 tRNA; other site 985080000674 putative tRNA binding site [nucleotide binding]; other site 985080000675 putative NADP binding site [chemical binding]; other site 985080000676 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 985080000677 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 985080000678 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 985080000679 substrate binding pocket [chemical binding]; other site 985080000680 chain length determination region; other site 985080000681 substrate-Mg2+ binding site; other site 985080000682 catalytic residues [active] 985080000683 aspartate-rich region 1; other site 985080000684 active site lid residues [active] 985080000685 aspartate-rich region 2; other site 985080000686 Domain of unknown function (DUF2018); Region: DUF2018; pfam09442 985080000687 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 985080000688 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 985080000689 dimerization interface [polypeptide binding]; other site 985080000690 DPS ferroxidase diiron center [ion binding]; other site 985080000691 ion pore; other site 985080000692 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 985080000693 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 985080000694 dimer interface [polypeptide binding]; other site 985080000695 phosphorylation site [posttranslational modification] 985080000696 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 985080000697 ATP binding site [chemical binding]; other site 985080000698 Mg2+ binding site [ion binding]; other site 985080000699 G-X-G motif; other site 985080000700 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 985080000701 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 985080000702 helicase 45; Provisional; Region: PTZ00424 985080000703 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 985080000704 ATP binding site [chemical binding]; other site 985080000705 Mg++ binding site [ion binding]; other site 985080000706 motif III; other site 985080000707 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 985080000708 nucleotide binding region [chemical binding]; other site 985080000709 ATP-binding site [chemical binding]; other site 985080000710 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 985080000711 SPFH domain / Band 7 family; Region: Band_7; pfam01145 985080000712 Protein of unknown function (DUF2393); Region: DUF2393; pfam09624 985080000713 potential frameshift: common BLAST hit: gi|383750099|ref|YP_005425202.1| oligopeptide permease ATPase protein 985080000714 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 985080000715 ABC transporter signature motif; other site 985080000716 Walker B; other site 985080000717 D-loop; other site 985080000718 H-loop/switch region; other site 985080000719 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 985080000720 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 985080000721 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 985080000722 Walker A/P-loop; other site 985080000723 ATP binding site [chemical binding]; other site 985080000724 Q-loop/lid; other site 985080000725 ABC transporter signature motif; other site 985080000726 Walker B; other site 985080000727 D-loop; other site 985080000728 H-loop/switch region; other site 985080000729 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 985080000730 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 985080000731 Walker A/P-loop; other site 985080000732 ATP binding site [chemical binding]; other site 985080000733 Q-loop/lid; other site 985080000734 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4239 985080000735 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 985080000736 dimer interface [polypeptide binding]; other site 985080000737 conserved gate region; other site 985080000738 putative PBP binding loops; other site 985080000739 ABC-ATPase subunit interface; other site 985080000740 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 985080000741 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 985080000742 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 985080000743 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 985080000744 GDP-binding site [chemical binding]; other site 985080000745 ACT binding site; other site 985080000746 IMP binding site; other site 985080000747 Flagellar FliJ protein; Region: FliJ; pfam02050 985080000748 Uncharacterized conserved protein [Function unknown]; Region: COG3334 985080000749 RIP metalloprotease RseP; Region: TIGR00054 985080000750 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 985080000751 active site 985080000752 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 985080000753 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic...; Region: S2P-M50; cl10020 985080000754 putative substrate binding region [chemical binding]; other site 985080000755 exodeoxyribonuclease VII, large subunit; Region: xseA; TIGR00237 985080000756 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 985080000757 generic binding surface II; other site 985080000758 generic binding surface I; other site 985080000759 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 985080000760 DNA methylase; Region: N6_N4_Mtase; pfam01555 985080000761 DNA methylase; Region: N6_N4_Mtase; pfam01555 985080000762 potential frameshift: common BLAST hit: gi|208434208|ref|YP_002265874.1| type II DNA modification enzyme 985080000763 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 985080000764 DNA methylase; Region: N6_N4_Mtase; pfam01555 985080000765 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 985080000766 Clp amino terminal domain; Region: Clp_N; pfam02861 985080000767 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 985080000768 Walker A motif; other site 985080000769 ATP binding site [chemical binding]; other site 985080000770 Walker B motif; other site 985080000771 arginine finger; other site 985080000772 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 985080000773 Walker A motif; other site 985080000774 ATP binding site [chemical binding]; other site 985080000775 Walker B motif; other site 985080000776 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 985080000777 Cytochrome c biogenesis protein [Posttranslational modification, protein turnover, chaperones]; Region: CcdA; COG0785 985080000778 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; pfam02683 985080000779 Dihydroorotase and related cyclic amidohydrolases [Nucleotide transport and metabolism]; Region: PyrC; COG0044 985080000780 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 985080000781 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 985080000782 active site 985080000783 chlorohydrolase; Provisional; Region: PRK08418 985080000784 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 985080000785 active site 985080000786 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 985080000787 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14339 985080000788 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 985080000789 FeS/SAM binding site; other site 985080000790 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: DUF374; Region: LPLAT_DUF374-like; cd07983 985080000791 putative acyl-acceptor binding pocket; other site 985080000792 urocanate hydratase; Provisional; Region: PRK05414 985080000793 Predicted Fe-S-cluster oxidoreductase [General function prediction only]; Region: COG0727 985080000794 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]; Region: COG2956 985080000795 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl09108 985080000796 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 985080000797 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 985080000798 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 985080000799 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 985080000800 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 985080000801 putative active site [active] 985080000802 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 985080000803 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 985080000804 putative acyl-acceptor binding pocket; other site 985080000805 potential frameshift: common BLAST hit: gi|15611336|ref|NP_222987.1| queuine tRNA-ribosyltransferase 985080000806 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; cl00409 985080000807 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; cl00409 985080000808 tRNA-guanine family transglycosylase; Region: tgt_general; TIGR00449 985080000809 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3400 985080000810 TrkA-C domain; Region: TrkA_C; pfam02080 985080000811 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 985080000812 active site 985080000813 dimer interface [polypeptide binding]; other site 985080000814 metal binding site [ion binding]; metal-binding site 985080000815 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 985080000816 Mechanosensitive ion channel; Region: MS_channel; pfam00924 985080000817 radical SAM methylthiotransferase, MiaB/RimO family; Region: TIGR00089 985080000818 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 985080000819 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 985080000820 FeS/SAM binding site; other site 985080000821 ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]; Region: HflB; COG0465 985080000822 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 985080000823 Walker B motif; other site 985080000824 arginine finger; other site 985080000825 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 985080000826 Domain of unknown function (DUF4149); Region: DUF4149; pfam13664 985080000827 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 985080000828 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 985080000829 PPE-repeat proteins [Cell motility and secretion]; Region: COG5651 985080000830 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 985080000831 Autotransporter beta-domain; Region: Autotransporter; pfam03797 985080000832 diaminopimelate decarboxylase; Region: lysA; TIGR01048 985080000833 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 985080000834 active site 985080000835 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 985080000836 substrate binding site [chemical binding]; other site 985080000837 catalytic residues [active] 985080000838 dimer interface [polypeptide binding]; other site 985080000839 Chorismate mutase [Amino acid transport and metabolism]; Region: PheA; COG1605 985080000840 Uncharacterized conserved protein [Function unknown]; Region: COG4866 985080000841 aminodeoxychorismate synthase; Provisional; Region: PRK07508 985080000842 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 985080000843 PyridoxaL 5'-Phosphate Dependent Enzymes class IV (PLPDE_IV). This D-amino acid superfamily, one of five classes of PLPDE, consists of branched-chain amino acid aminotransferases (BCAT), D-amino acid transferases (DAAT), and...; Region: PLPDE_IV; cl00224 985080000844 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 985080000845 substrate-cofactor binding pocket; other site 985080000846 pyridoxal 5'-phosphate binding site [chemical binding]; other site 985080000847 catalytic residue [active] 985080000848 acylamide amidohydrolase; Provisional; Region: amiE; PRK13286 985080000849 aliphatic amidases (class 2 nitrilases); Region: aliphatic_amidase; cd07565 985080000850 multimer interface [polypeptide binding]; other site 985080000851 active site 985080000852 catalytic triad [active] 985080000853 dimer interface [polypeptide binding]; other site 985080000854 flagellar hook-associated protein FlgL; Validated; Region: flgL; PRK08412 985080000855 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 985080000856 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 985080000857 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 985080000858 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 985080000859 The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; Region: PBP2_DppA_like; cd08493 985080000860 peptide binding site [polypeptide binding]; other site 985080000861 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 985080000862 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 985080000863 dimer interface [polypeptide binding]; other site 985080000864 conserved gate region; other site 985080000865 putative PBP binding loops; other site 985080000866 ABC-ATPase subunit interface; other site 985080000867 dipeptide transporter; Provisional; Region: PRK10913 985080000868 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 985080000869 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 985080000870 dimer interface [polypeptide binding]; other site 985080000871 conserved gate region; other site 985080000872 putative PBP binding loops; other site 985080000873 ABC-ATPase subunit interface; other site 985080000874 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 985080000875 nickel import ATP-binding protein NikD; Region: nickel_nikD; TIGR02770 985080000876 Walker A/P-loop; other site 985080000877 ATP binding site [chemical binding]; other site 985080000878 Q-loop/lid; other site 985080000879 ABC transporter signature motif; other site 985080000880 Walker B; other site 985080000881 D-loop; other site 985080000882 H-loop/switch region; other site 985080000883 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; pfam08352 985080000884 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 985080000885 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 985080000886 Walker A/P-loop; other site 985080000887 ATP binding site [chemical binding]; other site 985080000888 Q-loop/lid; other site 985080000889 ABC transporter signature motif; other site 985080000890 Walker B; other site 985080000891 D-loop; other site 985080000892 H-loop/switch region; other site 985080000893 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; pfam08352 985080000894 GTPase CgtA; Reviewed; Region: obgE; PRK12299 985080000895 GTP1/OBG; Region: GTP1_OBG; pfam01018 985080000896 Obg GTPase; Region: Obg; cd01898 985080000897 G1 box; other site 985080000898 GTP/Mg2+ binding site [chemical binding]; other site 985080000899 Switch I region; other site 985080000900 G2 box; other site 985080000901 G3 box; other site 985080000902 Switch II region; other site 985080000903 G4 box; other site 985080000904 G5 box; other site 985080000905 Alginate lyase; Region: Alginate_lyase; pfam05426 985080000906 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 985080000907 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 985080000908 inhibitor-cofactor binding pocket; inhibition site 985080000909 pyridoxal 5'-phosphate binding site [chemical binding]; other site 985080000910 catalytic residue [active] 985080000911 Putative F0F1-ATPase subunit (ATPase_gene1); Region: ATPase_gene1; pfam09527 985080000912 Predicted amidohydrolase [General function prediction only]; Region: COG0388 985080000913 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cd07197 985080000914 active site 985080000915 catalytic triad [active] 985080000916 dimer interface [polypeptide binding]; other site 985080000917 Catalytic domain of Helicobacter pylori peptidoglycan deacetylase (HpPgdA) and similar proteins; Region: CE4_HpPgdA_like; cd10938 985080000918 active site 985080000919 catalytic site [active] 985080000920 Zn binding site [ion binding]; other site 985080000921 tetramer interface [polypeptide binding]; other site 985080000922 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 985080000923 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 985080000924 CobW/HypB/UreG, nucleotide-binding domain; Region: cobW; pfam02492 985080000925 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; pfam07683 985080000926 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 985080000927 Major Facilitator Superfamily; Region: MFS_1; pfam07690 985080000928 putative substrate translocation pore; other site 985080000929 potential frameshift: common BLAST hit: gi|298736305|ref|YP_003728831.1| putative ABC transporter ATP-binding protein 985080000930 ABC-type protease/lipase transport system, ATPase and permease components [General function prediction only]; Region: ArpD; COG4618 985080000931 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 985080000932 Walker A/P-loop; other site 985080000933 ATP binding site [chemical binding]; other site 985080000934 ABC transporter; Region: ABC_tran; pfam00005 985080000935 Q-loop/lid; other site 985080000936 ABC transporter signature motif; other site 985080000937 Walker B; other site 985080000938 D-loop; other site 985080000939 heme oxygenase, HugZ family; Region: heme_ox_HugZ; TIGR04109 985080000940 Protein of unknown function (DUF2470); Region: DUF2470; pfam10615 985080000941 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 985080000942 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 985080000943 arginyl-tRNA synthetase; Region: argS; TIGR00456 985080000944 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 985080000945 active site 985080000946 HIGH motif; other site 985080000947 KMSK motif region; other site 985080000948 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 985080000949 tRNA binding surface [nucleotide binding]; other site 985080000950 anticodon binding site; other site 985080000951 twin arginine-targeting protein translocase, TatA/E family; Region: tatAE; TIGR01411 985080000952 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 985080000953 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 985080000954 catalytic site [active] 985080000955 G-X2-G-X-G-K; other site 985080000956 nuclease NucT; Provisional; Region: PRK13912 985080000957 Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6, and similar proteins; Region: PLDc_Nuc_like; cd09116 985080000958 putative active site [active] 985080000959 catalytic site [active] 985080000960 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 985080000961 Flagellar basal body L-ring protein [Cell motility and secretion]; Region: FlgH; COG2063 985080000962 flagellar basal body L-ring protein; Reviewed; Region: flgH; PRK00249 985080000963 CMP-NeuAc_Synthase activates N-acetylneuraminic acid by adding CMP moiety; Region: CMP-NeuAc_Synthase; cd02513 985080000964 ligand binding site; other site 985080000965 tetramer interface; other site 985080000966 Spore coat polysaccharide biosynthesis protein, predicted glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: spsG; COG3980 985080000967 pseudaminic acid biosynthesis N-acetyl transferase; Region: PseH; TIGR03585 985080000968 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 985080000969 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 985080000970 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 985080000971 NAD synthetase; Provisional; Region: PRK13980 985080000972 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 985080000973 homodimer interface [polypeptide binding]; other site 985080000974 NAD binding pocket [chemical binding]; other site 985080000975 ATP binding pocket [chemical binding]; other site 985080000976 Mg binding site [ion binding]; other site 985080000977 active-site loop [active] 985080000978 ketol-acid reductoisomerase; Provisional; Region: PRK05479 985080000979 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 985080000980 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 985080000981 Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]; Region: MinD; COG2894 985080000982 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 985080000983 Switch I; other site 985080000984 Switch II; other site 985080000985 cell division topological specificity factor MinE; Region: minE; TIGR01215 985080000986 DNA protecting protein DprA; Region: dprA; TIGR00732 985080000987 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 985080000988 Holliday junction resolvase-like protein; Reviewed; Region: PRK00109 985080000989 Sel1 repeat; Region: Sel1; cl02723 985080000990 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 985080000991 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 985080000992 active site 985080000993 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 985080000994 DHH family; Region: DHH; pfam01368 985080000995 DHHA1 domain; Region: DHHA1; pfam02272 985080000996 CTP synthetase; Validated; Region: pyrG; PRK05380 985080000997 CTP synthase N-terminus; Region: CTP_synth_N; pfam06418 985080000998 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 985080000999 active site 985080001000 putative oxyanion hole; other site 985080001001 catalytic triad [active] 985080001002 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 985080001003 flagellar basal-body M-ring protein/flagellar hook-basal body protein (fliF); Region: fliF; TIGR00206 985080001004 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; pfam01514 985080001005 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 985080001006 flagellar motor switch protein FliG; Region: fliG; TIGR00207 985080001007 FliG C-terminal domain; Region: FliG_C; pfam01706 985080001008 flagellar assembly protein H; Validated; Region: fliH; PRK06669 985080001009 Flagellar assembly protein FliH; Region: FliH; pfam02108 985080001010 1-deoxy-D-xylulose-5-phosphate synthase; Region: dxs; TIGR00204 985080001011 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 985080001012 TPP-binding site; other site 985080001013 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 985080001014 PYR/PP interface [polypeptide binding]; other site 985080001015 dimer interface [polypeptide binding]; other site 985080001016 TPP binding site [chemical binding]; other site 985080001017 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 985080001018 GTP-binding protein LepA; Provisional; Region: PRK05433 985080001019 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 985080001020 G1 box; other site 985080001021 putative GEF interaction site [polypeptide binding]; other site 985080001022 GTP/Mg2+ binding site [chemical binding]; other site 985080001023 Switch I region; other site 985080001024 G2 box; other site 985080001025 G3 box; other site 985080001026 Switch II region; other site 985080001027 G4 box; other site 985080001028 G5 box; other site 985080001029 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 985080001030 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 985080001031 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 985080001032 Domain of unknown function (DUF3883); Region: DUF3883; pfam13020 985080001033 Flagellar basal body rod protein [Cell motility and secretion]; Region: FlgG; COG4786 985080001034 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 985080001035 alpha-ketoglutarate transporter; Provisional; Region: PRK10406 985080001036 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 985080001037 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 985080001038 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 985080001039 TspO/MBR family; Region: TspO_MBR; cl01379 985080001040 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 985080001041 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 985080001042 Inactivated superfamily I helicase [DNA replication, recombination, and repair]; Region: COG3893 985080001043 RecB family exonuclease [DNA replication, recombination, and repair]; Region: COG2887 985080001044 transketolase, bacterial and yeast; Region: tktlase_bact; TIGR00232 985080001045 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 985080001046 TPP-binding site [chemical binding]; other site 985080001047 dimer interface [polypeptide binding]; other site 985080001048 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 985080001049 PYR/PP interface [polypeptide binding]; other site 985080001050 dimer interface [polypeptide binding]; other site 985080001051 TPP binding site [chemical binding]; other site 985080001052 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 985080001053 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 985080001054 riboflavin kinase/FMN adenylyltransferase; Region: ribF; TIGR00083 985080001055 active site 985080001056 Riboflavin kinase; Region: Flavokinase; pfam01687 985080001057 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 985080001058 S4 RNA-binding domain; Region: S4; smart00363 985080001059 RNA binding surface [nucleotide binding]; other site 985080001060 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 985080001061 S-adenosylmethionine binding site [chemical binding]; other site 985080001062 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 985080001063 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 985080001064 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 985080001065 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 985080001066 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 985080001067 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 985080001068 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 985080001069 Walker A/P-loop; other site 985080001070 ATP binding site [chemical binding]; other site 985080001071 Q-loop/lid; other site 985080001072 ABC transporter signature motif; other site 985080001073 Walker B; other site 985080001074 D-loop; other site 985080001075 H-loop/switch region; other site 985080001076 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 985080001077 Predicted endonuclease distantly related to archaeal Holliday junction resolvase and Mrr-like restriction enzymes [Defense mechanisms]; Region: COG1787 985080001078 Restriction endonuclease; Region: Mrr_cat; pfam04471 985080001079 Predicted ATPases [General function prediction only]; Region: COG1106 985080001080 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 985080001081 Walker A/P-loop; other site 985080001082 ATP binding site [chemical binding]; other site 985080001083 Predicted ATPases [General function prediction only]; Region: COG1106 985080001084 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 985080001085 Walker B; other site 985080001086 D-loop; other site 985080001087 H-loop/switch region; other site 985080001088 High-affinity nickel permease [Inorganic ion transport and metabolism]; Region: HoxN; COG3376 985080001089 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cd00596 985080001090 active site 985080001091 Zn binding site [ion binding]; other site 985080001092 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 985080001093 metal-binding site [ion binding] 985080001094 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 985080001095 metal-binding site [ion binding] 985080001096 copper-(or silver)-translocating P-type ATPase; Region: ATPase-IB1_Cu; TIGR01511 985080001097 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 985080001098 Soluble P-type ATPase [General function prediction only]; Region: COG4087 985080001099 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 985080001100 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 985080001101 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 985080001102 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 985080001103 Walker A motif; other site 985080001104 ATP binding site [chemical binding]; other site 985080001105 Walker B motif; other site 985080001106 arginine finger; other site 985080001107 Peptidase family M41; Region: Peptidase_M41; pfam01434 985080001108 ribosomal protein L11 methyltransferase; Region: prmA; TIGR00406 985080001109 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 985080001110 S-adenosylmethionine binding site [chemical binding]; other site 985080001111 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 985080001112 Response regulator receiver domain; Region: Response_reg; pfam00072 985080001113 active site 985080001114 phosphorylation site [posttranslational modification] 985080001115 intermolecular recognition site; other site 985080001116 dimerization interface [polypeptide binding]; other site 985080001117 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 985080001118 rRNA small subunit methyltransferase G; Region: GidB; pfam02527 985080001119 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 985080001120 S-adenosylmethionine binding site [chemical binding]; other site 985080001121 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 985080001122 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 985080001123 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 985080001124 sec-independent translocase; Provisional; Region: PRK04098 985080001125 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 985080001126 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 985080001127 Walker A motif; other site 985080001128 ATP binding site [chemical binding]; other site 985080001129 Walker B motif; other site 985080001130 arginine finger; other site 985080001131 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 985080001132 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 985080001133 oligomerization interface [polypeptide binding]; other site 985080001134 active site 985080001135 metal binding site [ion binding]; metal-binding site 985080001136 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 985080001137 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 985080001138 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 985080001139 septum formation inhibitor; Reviewed; Region: minC; PRK00556 985080001140 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 985080001141 UDP-3-0-acyl N-acetylglucosamine deacetylase; Region: lpxC; TIGR00325 985080001142 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 985080001143 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 985080001144 homoserine kinase; Region: thrB; TIGR00191 985080001145 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 985080001146 Predicted nucleic-acid-binding protein implicated in transcription termination [Transcription]; Region: COG2740 985080001147 putative RNA binding cleft [nucleotide binding]; other site 985080001148 translation initiation factor IF-2; Region: IF-2; TIGR00487 985080001149 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 985080001150 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 985080001151 G1 box; other site 985080001152 putative GEF interaction site [polypeptide binding]; other site 985080001153 GTP/Mg2+ binding site [chemical binding]; other site 985080001154 Switch I region; other site 985080001155 G2 box; other site 985080001156 G3 box; other site 985080001157 Switch II region; other site 985080001158 G4 box; other site 985080001159 G5 box; other site 985080001160 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 985080001161 Translation-initiation factor 2; Region: IF-2; pfam11987 985080001162 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 985080001163 ribosome-binding factor A; Region: rbfA; TIGR00082 985080001164 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG0779 985080001165 Sm and related proteins; Region: Sm_like; cl00259 985080001166 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 985080001167 putative oligomer interface [polypeptide binding]; other site 985080001168 putative RNA binding site [nucleotide binding]; other site 985080001169 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 985080001170 putative active site [active] 985080001171 putative metal binding site [ion binding]; other site 985080001172 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 985080001173 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 985080001174 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 985080001175 active site 985080001176 intermolecular recognition site; other site 985080001177 dimerization interface [polypeptide binding]; other site 985080001178 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 985080001179 DNA binding site [nucleotide binding] 985080001180 Predicted phosphohydrolase (DHH superfamily) [General function prediction only]; Region: COG2404 985080001181 DHH family; Region: DHH; pfam01368 985080001182 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 985080001183 FHIPEP family; Region: FHIPEP; pfam00771 985080001184 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 985080001185 16S/18S rRNA binding site [nucleotide binding]; other site 985080001186 S13e-L30e interaction site [polypeptide binding]; other site 985080001187 25S rRNA binding site [nucleotide binding]; other site 985080001188 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 985080001189 O-Antigen ligase; Region: Wzy_C; pfam04932 985080001190 Dehydroquinase class II; Region: DHquinase_II; pfam01220 985080001191 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 985080001192 trimer interface [polypeptide binding]; other site 985080001193 active site 985080001194 dimer interface [polypeptide binding]; other site 985080001195 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 985080001196 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 985080001197 active site 985080001198 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 985080001199 catalytic center binding site [active] 985080001200 ATP binding site [chemical binding]; other site 985080001201 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK05703 985080001202 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 985080001203 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 985080001204 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 985080001205 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 985080001206 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 985080001207 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 985080001208 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 985080001209 DNA binding residues [nucleotide binding] 985080001210 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 985080001211 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 985080001212 flagellar motor switch protein FliY; Validated; Region: PRK08432 985080001213 flagellar motor switch protein FliN; Region: fliN; TIGR02480 985080001214 Beta-galactosidase, beta subunit [Carbohydrate transport and metabolism]; Region: EbgC; COG2731 985080001215 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4731 985080001216 ferric uptake regulator; Provisional; Region: fur; PRK09462 985080001217 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 985080001218 metal binding site 2 [ion binding]; metal-binding site 985080001219 putative DNA binding helix; other site 985080001220 metal binding site 1 [ion binding]; metal-binding site 985080001221 dimer interface [polypeptide binding]; other site 985080001222 structural Zn2+ binding site [ion binding]; other site 985080001223 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]; Region: MGS1; COG2256 985080001224 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 985080001225 Walker A motif; other site 985080001226 ATP binding site [chemical binding]; other site 985080001227 Walker B motif; other site 985080001228 arginine finger; other site 985080001229 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 985080001230 Helix-Turn-Helix DNA binding domain of the HspR transcription regulator; Region: HTH_HspR; cd04766 985080001231 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 985080001232 DNA binding residues [nucleotide binding] 985080001233 putative dimer interface [polypeptide binding]; other site 985080001234 chaperone protein DnaJ; Provisional; Region: PRK14299 985080001235 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 985080001236 HSP70 interaction site [polypeptide binding]; other site 985080001237 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 985080001238 substrate binding site [polypeptide binding]; other site 985080001239 dimer interface [polypeptide binding]; other site 985080001240 5'-3' exonuclease; Provisional; Region: PRK14976 985080001241 PIN (PilT N terminus) domain: Superfamily; Region: PIN_SF; cl14812 985080001242 putative active site [active] 985080001243 Helix-hairpin-helix class 2 (Pol1 family) motifs; Region: HhH2; smart00279 985080001244 DNA binding site [nucleotide binding] 985080001245 metal binding site [ion binding]; metal-binding site 985080001246 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 985080001247 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 985080001248 active site 985080001249 dimerization interface [polypeptide binding]; other site 985080001250 bifunctional 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase/2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase protein; Provisional; Region: ispDF; PRK09382 985080001251 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 985080001252 substrate binding site; other site 985080001253 dimer interface; other site 985080001254 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 985080001255 homotrimer interaction site [polypeptide binding]; other site 985080001256 zinc binding site [ion binding]; other site 985080001257 CDP-binding sites; other site 985080001258 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 985080001259 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 985080001260 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 985080001261 protein binding site [polypeptide binding]; other site 985080001262 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 985080001263 S-methylmethionine transporter; Provisional; Region: PRK11387 985080001264 CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase; Region: pgsA; TIGR00560 985080001265 7-alpha-hydroxysteroid dehydrogenase; Provisional; Region: PRK08416 985080001266 1-cyclohexenylcarbonyl_coenzyme A_reductase (ChcA)_like, classical (c) SDRs; Region: ChcA_like_SDR_c; cd05359 985080001267 putative NAD(P) binding site [chemical binding]; other site 985080001268 active site 985080001269 dihydrodipicolinate synthase; Region: dapA; TIGR00674 985080001270 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 985080001271 dimer interface [polypeptide binding]; other site 985080001272 active site 985080001273 catalytic residue [active] 985080001274 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 985080001275 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 985080001276 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 985080001277 dihydroorotate dehydrogenase, subfamily 2; Region: pyrD_sub2; TIGR01036 985080001278 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 985080001279 quinone interaction residues [chemical binding]; other site 985080001280 active site 985080001281 catalytic residues [active] 985080001282 FMN binding site [chemical binding]; other site 985080001283 substrate binding site [chemical binding]; other site 985080001284 Polyphosphate kinase [Inorganic ion transport and metabolism]; Region: Ppk; COG0855 985080001285 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 985080001286 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 985080001287 Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C1_like; cd09165 985080001288 putative domain interface [polypeptide binding]; other site 985080001289 putative active site [active] 985080001290 catalytic site [active] 985080001291 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 985080001292 putative active site [active] 985080001293 putative domain interface [polypeptide binding]; other site 985080001294 catalytic site [active] 985080001295 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 985080001296 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 985080001297 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 985080001298 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 985080001299 S-adenosylmethionine binding site [chemical binding]; other site 985080001300 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 985080001301 Type III restriction enzyme, res subunit; Region: ResIII; pfam04851 985080001302 ATP binding site [chemical binding]; other site 985080001303 Type III restriction enzyme, res subunit; Region: ResIII; pfam04851 985080001304 putative Mg++ binding site [ion binding]; other site 985080001305 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 985080001306 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 985080001307 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2604 985080001308 N-terminal tellurium resistance protein terB-like domain of heat shock DnaJ-like proteins; Region: terB_like_DjlA; cd07316 985080001309 putative metal binding site [ion binding]; other site 985080001310 CoB--CoM heterodisulfide reductase, subunit B; Region: CoB_CoM_SS_B; TIGR03288 985080001311 oligoendopeptidase, pepF/M3 family; Region: M3_fam_3; TIGR02290 985080001312 Peptidase family M3B Oligopeptidase F (PepF); Region: M3B_PepF_5; cd09610 985080001313 active site 985080001314 Zn binding site [ion binding]; other site 985080001315 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 985080001316 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 985080001317 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 985080001318 ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: ModA; COG0725 985080001319 molybdenum ABC transporter, periplasmic molybdate-binding protein; Region: modA; TIGR01256 985080001320 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 985080001321 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 985080001322 dimer interface [polypeptide binding]; other site 985080001323 conserved gate region; other site 985080001324 putative PBP binding loops; other site 985080001325 ABC-ATPase subunit interface; other site 985080001326 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 985080001327 putative bacteriocin export ABC transporter, lactococcin 972 group; Region: L_ocin_972_ABC; TIGR03608 985080001328 Walker A/P-loop; other site 985080001329 ATP binding site [chemical binding]; other site 985080001330 Q-loop/lid; other site 985080001331 ABC transporter signature motif; other site 985080001332 Walker B; other site 985080001333 D-loop; other site 985080001334 H-loop/switch region; other site 985080001335 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 985080001336 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 985080001337 active site 985080001338 HIGH motif; other site 985080001339 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 985080001340 active site 985080001341 KMSKS motif; other site 985080001342 potential frameshift: common BLAST hit: gi|15611497|ref|NP_223148.1| type II DNA modification (methyltransferase 985080001343 Helix-turn-helix domain; Region: HTH_17; pfam12728 985080001344 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0827 985080001345 Methyltransferase domain; Region: Methyltransf_26; pfam13659 985080001346 TaqI-like C-terminal specificity domain; Region: TaqI_C; pfam12950 985080001347 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 985080001348 ADP-heptose:LPS heptosyl transferase I; Provisional; Region: PRK10964; cl15782 985080001349 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 985080001350 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 985080001351 G1 box; other site 985080001352 putative GEF interaction site [polypeptide binding]; other site 985080001353 GTP/Mg2+ binding site [chemical binding]; other site 985080001354 Switch I region; other site 985080001355 G2 box; other site 985080001356 G3 box; other site 985080001357 Switch II region; other site 985080001358 G4 box; other site 985080001359 G5 box; other site 985080001360 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 985080001361 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 985080001362 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dam; COG0338 985080001363 potential frameshift: common BLAST hit: gi|308184263|ref|YP_003928396.1| type II restriction endonuclease 985080001364 GIY-YIG nuclease domain superfamily; Region: GIY-YIG_SF; cl15257 985080001365 GIY-YIG motif/motif A; other site 985080001366 active site 985080001367 catalytic site [active] 985080001368 GIY-YIG nuclease domain superfamily; Region: GIY-YIG_SF; cl15257 985080001369 catalytic site [active] 985080001370 metal binding site [ion binding]; metal-binding site 985080001371 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 985080001372 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 985080001373 cofactor binding site; other site 985080001374 DNA binding site [nucleotide binding] 985080001375 substrate interaction site [chemical binding]; other site 985080001376 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 985080001377 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 985080001378 potential frameshift: common BLAST hit: gi|254779149|ref|YP_003057254.1| non-functional type II restriction endonuclease 985080001379 Catalase-like heme-binding proteins similar to the uncharacterized srpA; Region: srpA_like; cd08153 985080001380 putative heme binding pocket [chemical binding]; other site 985080001381 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 985080001382 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 985080001383 Kef-type K+ transport systems, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: Kch; COG1226 985080001384 TrkA-N domain; Region: TrkA_N; pfam02254 985080001385 TrkA-C domain; Region: TrkA_C; pfam02080 985080001386 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 985080001387 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 985080001388 phospho-N-acetylmuramoyl-pentapeptide-transferase; Region: mraY; TIGR00445 985080001389 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 985080001390 Mg++ binding site [ion binding]; other site 985080001391 putative catalytic motif [active] 985080001392 putative substrate binding site [chemical binding]; other site 985080001393 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK03815 985080001394 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 985080001395 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 985080001396 Protein of unknown function (DUF493); Region: DUF493; pfam04359 985080001397 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 985080001398 active site 985080001399 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 985080001400 Na2 binding site [ion binding]; other site 985080001401 putative substrate binding site 1 [chemical binding]; other site 985080001402 Na binding site 1 [ion binding]; other site 985080001403 putative substrate binding site 2 [chemical binding]; other site 985080001404 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 985080001405 Na2 binding site [ion binding]; other site 985080001406 putative substrate binding site 1 [chemical binding]; other site 985080001407 Na binding site 1 [ion binding]; other site 985080001408 putative substrate binding site 2 [chemical binding]; other site 985080001409 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 985080001410 dimerization interface [polypeptide binding]; other site 985080001411 substrate binding site [chemical binding]; other site 985080001412 active site 985080001413 calcium binding site [ion binding]; other site 985080001414 DNA polymerase III, beta subunit; Region: dnan; TIGR00663 985080001415 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 985080001416 putative DNA binding surface [nucleotide binding]; other site 985080001417 dimer interface [polypeptide binding]; other site 985080001418 beta-clamp/translesion DNA polymerase binding surface; other site 985080001419 beta-clamp/clamp loader binding surface; other site 985080001420 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 985080001421 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 985080001422 Mg2+ binding site [ion binding]; other site 985080001423 G-X-G motif; other site 985080001424 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 985080001425 anchoring element; other site 985080001426 dimer interface [polypeptide binding]; other site 985080001427 ATP binding site [chemical binding]; other site 985080001428 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 985080001429 active site 985080001430 putative metal-binding site [ion binding]; other site 985080001431 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 985080001432 R.Pab1 restriction endonuclease; Region: RE_R_Pab1; pfam09522 985080001433 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 985080001434 Peptidase family M23; Region: Peptidase_M23; pfam01551 985080001435 nudix-type nucleoside diphosphatase, YffH/AdpP family; Region: TIGR00052 985080001436 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 985080001437 dimer interface [polypeptide binding]; other site 985080001438 ADP-ribose binding site [chemical binding]; other site 985080001439 active site 985080001440 nudix motif; other site 985080001441 metal binding site [ion binding]; metal-binding site 985080001442 FAD binding domain; Region: FAD_binding_4; pfam01565 985080001443 glycolate oxidase, subunit GlcD; Region: glcD; TIGR00387 985080001444 Protein-interacting Bro1-like domain of mammalian Alix and related domains; Region: BRO1_Alix_like; cl14649 985080001445 dihydrodipicolinate reductase; Region: dapB; TIGR00036 985080001446 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 985080001447 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 985080001448 glutamine synthetase, type I; Region: GlnA; TIGR00653 985080001449 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 985080001450 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 985080001451 Uncharacterized conserved protein [Function unknown]; Region: COG1479 985080001452 Protein of unknown function DUF262; Region: DUF262; pfam03235 985080001453 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 985080001454 Uncharacterized conserved protein [Function unknown]; Region: COG3586 985080001455 ribosomal protein L9; Region: L9; TIGR00158 985080001456 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 985080001457 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 985080001458 Protease HslV and the ATPase/chaperone HslU are part of an ATP-dependent proteolytic system that is the prokaryotic homolog of the proteasome. HslV is a dimer of hexamers (a dodecamer) that forms a central proteolytic chamber with active sites on the...; Region: protease_HslV; cd01913 985080001459 active site 985080001460 HslU subunit interaction site [polypeptide binding]; other site 985080001461 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 985080001462 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 985080001463 Walker A motif; other site 985080001464 ATP binding site [chemical binding]; other site 985080001465 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 985080001466 Walker B motif; other site 985080001467 arginine finger; other site 985080001468 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 985080001469 GTPase [General function prediction only]; Region: Era; COG1159 985080001470 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 985080001471 G1 box; other site 985080001472 GTP/Mg2+ binding site [chemical binding]; other site 985080001473 Switch I region; other site 985080001474 G2 box; other site 985080001475 Switch II region; other site 985080001476 G3 box; other site 985080001477 G4 box; other site 985080001478 G5 box; other site 985080001479 KH domain; Region: KH_2; pfam07650 985080001480 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3034 985080001481 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 985080001482 Sel1-like repeats; Region: SEL1; smart00671 985080001483 Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]; Region: TopA; COG0551 985080001484 Type IV secretory pathway, VirD4 components [Intracellular trafficking and secretion]; Region: VirD4; COG3505 985080001485 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 985080001486 Walker A motif; other site 985080001487 ATP binding site [chemical binding]; other site 985080001488 Walker B motif; other site 985080001489 P-type DNA transfer ATPase VirB11; Region: VirB11; TIGR02788 985080001490 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 985080001491 ATP binding site [chemical binding]; other site 985080001492 Walker A motif; other site 985080001493 hexamer interface [polypeptide binding]; other site 985080001494 Walker B motif; other site 985080001495 CagZ; Region: CagZ; pfam09053 985080001496 potential frameshift: common BLAST hit: gi|15611543|ref|NP_223194.1| cag island protein 985080001497 DC-EC Repeat; Region: CagY_M; pfam07337 985080001498 Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion]; Region: VirB10; COG2948 985080001499 potential frameshift: common BLAST hit: gi|383749812|ref|YP_005424915.1| cag pathogenicity island protein (cag7) 985080001500 DC-EC Repeat; Region: CagY_M; pfam07337 985080001501 DC-EC Repeat; Region: CagY_M; pfam07337 985080001502 potential frameshift: common BLAST hit: gi|15611543|ref|NP_223194.1| cag island protein 985080001503 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cl11423 985080001504 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cl11423 985080001505 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 985080001506 VirB7 interaction site; other site 985080001507 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 985080001508 Cag pathogenicity island protein Cag12; Region: Cag12; pfam13117 985080001509 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK06945 985080001510 prolyl-tRNA synthetase; Provisional; Region: PRK08661 985080001511 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 985080001512 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 985080001513 CagA exotoxin; Region: CagA; pfam03507 985080001514 CagA exotoxin; Region: CagA; pfam03507 985080001515 AAA domain; Region: AAA_12; pfam13087 985080001516 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 985080001517 transcription termination factor Rho; Provisional; Region: rho; PRK09376 985080001518 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 985080001519 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 985080001520 RNA binding site [nucleotide binding]; other site 985080001521 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 985080001522 multimer interface [polypeptide binding]; other site 985080001523 Walker A motif; other site 985080001524 ATP binding site [chemical binding]; other site 985080001525 Walker B motif; other site 985080001526 Ribosomal protein L31; Region: Ribosomal_L31; pfam01197 985080001527 Predicted methyltransferases [General function prediction only]; Region: COG0313 985080001528 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 985080001529 putative SAM binding site [chemical binding]; other site 985080001530 putative homodimer interface [polypeptide binding]; other site 985080001531 rRNA methylase, putative, group 3; Region: rRNA_methyl_3; TIGR00186 985080001532 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 985080001533 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 985080001534 acetyl-CoA carboxylase, carboxyl transferase, alpha subunit; Region: accA; TIGR00513 985080001535 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 985080001536 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK08439 985080001537 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 985080001538 dimer interface [polypeptide binding]; other site 985080001539 active site 985080001540 acyl carrier protein; Provisional; Region: acpP; PRK00982 985080001541 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 985080001542 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 985080001543 NAD(P) binding site [chemical binding]; other site 985080001544 active site 985080001545 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 985080001546 Predicted membrane protein [Function unknown]; Region: COG3059 985080001547 diaminopimelate epimerase; Region: DapF; TIGR00652 985080001548 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 985080001549 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 985080001550 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 985080001551 Domain of unknown function DUF20; Region: UPF0118; pfam01594 985080001552 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 985080001553 FeS/SAM binding site; other site 985080001554 Domain of unknown function (DUF4008); Region: DUF4008; pfam13186 985080001555 GTP-binding protein YchF; Reviewed; Region: PRK09601 985080001556 YchF GTPase; Region: YchF; cd01900 985080001557 G1 box; other site 985080001558 GTP/Mg2+ binding site [chemical binding]; other site 985080001559 Switch I region; other site 985080001560 G2 box; other site 985080001561 Switch II region; other site 985080001562 G3 box; other site 985080001563 G4 box; other site 985080001564 G5 box; other site 985080001565 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 985080001566 multifunctional aminopeptidase A; Provisional; Region: PRK00913 985080001567 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 985080001568 interface (dimer of trimers) [polypeptide binding]; other site 985080001569 Substrate-binding/catalytic site; other site 985080001570 Zn-binding sites [ion binding]; other site 985080001571 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 985080001572 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 985080001573 active site 985080001574 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 985080001575 ribose 5-phosphate isomerase B; Region: rpiB; TIGR01120 985080001576 Peptidase family M50; Region: Peptidase_M50; pfam02163 985080001577 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 985080001578 active site 985080001579 putative substrate binding region [chemical binding]; other site 985080001580 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 985080001581 signal peptidase I; Provisional; Region: PRK10861 985080001582 Catalytic site [active] 985080001583 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 985080001584 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14191 985080001585 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 985080001586 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 985080001587 homodimer interface [polypeptide binding]; other site 985080001588 NADP binding site [chemical binding]; other site 985080001589 substrate binding site [chemical binding]; other site 985080001590 Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]; Region: MdoB; COG1368 985080001591 Sulfatase; Region: Sulfatase; pfam00884 985080001592 Predicted neuraminidase (sialidase) [Carbohydrate transport and metabolism]; Region: COG4692 985080001593 BNR repeat-like domain; Region: BNR_2; pfam13088 985080001594 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 985080001595 active site 985080001596 substrate binding pocket [chemical binding]; other site 985080001597 dimer interface [polypeptide binding]; other site 985080001598 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 985080001599 TonB family C-terminal domain; Region: tonB_Cterm; TIGR01352 985080001600 flagellar motor switch protein; Validated; Region: PRK08433 985080001601 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 985080001602 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 985080001603 minor groove reading motif; other site 985080001604 helix-hairpin-helix signature motif; other site 985080001605 substrate binding pocket [chemical binding]; other site 985080001606 active site 985080001607 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 985080001608 Fe2+ transport system protein A [Inorganic ion transport and metabolism]; Region: FeoA; COG1918 985080001609 Protein of unknown function; Region: DUF3971; pfam13116 985080001610 AsmA-like C-terminal region; Region: AsmA_1; pfam13109 985080001611 YceG-like family; Region: YceG; pfam02618 985080001612 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 985080001613 dimerization interface [polypeptide binding]; other site 985080001614 2-oxoglutarate-acceptor oxidoreductase subunit OorD; Reviewed; Region: oorD; PRK09626 985080001615 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 985080001616 2-oxoglutarate-acceptor oxidoreductase subunit OorA; Reviewed; Region: oorA; PRK09627 985080001617 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 985080001618 dimer interface [polypeptide binding]; other site 985080001619 PYR/PP interface [polypeptide binding]; other site 985080001620 TPP binding site [chemical binding]; other site 985080001621 substrate binding site [chemical binding]; other site 985080001622 2-oxoglutarate-acceptor oxidoreductase subunit OorB; Reviewed; Region: oorB; PRK09628 985080001623 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 985080001624 TPP-binding site [chemical binding]; other site 985080001625 2-oxoglutarate-acceptor oxidoreductase subunit OorC; Reviewed; Region: oorC; PRK08441 985080001626 2-oxoglutarate ferredoxin oxidoreductase subunit gamma; Validated; Region: PRK08537 985080001627 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG5610 985080001628 haloacid dehalogenase superfamily, subfamily IA, variant 1 with third motif having Dx(3-4)D or Dx(3-4)E; Region: HAD-SF-IA-v1; TIGR01549 985080001629 Disulfide bond formation protein DsbB [Posttranslational modification, protein turnover, chaperones]; Region: DsbB; COG1495 985080001630 tumor necrosis factor alpha-inducing protein; Reviewed; Region: PRK12303 985080001631 Membrane carboxypeptidase (penicillin-binding protein) [Cell envelope biogenesis, outer membrane]; Region: MrcB; COG0744 985080001632 Transglycosylase; Region: Transgly; pfam00912 985080001633 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 985080001634 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 985080001635 Aminotransferase class I and II; Region: Aminotran_1_2; pfam00155 985080001636 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 985080001637 catalytic residue [active] 985080001638 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 985080001639 dimer interface [polypeptide binding]; other site 985080001640 putative CheW interface [polypeptide binding]; other site 985080001641 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 985080001642 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 985080001643 ATP-binding cassette domain of multidrug resistance protein-like transporters; Region: ABCC_MRP_Like; cd03228 985080001644 Walker A/P-loop; other site 985080001645 ATP binding site [chemical binding]; other site 985080001646 Q-loop/lid; other site 985080001647 ABC transporter signature motif; other site 985080001648 Walker B; other site 985080001649 D-loop; other site 985080001650 H-loop/switch region; other site 985080001651 flagellin A; Reviewed; Region: PRK12584 985080001652 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 985080001653 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 985080001654 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 985080001655 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 985080001656 3-methyladenine DNA glycosylase; Provisional; Region: PRK13913 985080001657 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 985080001658 minor groove reading motif; other site 985080001659 helix-hairpin-helix signature motif; other site 985080001660 active site 985080001661 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 985080001662 substrate binding site [chemical binding]; other site 985080001663 active site 985080001664 Outer membrane efflux protein; Region: OEP; pfam02321 985080001665 Outer membrane efflux protein; Region: OEP; pfam02321 985080001666 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 985080001667 HlyD family secretion protein; Region: HlyD_3; pfam13437 985080001668 AcrB/AcrD/AcrF family; Region: ACR_tran; pfam00873 985080001669 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 985080001670 potential frameshift: common BLAST hit: gi|298736303|ref|YP_003728829.1| putative vacuolating cytotoxin VacA 985080001671 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 985080001672 PPE-repeat proteins [Cell motility and secretion]; Region: COG5651 985080001673 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 985080001674 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 985080001675 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 985080001676 PPE-repeat proteins [Cell motility and secretion]; Region: COG5651 985080001677 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 985080001678 Autotransporter beta-domain; Region: Autotransporter; pfam03797 985080001679 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 985080001680 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 985080001681 nucleotide binding pocket [chemical binding]; other site 985080001682 K-X-D-G motif; other site 985080001683 catalytic site [active] 985080001684 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 985080001685 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 985080001686 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 985080001687 Dimer interface [polypeptide binding]; other site 985080001688 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 985080001689 Response regulator receiver domain; Region: Response_reg; pfam00072 985080001690 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 985080001691 active site 985080001692 phosphorylation site [posttranslational modification] 985080001693 intermolecular recognition site; other site 985080001694 dimerization interface [polypeptide binding]; other site 985080001695 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 985080001696 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 985080001697 dimer interface [polypeptide binding]; other site 985080001698 anticodon binding site; other site 985080001699 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 985080001700 homodimer interface [polypeptide binding]; other site 985080001701 motif 1; other site 985080001702 active site 985080001703 motif 2; other site 985080001704 GAD domain; Region: GAD; pfam02938 985080001705 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 985080001706 active site 985080001707 motif 3; other site 985080001708 adenylate kinase; Reviewed; Region: adk; PRK00279 985080001709 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 985080001710 AMP-binding site [chemical binding]; other site 985080001711 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 985080001712 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 985080001713 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; cl01298 985080001714 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 985080001715 Glycosyltransferase involved in LPS biosynthesis [Cell envelope biogenesis, outer membrane]; Region: COG3306 985080001716 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 985080001717 dimer interface [polypeptide binding]; other site 985080001718 substrate binding site [chemical binding]; other site 985080001719 metal binding sites [ion binding]; metal-binding site 985080001720 MutS2 family protein; Region: mutS2; TIGR01069 985080001721 ATPase domain of DNA mismatch repair MUTS family; Region: MUTSac; smart00534 985080001722 Walker A/P-loop; other site 985080001723 ATP binding site [chemical binding]; other site 985080001724 Q-loop/lid; other site 985080001725 ABC transporter signature motif; other site 985080001726 Walker B; other site 985080001727 D-loop; other site 985080001728 H-loop/switch region; other site 985080001729 Smr domain; Region: Smr; pfam01713 985080001730 UDP-N-acetylmuramate--alanine ligase; Region: murC; TIGR01082 985080001731 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 985080001732 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 985080001733 hypothetical protein; Provisional; Region: PRK05839 985080001734 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 985080001735 pyridoxal 5'-phosphate binding site [chemical binding]; other site 985080001736 homodimer interface [polypeptide binding]; other site 985080001737 catalytic residue [active] 985080001738 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 985080001739 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 985080001740 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 985080001741 Tetrahydrodipicolinate N-succinyltransferase [Amino acid transport and metabolism]; Region: DapD; COG2171 985080001742 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 985080001743 putative trimer interface [polypeptide binding]; other site 985080001744 putative CoA binding site [chemical binding]; other site 985080001745 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 985080001746 Sel1-like repeats; Region: SEL1; smart00671 985080001747 Sel1-like repeats; Region: SEL1; smart00671 985080001748 Sel1 repeat; Region: Sel1; cl02723 985080001749 Sel1-like repeats; Region: SEL1; smart00671 985080001750 Uncharacterized conserved protein [Function unknown]; Region: COG1479 985080001751 Protein of unknown function DUF262; Region: DUF262; pfam03235 985080001752 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 985080001753 Putative NADPH-quinone reductase (modulator of drug activity B) [General function prediction only]; Region: MdaB; COG2249 985080001754 hydrogenase (NiFe) small subunit (hydA); Region: hydA; TIGR00391 985080001755 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 985080001756 Ni,Fe-hydrogenase I large subunit [Energy production and conversion]; Region: HyaB; COG0374 985080001757 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; pfam00374 985080001758 Ni,Fe-hydrogenase I cytochrome b subunit [Energy production and conversion]; Region: HyaC; COG1969 985080001759 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 985080001760 nickel binding site [ion binding]; other site 985080001761 putative substrate-binding site; other site 985080001762 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 985080001763 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 985080001764 Ligand Binding Site [chemical binding]; other site 985080001765 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 985080001766 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 985080001767 active site 985080001768 NTP binding site [chemical binding]; other site 985080001769 metal binding triad [ion binding]; metal-binding site 985080001770 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 985080001771 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 985080001772 hydrophobic ligand binding site; other site 985080001773 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 985080001774 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 985080001775 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 985080001776 dimer interface [polypeptide binding]; other site 985080001777 FMN binding site [chemical binding]; other site 985080001778 glutamylglutaminyl-tRNA synthetase; Provisional; Region: PRK12410 985080001779 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 985080001780 active site 985080001781 HIGH motif; other site 985080001782 nucleotide binding site [chemical binding]; other site 985080001783 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 985080001784 active site 985080001785 KMSKS motif; other site 985080001786 YGGT family; Region: YGGT; pfam02325 985080001787 Glycosyl hydrolase families: GH43, GH62, GH32, GH68; Region: GH43_62_32_68; cl14647 985080001788 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 985080001789 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 985080001790 N-acetyl-D-glucosamine binding site [chemical binding]; other site 985080001791 catalytic residue [active] 985080001792 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 985080001793 dTDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]; Region: RfbA; COG1209 985080001794 active site 985080001795 tetramer interface; other site 985080001796 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 985080001797 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 985080001798 hinge; other site 985080001799 active site 985080001800 aspartate ammonia-lyase; Provisional; Region: aspA; PRK12273 985080001801 Aspartase; Region: Aspartase; cd01357 985080001802 active sites [active] 985080001803 tetramer interface [polypeptide binding]; other site 985080001804 Uracil-DNA glycosylases (UDG) and related enzymes; Region: UDG_like; cl00483 985080001805 ligand binding site [chemical binding]; other site 985080001806 active site 985080001807 Glycosyltransferase family 10 (fucosyltransferase); Region: Glyco_transf_10; pfam00852 985080001808 phosphoserine phosphatase SerB; Region: serB; TIGR00338 985080001809 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 985080001810 motif II; other site 985080001811 nonheme-containing ferritins; Region: Nonheme_Ferritin; cd01055 985080001812 Ferritin-like domain; Region: Ferritin; pfam00210 985080001813 ferroxidase diiron center [ion binding]; other site 985080001814 hypothetical protein; Provisional; Region: PRK08444 985080001815 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 985080001816 FeS/SAM binding site; other site 985080001817 Outer membrane protein/protective antigen OMA87 [Cell envelope biogenesis, outer membrane]; Region: COG4775 985080001818 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 985080001819 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 985080001820 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 985080001821 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 985080001822 Surface antigen; Region: Bac_surface_Ag; pfam01103 985080001823 hypothetical protein; Provisional; Region: PRK08445 985080001824 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 985080001825 FeS/SAM binding site; other site 985080001826 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 985080001827 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 985080001828 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 985080001829 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 985080001830 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 985080001831 GatB domain; Region: GatB_Yqey; smart00845 985080001832 SurA N-terminal domain; Region: SurA_N; pfam09312 985080001833 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]; Region: COG2956 985080001834 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]; Region: COG1439 985080001835 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 985080001836 RNA/DNA hybrid binding site [nucleotide binding]; other site 985080001837 active site 985080001838 ribonuclease III; Reviewed; Region: rnc; PRK00102 985080001839 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 985080001840 dimerization interface [polypeptide binding]; other site 985080001841 active site 985080001842 metal binding site [ion binding]; metal-binding site 985080001843 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 985080001844 dsRNA binding site [nucleotide binding]; other site 985080001845 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 985080001846 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 985080001847 Tetramer interface [polypeptide binding]; other site 985080001848 active site 985080001849 FMN-binding site [chemical binding]; other site 985080001850 Protein of unknown function (DUF2603); Region: DUF2603; pfam10788 985080001851 oxygen-independent coproporphyrinogen III oxidase; Region: hemN; TIGR00538 985080001852 RNase PH-like 3'-5' exoribonucleases; Region: RNase_PH; cl03114 985080001853 HemN C-terminal domain; Region: HemN_C; pfam06969 985080001854 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 985080001855 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 985080001856 Cysteine-rich domain; Region: CCG; pfam02754 985080001857 Cysteine-rich domain; Region: CCG; pfam02754 985080001858 Predicted helicase [General function prediction only]; Region: COG4889 985080001859 Restriction endonuclease; Region: Mrr_cat; pfam04471 985080001860 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 985080001861 ATP binding site [chemical binding]; other site 985080001862 putative Mg++ binding site [ion binding]; other site 985080001863 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 985080001864 nucleotide binding region [chemical binding]; other site 985080001865 ATP-binding site [chemical binding]; other site 985080001866 Predicted helicase [General function prediction only]; Region: COG4889 985080001867 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 985080001868 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 985080001869 aspartate aminotransferase; Provisional; Region: PRK05764 985080001870 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 985080001871 pyridoxal 5'-phosphate binding site [chemical binding]; other site 985080001872 homodimer interface [polypeptide binding]; other site 985080001873 catalytic residue [active] 985080001874 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 985080001875 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 985080001876 active site 985080001877 DNA binding site [nucleotide binding] 985080001878 Int/Topo IB signature motif; other site 985080001879 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 985080001880 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 985080001881 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 985080001882 DNA binding site [nucleotide binding] 985080001883 active site 985080001884 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 985080001885 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 985080001886 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 985080001887 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 985080001888 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK08447 985080001889 ATP cone domain; Region: ATP-cone; pfam03477 985080001890 Class I ribonucleotide reductase; Region: RNR_I; cd01679 985080001891 active site 985080001892 dimer interface [polypeptide binding]; other site 985080001893 catalytic residues [active] 985080001894 effector binding site; other site 985080001895 R2 peptide binding site; other site 985080001896 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK14359 985080001897 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 985080001898 Substrate binding site; other site 985080001899 Mg++ binding site; other site 985080001900 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 985080001901 active site 985080001902 substrate binding site [chemical binding]; other site 985080001903 CoA binding site [chemical binding]; other site 985080001904 Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]; Region: FecA; COG4772 985080001905 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 985080001906 N-terminal plug; other site 985080001907 ligand-binding site [chemical binding]; other site 985080001908 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 985080001909 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 985080001910 G1 box; other site 985080001911 GTP/Mg2+ binding site [chemical binding]; other site 985080001912 Switch I region; other site 985080001913 G2 box; other site 985080001914 G3 box; other site 985080001915 Switch II region; other site 985080001916 G4 box; other site 985080001917 G5 box; other site 985080001918 Nucleoside recognition; Region: Gate; pfam07670 985080001919 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 985080001920 Nucleoside recognition; Region: Gate; pfam07670 985080001921 Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; Region: DNA_polB_like1_exo; cd05782 985080001922 active site 985080001923 catalytic site [active] 985080001924 substrate binding site [chemical binding]; other site 985080001925 Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; Region: DNA_pol_B_exo2; pfam10108 985080001926 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 985080001927 DNA methylase; Region: N6_N4_Mtase; pfam01555 985080001928 CfrBI restriction endonuclease; Region: RE_CfrBI; pfam09516 985080001929 Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcxC; COG4647 985080001930 Acetone carboxylase gamma subunit; Region: Acetone_carb_G; pfam08882 985080001931 N-methylhydantoinase B/acetone carboxylase, alpha subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuB; COG0146 985080001932 N-methylhydantoinase B/acetone carboxylase, alpha subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuB; COG0146 985080001933 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3528 985080001934 Short chain fatty acid transporter; Region: SCFA_trans; pfam02667 985080001935 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 985080001936 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 985080001937 putative acyltransferase; Provisional; Region: PRK05790 985080001938 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 985080001939 dimer interface [polypeptide binding]; other site 985080001940 active site 985080001941 Diacylglycerol kinase [Cell envelope biogenesis, outer membrane]; Region: DgkA; COG0818 985080001942 DNA gyrase subunit A; Validated; Region: PRK05560 985080001943 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 985080001944 CAP-like domain; other site 985080001945 active site 985080001946 primary dimer interface [polypeptide binding]; other site 985080001947 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 985080001948 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 985080001949 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 985080001950 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 985080001951 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 985080001952 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 985080001953 Response regulator receiver domain; Region: Response_reg; pfam00072 985080001954 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 985080001955 active site 985080001956 phosphorylation site [posttranslational modification] 985080001957 intermolecular recognition site; other site 985080001958 dimerization interface [polypeptide binding]; other site 985080001959 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 985080001960 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 985080001961 Walker A motif; other site 985080001962 ATP binding site [chemical binding]; other site 985080001963 Walker B motif; other site 985080001964 arginine finger; other site 985080001965 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 985080001966 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 985080001967 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 985080001968 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 985080001969 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 985080001970 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG0275 985080001971 16S rRNA (cytosine(1402)-N(4))-methyltransferase; Region: TIGR00006 985080001972 Uncharacterized conserved protein [Function unknown]; Region: COG1912 985080001973 Competence protein ComGF [Intracellular trafficking and secretion]; Region: ComGF; COG4940 985080001974 Predicted hydrolases of HD superfamily [General function prediction only]; Region: COG1896 985080001975 Fic family protein [Function unknown]; Region: COG3177 985080001976 Fic/DOC family; Region: Fic; pfam02661 985080001977 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 985080001978 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 985080001979 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 985080001980 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 985080001981 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 985080001982 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 985080001983 Walker A/P-loop; other site 985080001984 ATP binding site [chemical binding]; other site 985080001985 Q-loop/lid; other site 985080001986 ABC transporter signature motif; other site 985080001987 Walker B; other site 985080001988 D-loop; other site 985080001989 H-loop/switch region; other site 985080001990 Uncharacterized P-loop hydrolase UPF0079; Region: UPF0079; cl00520 985080001991 DNA polymerase III subunits gamma and tau; Validated; Region: PRK08451 985080001992 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 985080001993 Walker A motif; other site 985080001994 ATP binding site [chemical binding]; other site 985080001995 Walker B motif; other site 985080001996 arginine finger; other site 985080001997 L-lysine exporter; Region: 2a75; TIGR00948 985080001998 Protein of unknown function (DUF1104); Region: DUF1104; pfam06518 985080001999 Protein of unknown function (DUF1104); Region: DUF1104; pfam06518 985080002000 tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; Region: COG0042 985080002001 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 985080002002 FMN binding site [chemical binding]; other site 985080002003 active site 985080002004 catalytic residues [active] 985080002005 substrate binding site [chemical binding]; other site 985080002006 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 985080002007 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 985080002008 Ligand Binding Site [chemical binding]; other site 985080002009 potential frameshift: common BLAST hit: gi|208434641|ref|YP_002266307.1| labile enterotoxin outputA 985080002010 potential frameshift: common BLAST hit: gi|254779290|ref|YP_003057395.1| LeoA protein 985080002011 potential frameshift: common BLAST hit: gi|254779290|ref|YP_003057395.1| LeoA protein 985080002012 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 985080002013 Walker A/P-loop; other site 985080002014 ATP binding site [chemical binding]; other site 985080002015 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 985080002016 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 985080002017 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 985080002018 FeS/SAM binding site; other site 985080002019 Predicted phosphoribosyltransferases [General function prediction only]; Region: COG2236 985080002020 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 985080002021 active site 985080002022 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]; Region: COG0075 985080002023 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 985080002024 catalytic residue [active] 985080002025 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 985080002026 tetramer interfaces [polypeptide binding]; other site 985080002027 binuclear metal-binding site [ion binding]; other site 985080002028 D-alanyl-alanine synthetase A; Reviewed; Region: ddl; PRK01966 985080002029 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 985080002030 ATP-grasp domain; Region: ATP-grasp_4; cl17255 985080002031 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 985080002032 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 985080002033 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 985080002034 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 985080002035 nucleotide binding site/active site [active] 985080002036 HIT family signature motif; other site 985080002037 catalytic residue [active] 985080002038 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 985080002039 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 985080002040 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 985080002041 active site 985080002042 Uncharacterized protein/domain associated with GTPases [Function unknown]; Region: COG3597 985080002043 Uncharacterized protein/domain associated with GTPases [Function unknown]; Region: COG3597 985080002044 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 985080002045 G1 box; other site 985080002046 GTP/Mg2+ binding site [chemical binding]; other site 985080002047 G2 box; other site 985080002048 Switch I region; other site 985080002049 G3 box; other site 985080002050 Switch II region; other site 985080002051 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 985080002052 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 985080002053 RNA binding surface [nucleotide binding]; other site 985080002054 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 985080002055 active site 985080002056 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cl00065 985080002057 Fibronectin type 3 domain-containing protein [General function prediction only]; Region: COG3401 985080002058 Interdomain contacts; other site 985080002059 Cytokine receptor motif; other site 985080002060 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 985080002061 Interdomain contacts; other site 985080002062 Cytokine receptor motif; other site 985080002063 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 985080002064 Interdomain contacts; other site 985080002065 Cytokine receptor motif; other site 985080002066 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 985080002067 S-adenosylmethionine binding site [chemical binding]; other site 985080002068 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 985080002069 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 985080002070 Walker A/P-loop; other site 985080002071 ATP binding site [chemical binding]; other site 985080002072 Q-loop/lid; other site 985080002073 ABC transporter signature motif; other site 985080002074 Walker B; other site 985080002075 D-loop; other site 985080002076 H-loop/switch region; other site 985080002077 putative protein insertion permease FtsX; Region: ftsX; TIGR00439 985080002078 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 985080002079 Peptidase family M23; Region: Peptidase_M23; pfam01551 985080002080 flagellar protein FlaG; Provisional; Region: PRK08452 985080002081 flagellar capping protein; Validated; Region: fliD; PRK08453 985080002082 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 985080002083 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 985080002084 flagellar biosynthetic protein FliS; Region: fliS; TIGR00208 985080002085 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 985080002086 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 985080002087 putative ATP binding site [chemical binding]; other site 985080002088 putative substrate interface [chemical binding]; other site 985080002089 N-carbamoylputrescine amidohydrolase (CPA) (class 11 nitrilases); Region: CPA; cd07573 985080002090 N-carbamoylputrescine amidase; Region: agmatine_aguB; TIGR03381 985080002091 putative active site; other site 985080002092 catalytic triad [active] 985080002093 putative dimer interface [polypeptide binding]; other site 985080002094 Predicted permease [General function prediction only]; Region: COG2056 985080002095 Na+-H+ antiporter family; Region: Na_H_antiport_2; pfam13726 985080002096 Predicted membrane protein [Function unknown]; Region: COG1288; cl17886 985080002097 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Thermotoga marina NorM; Region: MATE_NorM_like; cd13137 985080002098 putative efflux protein, MATE family; Region: matE; TIGR00797 985080002099 phosphodiesterase; Provisional; Region: PRK12704 985080002100 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 985080002101 nucleic acid binding region [nucleotide binding]; other site 985080002102 G-X-X-G motif; other site 985080002103 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 985080002104 Zn2+ binding site [ion binding]; other site 985080002105 Mg2+ binding site [ion binding]; other site 985080002106 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212; cl00360 985080002107 signal recognition particle-docking protein FtsY; Region: ftsY; TIGR00064 985080002108 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 985080002109 Predicted Fe-S-cluster oxidoreductase [General function prediction only]; Region: COG0727 985080002110 Mu-like prophage protein [General function prediction only]; Region: COG3941 985080002111 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 985080002112 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 985080002113 FeS/SAM binding site; other site 985080002114 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 985080002115 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 985080002116 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 985080002117 GTP binding site; other site 985080002118 flagellar biosynthetic protein FlhB; Region: flhB; TIGR00328 985080002119 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 985080002120 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 985080002121 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 985080002122 active site 985080002123 metal binding site [ion binding]; metal-binding site 985080002124 Nitronate monooxygenase; Region: NMO; pfam03060 985080002125 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 985080002126 FMN binding site [chemical binding]; other site 985080002127 substrate binding site [chemical binding]; other site 985080002128 putative catalytic residue [active] 985080002129 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 985080002130 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 985080002131 active site 985080002132 HIGH motif; other site 985080002133 dimer interface [polypeptide binding]; other site 985080002134 KMSKS motif; other site 985080002135 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 985080002136 RNA binding surface [nucleotide binding]; other site 985080002137 (p)ppGpp synthetase, RelA/SpoT family; Region: spoT_relA; TIGR00691 985080002138 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 985080002139 Zn2+ binding site [ion binding]; other site 985080002140 Mg2+ binding site [ion binding]; other site 985080002141 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 985080002142 synthetase active site [active] 985080002143 NTP binding site [chemical binding]; other site 985080002144 metal binding site [ion binding]; metal-binding site 985080002145 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 985080002146 DNA-directed RNA polymerase, subunit K/omega [Transcription]; Region: RpoZ; COG1758 985080002147 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 985080002148 putative nucleotide binding site [chemical binding]; other site 985080002149 uridine monophosphate binding site [chemical binding]; other site 985080002150 homohexameric interface [polypeptide binding]; other site 985080002151 Predicted periplasmic solute-binding protein [General function prediction only]; Region: COG1427 985080002152 aconitate hydratase 2; Region: acnB; TIGR00117 985080002153 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 985080002154 substrate binding site [chemical binding]; other site 985080002155 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 985080002156 substrate binding site [chemical binding]; other site 985080002157 ligand binding site [chemical binding]; other site 985080002158 FOG: Transposase [DNA replication, recombination, and repair]; Region: COG5659 985080002159 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 985080002160 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 985080002161 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 985080002162 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 985080002163 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 985080002164 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 985080002165 nucleotide binding region [chemical binding]; other site 985080002166 ATP-binding site [chemical binding]; other site 985080002167 SEC-C motif; Region: SEC-C; pfam02810 985080002168 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 985080002169 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 985080002170 FtsX-like permease family; Region: FtsX; pfam02687 985080002171 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 985080002172 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 985080002173 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; cl00207 985080002174 metal-binding site [ion binding] 985080002175 heavy metal-(Cd/Co/Hg/Pb/Zn)-translocating P-type ATPase; Region: ATPase-IB2_Cd; TIGR01512 985080002176 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 985080002177 Soluble P-type ATPase [General function prediction only]; Region: COG4087 985080002178 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 985080002179 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 985080002180 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 985080002181 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 985080002182 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 985080002183 active site 985080002184 catalytic residues [active] 985080002185 metal binding site [ion binding]; metal-binding site 985080002186 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 985080002187 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 985080002188 oligomer interface [polypeptide binding]; other site 985080002189 active site residues [active] 985080002190 trigger factor; Provisional; Region: tig; PRK01490 985080002191 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 985080002192 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 985080002193 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 985080002194 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 985080002195 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 985080002196 trimer interface [polypeptide binding]; other site 985080002197 dimer interface [polypeptide binding]; other site 985080002198 putative active site [active] 985080002199 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 985080002200 MPT binding site; other site 985080002201 trimer interface [polypeptide binding]; other site 985080002202 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 985080002203 MoaE homodimer interface [polypeptide binding]; other site 985080002204 MoaD interaction [polypeptide binding]; other site 985080002205 active site residues [active] 985080002206 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 985080002207 MoaE interaction surface [polypeptide binding]; other site 985080002208 MoeB interaction surface [polypeptide binding]; other site 985080002209 thiocarboxylated glycine; other site 985080002210 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 985080002211 dimerization interface [polypeptide binding]; other site 985080002212 active site 985080002213 Domain of unknown function (DUF3943); Region: DUF3943; pfam13084 985080002214 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional; Region: PRK09314 985080002215 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: ribB; TIGR00506 985080002216 GTP cyclohydrolase II [Coenzyme metabolism]; Region: RibA; COG0807 985080002217 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 985080002218 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG1451 985080002219 Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]; Region: FecA; COG4772 985080002220 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 985080002221 N-terminal plug; other site 985080002222 ligand-binding site [chemical binding]; other site 985080002223 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 985080002224 flagellar basal body-associated protein FliL; Reviewed; Region: fliL; PRK08455 985080002225 RNA methyltransferase, RsmD family; Region: TIGR00095 985080002226 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 985080002227 Uncharacterized conserved protein [Function unknown]; Region: COG1565 985080002228 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 985080002229 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 2 [Coenzyme metabolism]; Region: ThiF; COG0476 985080002230 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 985080002231 ATP binding site [chemical binding]; other site 985080002232 substrate interface [chemical binding]; other site 985080002233 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 985080002234 flagellar motor protein MotA; Validated; Region: PRK08456 985080002235 flagellar motor protein MotB; Reviewed; Region: motB; PRK08457 985080002236 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 985080002237 ligand binding site [chemical binding]; other site 985080002238 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 985080002239 dimer interface [polypeptide binding]; other site 985080002240 conserved gate region; other site 985080002241 ABC-ATPase subunit interface; other site 985080002242 Periplasmic glycine betaine/choline-binding (lipo)protein of an ABC-type transport system (osmoprotectant binding protein) [Cell envelope biogenesis, outer membrane]; Region: OpuBC; COG1732 985080002243 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 985080002244 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 985080002245 Walker A/P-loop; other site 985080002246 ATP binding site [chemical binding]; other site 985080002247 Q-loop/lid; other site 985080002248 ABC transporter signature motif; other site 985080002249 Walker B; other site 985080002250 D-loop; other site 985080002251 H-loop/switch region; other site 985080002252 excinuclease ABC, C subunit; Region: uvrC; TIGR00194 985080002253 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 985080002254 GIY-YIG motif/motif A; other site 985080002255 active site 985080002256 catalytic site [active] 985080002257 putative DNA binding site [nucleotide binding]; other site 985080002258 metal binding site [ion binding]; metal-binding site 985080002259 UvrB/uvrC motif; Region: UVR; pfam02151 985080002260 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 985080002261 homoserine dehydrogenase; Provisional; Region: PRK06349 985080002262 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 985080002263 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 985080002264 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 985080002265 Predicted endonuclease distantly related to archaeal Holliday junction resolvase [DNA replication, recombination, and repair]; Region: COG0792 985080002266 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 985080002267 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 985080002268 catalytic residues [active] 985080002269 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 985080002270 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 985080002271 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 985080002272 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 985080002273 RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins; Region: RRM_HP0827_like; cd12399 985080002274 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 985080002275 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 985080002276 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 985080002277 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 985080002278 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 985080002279 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 985080002280 active site 985080002281 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit; Region: gatA; TIGR00132 985080002282 indole acetimide hydrolase; Validated; Region: PRK07488 985080002283 dephospho-CoA kinase; Region: TIGR00152 985080002284 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 985080002285 CoA-binding site [chemical binding]; other site 985080002286 ATP-binding [chemical binding]; other site 985080002287 spermidine synthase; Provisional; Region: speE; PRK00536 985080002288 spermidine synthase; Provisional; Region: PRK00811 985080002289 GTP-binding protein Der; Reviewed; Region: PRK00093 985080002290 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 985080002291 G1 box; other site 985080002292 GTP/Mg2+ binding site [chemical binding]; other site 985080002293 Switch I region; other site 985080002294 G2 box; other site 985080002295 Switch II region; other site 985080002296 G3 box; other site 985080002297 G4 box; other site 985080002298 G5 box; other site 985080002299 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 985080002300 G1 box; other site 985080002301 GTP/Mg2+ binding site [chemical binding]; other site 985080002302 Switch I region; other site 985080002303 G2 box; other site 985080002304 G3 box; other site 985080002305 Switch II region; other site 985080002306 G4 box; other site 985080002307 G5 box; other site 985080002308 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 985080002309 IHF dimer interface [polypeptide binding]; other site 985080002310 IHF - DNA interface [nucleotide binding]; other site 985080002311 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3018 985080002312 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3018 985080002313 Long-chain fatty acid transport protein [Lipid metabolism]; Region: FadL; COG2067 985080002314 UDP-N-acetylglucosamine 4,6-dehydratase; Region: PseB; TIGR03589 985080002315 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 985080002316 NAD(P) binding site [chemical binding]; other site 985080002317 homodimer interface [polypeptide binding]; other site 985080002318 substrate binding site [chemical binding]; other site 985080002319 active site 985080002320 phosphopantothenoylcysteine decarboxylase / phosphopantothenate--cysteine ligase; Region: coaBC_dfp; TIGR00521 985080002321 Flavoprotein; Region: Flavoprotein; pfam02441 985080002322 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 985080002323 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 985080002324 thiamine phosphate binding site [chemical binding]; other site 985080002325 active site 985080002326 pyrophosphate binding site [ion binding]; other site 985080002327 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 985080002328 dimer interface [polypeptide binding]; other site 985080002329 substrate binding site [chemical binding]; other site 985080002330 ATP binding site [chemical binding]; other site 985080002331 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 985080002332 substrate binding site [chemical binding]; other site 985080002333 multimerization interface [polypeptide binding]; other site 985080002334 ATP binding site [chemical binding]; other site 985080002335 type I site-specific deoxyribonuclease, HsdR family; Region: hsdR; TIGR00348 985080002336 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 985080002337 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 985080002338 ATP binding site [chemical binding]; other site 985080002339 putative Mg++ binding site [ion binding]; other site 985080002340 Type I restriction and modification enzyme - subunit R C terminal; Region: EcoR124_C; pfam12008 985080002341 type I site-specific deoxyribonuclease, HsdR family; Region: hsdR; TIGR00348 985080002342 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 985080002343 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 985080002344 type I restriction system adenine methylase (hsdM); Region: hsdM; TIGR00497 985080002345 HsdM N-terminal domain; Region: HsdM_N; pfam12161 985080002346 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 985080002347 S-adenosylmethionine binding site [chemical binding]; other site 985080002348 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 985080002349 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 985080002350 active site 985080002351 Protein of unknown function (DUF511); Region: DUF511; cl01114 985080002352 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 985080002353 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 985080002354 Walker A/P-loop; other site 985080002355 ATP binding site [chemical binding]; other site 985080002356 Q-loop/lid; other site 985080002357 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 985080002358 ABC transporter; Region: ABC_tran_2; pfam12848 985080002359 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 985080002360 guanosine 5'-monophosphate oxidoreductase; Provisional; Region: PRK05458 985080002361 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 985080002362 active site 985080002363 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 985080002364 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 985080002365 dimer interface [polypeptide binding]; other site 985080002366 active site 985080002367 ADP-heptose synthase, bifunctional sugar kinase/adenylyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaE; COG2870 985080002368 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 985080002369 putative ribose interaction site [chemical binding]; other site 985080002370 putative ADP binding site [chemical binding]; other site 985080002371 rfaE bifunctional protein, domain II; Region: rfaE_dom_II; TIGR02199 985080002372 active site 985080002373 nucleotide binding site [chemical binding]; other site 985080002374 HIGH motif; other site 985080002375 KMSKS motif; other site 985080002376 ADP-L-glycero-D-mannoheptose 6-epimerase (GME), extended (e) SDRs; Region: ADP_GME_SDR_e; cd05248 985080002377 ADP-L-glycero-D-manno-heptose-6-epimerase; Region: heptose_epim; TIGR02197 985080002378 NADP binding site [chemical binding]; other site 985080002379 homopentamer interface [polypeptide binding]; other site 985080002380 substrate binding site [chemical binding]; other site 985080002381 active site 985080002382 D,D-heptose 1,7-bisphosphate phosphatase; Region: GmhB_yaeD; TIGR00213 985080002383 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 985080002384 active site 985080002385 motif I; other site 985080002386 motif II; other site 985080002387 Uncharacterized conserved protein [Function unknown]; Region: COG2836 985080002388 pantothenate kinase; Reviewed; Region: PRK13333 985080002389 PQQ-like domain; Region: PQQ_2; pfam13360 985080002390 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 985080002391 trimer interface [polypeptide binding]; other site 985080002392 active site 985080002393 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 985080002394 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 985080002395 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 985080002396 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 985080002397 lipid-A-disaccharide synthase; Region: lpxB; TIGR00215 985080002398 hydrogenase nickel incorporation protein; Provisional; Region: hypA; PRK00564 985080002399 Hydrogenase expression/synthesis hypA family; Region: HypA; pfam01155 985080002400 flagellar hook protein FlgE; Validated; Region: flgE; PRK08425 985080002401 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 985080002402 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 985080002403 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 985080002404 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 985080002405 CDP-diacylglycerol pyrophosphatase, bacterial type; Region: cdh; TIGR00672 985080002406 alkylphosphonate utilization operon protein PhnA; Region: phnA; TIGR00686 985080002407 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; pfam08274 985080002408 PhnA protein; Region: PhnA; pfam03831 985080002409 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 985080002410 Clade 3 of the heme-binding enzyme catalase; Region: catalase_clade_3; cd08156 985080002411 tetramer interface [polypeptide binding]; other site 985080002412 heme binding pocket [chemical binding]; other site 985080002413 NADPH binding site [chemical binding]; other site 985080002414 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 985080002415 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 985080002416 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 985080002417 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 985080002418 active site 985080002419 putative DNA-binding cleft [nucleotide binding]; other site 985080002420 dimer interface [polypeptide binding]; other site 985080002421 Uncharacterized conserved protein [Function unknown]; Region: COG1432 985080002422 LabA_like proteins; Region: LabA_like; cd06167 985080002423 putative metal binding site [ion binding]; other site 985080002424 Glutaminase; Region: Glutaminase; cl00907 985080002425 Holliday junction DNA helicase, RuvA subunit; Region: ruvA; TIGR00084 985080002426 RuvA N terminal domain; Region: RuvA_N; pfam01330 985080002427 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 985080002428 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 985080002429 MviN-like protein; Region: MVIN; pfam03023 985080002430 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 985080002431 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 985080002432 active site 985080002433 HIGH motif; other site 985080002434 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 985080002435 KMSKS motif; other site 985080002436 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 985080002437 tRNA binding surface [nucleotide binding]; other site 985080002438 anticodon binding site; other site 985080002439 Vacuolating cyotoxin; Region: VacA; pfam02691 985080002440 Autotransporter beta-domain; Region: Autotransporter; pfam03797 985080002441 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 985080002442 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 985080002443 Ligand binding site; other site 985080002444 metal-binding site 985080002445 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 985080002446 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 985080002447 Walker A/P-loop; other site 985080002448 ATP binding site [chemical binding]; other site 985080002449 Q-loop/lid; other site 985080002450 ABC transporter signature motif; other site 985080002451 Walker B; other site 985080002452 D-loop; other site 985080002453 H-loop/switch region; other site 985080002454 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; cl00462 985080002455 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 985080002456 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 985080002457 ABC-ATPase subunit interface; other site 985080002458 dimer interface [polypeptide binding]; other site 985080002459 putative PBP binding regions; other site 985080002460 short chain dehydrogenase; Validated; Region: PRK06182 985080002461 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 985080002462 NADP binding site [chemical binding]; other site 985080002463 active site 985080002464 steroid binding site; other site 985080002465 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 985080002466 RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; Region: Rel-Spo_like; cl11966 985080002467 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3041; cl17396 985080002468 hydrogenase expression/formation protein HypD; Region: hypD; TIGR00075 985080002469 hydrogenase isoenzymes formation protein HypD; Provisional; Region: PRK15062 985080002470 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypC; COG0298 985080002471 hydrogenase accessory protein HypB; Region: hypB; TIGR00073 985080002472 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 985080002473 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 985080002474 acetate kinase A/propionate kinase 2; Reviewed; Region: PRK00180 985080002475 propionate/acetate kinase; Provisional; Region: PRK12379 985080002476 BioD-like N-terminal domain of phosphotransacetylase [General function prediction only]; Region: Pta; COG0857 985080002477 phosphotransacetylase; Reviewed; Region: eutD; PRK09653 985080002478 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 985080002479 flagellar basal body rod modification protein; Reviewed; Region: flgD; PRK05842 985080002480 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 985080002481 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 985080002482 flagellar hook protein FlgE; Validated; Region: flgE; PRK05841 985080002483 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 985080002484 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0827 985080002485 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 985080002486 S-adenosylmethionine binding site [chemical binding]; other site 985080002487 potential frameshift: common BLAST hit: gi|15611914|ref|NP_223565.1| ATP-dependent helicase 985080002488 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 985080002489 Part of AAA domain; Region: AAA_19; pfam13245 985080002490 Family description; Region: UvrD_C_2; pfam13538 985080002491 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 985080002492 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 985080002493 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 985080002494 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 985080002495 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 985080002496 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 985080002497 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 985080002498 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 985080002499 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 985080002500 ATP-grasp domain; Region: ATP-grasp_4; cl17255 985080002501 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 985080002502 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 985080002503 ATP-grasp domain; Region: ATP-grasp_4; cl17255 985080002504 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 985080002505 IMP binding site; other site 985080002506 dimer interface [polypeptide binding]; other site 985080002507 interdomain contacts; other site 985080002508 partial ornithine binding site; other site 985080002509 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 985080002510 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 985080002511 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; pfam00044 985080002512 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 985080002513 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 985080002514 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 985080002515 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 985080002516 PPE-repeat proteins [Cell motility and secretion]; Region: COG5651 985080002517 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 985080002518 Autotransporter beta-domain; Region: Autotransporter; pfam03797 985080002519 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 985080002520 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 985080002521 active site 1 [active] 985080002522 dimer interface [polypeptide binding]; other site 985080002523 hexamer interface [polypeptide binding]; other site 985080002524 active site 2 [active] 985080002525 recombination protein RecR; Region: recR; TIGR00615 985080002526 RecR protein; Region: RecR; pfam02132 985080002527 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 985080002528 putative active site [active] 985080002529 putative metal-binding site [ion binding]; other site 985080002530 tetramer interface [polypeptide binding]; other site 985080002531 tRNA pseudouridine synthase, TruD family; Region: tRNA_TruD_broad; TIGR00094 985080002532 Pseudouridine synthase, similar to Escherichia coli TruD; Region: PseudoU_synth_EcTruD; cd02575 985080002533 Permutation of conserved domain; other site 985080002534 active site 985080002535 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 985080002536 heat shock protein HtpX; Provisional; Region: PRK02870 985080002537 GTP cyclohydrolase I; Region: folE; TIGR00063 985080002538 GTP cyclohydrolase I; Provisional; Region: PLN03044 985080002539 active site 985080002540 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 985080002541 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 985080002542 substrate binding pocket [chemical binding]; other site 985080002543 chain length determination region; other site 985080002544 substrate-Mg2+ binding site; other site 985080002545 catalytic residues [active] 985080002546 aspartate-rich region 1; other site 985080002547 active site lid residues [active] 985080002548 aspartate-rich region 2; other site 985080002549 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 985080002550 6-pyruvoyl-tetrahydropterin synthase [Coenzyme metabolism]; Region: COG0720 985080002551 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 985080002552 putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE; Region: rSAM_QueE_Ecoli; TIGR04322 985080002553 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 985080002554 Coenzyme A binding pocket [chemical binding]; other site 985080002555 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 985080002556 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 985080002557 metabolite-proton symporter; Region: 2A0106; TIGR00883 985080002558 putative substrate translocation pore; other site 985080002559 peptide chain release factor 1; Validated; Region: prfA; PRK00591 985080002560 Uncharacterized conserved protein [Function unknown]; Region: COG1479 985080002561 Protein of unknown function DUF262; Region: DUF262; pfam03235 985080002562 Protein of unknown function DUF262; Region: DUF262; pfam03235 985080002563 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 985080002564 dimer interface [polypeptide binding]; other site 985080002565 conserved gate region; other site 985080002566 putative PBP binding loops; other site 985080002567 ABC-ATPase subunit interface; other site 985080002568 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 985080002569 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 985080002570 substrate binding pocket [chemical binding]; other site 985080002571 membrane-bound complex binding site; other site 985080002572 hinge residues; other site 985080002573 alanine racemase; Region: alr; TIGR00492 985080002574 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 985080002575 active site 985080002576 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 985080002577 dimer interface [polypeptide binding]; other site 985080002578 substrate binding site [chemical binding]; other site 985080002579 catalytic residues [active] 985080002580 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 985080002581 amino acid carrier protein; Region: agcS; TIGR00835 985080002582 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 985080002583 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 985080002584 homotrimer interaction site [polypeptide binding]; other site 985080002585 putative active site [active] 985080002586 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 985080002587 TIGR01210 family protein; Region: TIGR01210 985080002588 Uncharacterized conserved protein [Function unknown]; Region: COG1576 985080002589 acetyl-CoA carboxylase, carboxyl transferase, beta subunit; Region: accD; TIGR00515 985080002590 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 985080002591 putative recombination protein RecO; Provisional; Region: PRK13908 985080002592 competence/damage-inducible protein CinA C-terminal domain; Region: cinA_cterm; TIGR00199 985080002593 potential frameshift: common BLAST hit: gi|15611955|ref|NP_223606.1| aldehyde dehydrogenase 985080002594 Proteins of this family catalyze the reduction of flavin or nitrocompounds using NAD(P)H as electron donor in a obligatory two-electron transfer, utilizing FMN or FAD as cofactor. They are often found to be homodimers. Enzymes of this family are...; Region: Nitro_FMN_reductase; cl00514 985080002595 dimer interface [polypeptide binding]; other site 985080002596 Proteins of this family catalyze the reduction of flavin or nitrocompounds using NAD(P)H as electron donor in a obligatory two-electron transfer, utilizing FMN or FAD as cofactor. They are often found to be homodimers. Enzymes of this family are...; Region: Nitro_FMN_reductase; cl00514 985080002597 FMN binding site [chemical binding]; other site 985080002598 prolipoprotein diacylglyceryl transferase; Region: lgt; TIGR00544 985080002599 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 985080002600 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 985080002601 active site 985080002602 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 985080002603 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 985080002604 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 985080002605 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]; Region: COG1579 985080002606 Putative zinc ribbon domain; Region: DUF164; pfam02591 985080002607 dinuclear metal center protein, YbgI/SA1388 family; Region: YbgI_SA1388; TIGR00486 985080002608 Uncharacterized conserved protein [Function unknown]; Region: COG0327 985080002609 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 985080002610 dimer interface [polypeptide binding]; other site 985080002611 motif 1; other site 985080002612 active site 985080002613 motif 2; other site 985080002614 motif 3; other site 985080002615 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 985080002616 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 985080002617 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 985080002618 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 985080002619 Dynamin family; Region: Dynamin_N; pfam00350 985080002620 G1 box; other site 985080002621 GTP/Mg2+ binding site [chemical binding]; other site 985080002622 G2 box; other site 985080002623 Switch I region; other site 985080002624 G3 box; other site 985080002625 Switch II region; other site 985080002626 G4 box; other site 985080002627 G5 box; other site 985080002628 potential frameshift: common BLAST hit: gi|298736077|ref|YP_003728602.1| putative tRNA modification GTPase TrmE 985080002629 potential frameshift: common BLAST hit: gi|210135153|ref|YP_002301592.1| ATP/GTP-binding protein 985080002630 Predicted GTPases (dynamin-related) [General function prediction only]; Region: COG0699 985080002631 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 985080002632 G3 box; other site 985080002633 Switch II region; other site 985080002634 G4 box; other site 985080002635 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 985080002636 G1 box; other site 985080002637 GTP/Mg2+ binding site [chemical binding]; other site 985080002638 G2 box; other site 985080002639 Switch I region; other site 985080002640 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 985080002641 G1 box; other site 985080002642 GTP/Mg2+ binding site [chemical binding]; other site 985080002643 G2 box; other site 985080002644 Switch I region; other site 985080002645 G3 box; other site 985080002646 Switch II region; other site 985080002647 G4 box; other site 985080002648 Protein of unknown function (DUF3240); Region: DUF3240; pfam11582 985080002649 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 985080002650 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 985080002651 Outer membrane efflux protein; Region: OEP; pfam02321 985080002652 Outer membrane efflux protein; Region: OEP; pfam02321 985080002653 glycyl-tRNA synthetase, tetrameric type, beta subunit; Region: glyS; TIGR00211 985080002654 phosphoglyceromutase; Provisional; Region: PRK05434 985080002655 2,3-bisphosphoglycerate-independent phosphoglycerate mutase; Region: pgm_bpd_ind; TIGR01307 985080002656 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C subunit; Region: gatC; TIGR00135 985080002657 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK05964 985080002658 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 985080002659 inhibitor-cofactor binding pocket; inhibition site 985080002660 pyridoxal 5'-phosphate binding site [chemical binding]; other site 985080002661 catalytic residue [active] 985080002662 SurA N-terminal domain; Region: SurA_N_3; cl07813 985080002663 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 985080002664 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 985080002665 cell division protein FtsA; Region: ftsA; TIGR01174 985080002666 Cell division protein FtsA; Region: FtsA; smart00842 985080002667 Cell division protein FtsA; Region: FtsA; pfam14450 985080002668 cell division protein FtsZ; Validated; Region: PRK09330 985080002669 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 985080002670 nucleotide binding site [chemical binding]; other site 985080002671 SulA interaction site; other site 985080002672 Mechanosensitive ion channel; Region: MS_channel; pfam00924 985080002673 potential frameshift: common BLAST hit: gi|188527700|ref|YP_001910387.1| topoisomerase I 985080002674 Topoisomerase IA [DNA replication, recombination, and repair]; Region: TopA; COG0550 985080002675 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 985080002676 active site 985080002677 interdomain interaction site; other site 985080002678 putative metal-binding site [ion binding]; other site 985080002679 nucleotide binding site [chemical binding]; other site 985080002680 DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA...; Region: TOP1Ac; cl11986 985080002681 domain I; other site 985080002682 DNA binding groove [nucleotide binding] 985080002683 phosphate binding site [ion binding]; other site 985080002684 domain II; other site 985080002685 domain III; other site 985080002686 nucleotide binding site [chemical binding]; other site 985080002687 catalytic site [active] 985080002688 DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA...; Region: TOP1Ac; cl11986 985080002689 Topoisomerase IA [DNA replication, recombination, and repair]; Region: TopA; COG0550 985080002690 domain IV; other site 985080002691 potential frameshift: common BLAST hit: gi|15612561|ref|NP_223640.1| conjugal plasmid transfer system protein 985080002692 Type IV secretory pathway, VirB9 components [Intracellular trafficking and secretion]; Region: VirB9; COG3504 985080002693 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 985080002694 potential frameshift: common BLAST hit: gi|308183674|ref|YP_003927801.1| VirB11 type IV secretion ATPase 985080002695 Type IV secretory pathway, VirB11 components, and related ATPases involved in archaeal flagella biosynthesis [Cell motility and secretion / Intracellular trafficking and secretion]; Region: VirB11; COG0630 985080002696 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 985080002697 Walker A motif; other site 985080002698 ATP binding site [chemical binding]; other site 985080002699 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 985080002700 Walker B motif; other site 985080002701 Type IV secretory pathway, VirD4 components [Intracellular trafficking and secretion]; Region: VirD4; COG3505 985080002702 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 985080002703 Walker A motif; other site 985080002704 ATP binding site [chemical binding]; other site 985080002705 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 985080002706 Walker B motif; other site 985080002707 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3041; cl17396 985080002708 potential frameshift: common BLAST hit: gi|210134634|ref|YP_002301073.1| integrase/recombinase XercD family 985080002709 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 985080002710 active site 985080002711 catalytic residues [active] 985080002712 DNA binding site [nucleotide binding] 985080002713 Int/Topo IB signature motif; other site 985080002714 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 985080002715 Uncharacterized conserved protein [Function unknown]; Region: COG1479 985080002716 Protein of unknown function DUF262; Region: DUF262; pfam03235 985080002717 Uncharacterized conserved protein [Function unknown]; Region: COG1479 985080002718 Protein of unknown function DUF262; Region: DUF262; pfam03235 985080002719 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 985080002720 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: COG1598 985080002721 YcfA-like protein; Region: YcfA; cl00752 985080002722 Arginine decarboxylase (spermidine biosynthesis) [Amino acid transport and metabolism]; Region: SpeA; COG1166 985080002723 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase; Region: PLPDE_III_ADC; cd06830 985080002724 active site 985080002725 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 985080002726 catalytic residues [active] 985080002727 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 985080002728 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 985080002729 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 985080002730 putative ADP-binding pocket [chemical binding]; other site 985080002731 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 985080002732 Methyltransferase domain; Region: Methyltransf_23; pfam13489 985080002733 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 985080002734 S-adenosylmethionine binding site [chemical binding]; other site 985080002735 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 985080002736 potential frameshift: common BLAST hit: gi|383749342|ref|YP_005424445.1| methionyl-tRNA synthetase 985080002737 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 985080002738 putative tRNA-binding site [nucleotide binding]; other site 985080002739 dimer interface [polypeptide binding]; other site 985080002740 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 985080002741 methionyl-tRNA synthetase; Reviewed; Region: PRK11893 985080002742 active site 985080002743 HIGH motif; other site 985080002744 KMSKS motif; other site 985080002745 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 985080002746 anticodon binding site; other site 985080002747 tRNA binding surface [nucleotide binding]; other site 985080002748 Mycolic acid cyclopropane synthetase; Region: CMAS; pfam02353 985080002749 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 985080002750 S-adenosylmethionine binding site [chemical binding]; other site 985080002751 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 985080002752 Mechanosensitive ion channel; Region: MS_channel; pfam00924 985080002753 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 985080002754 GMP synthase; Reviewed; Region: guaA; PRK00074 985080002755 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 985080002756 AMP/PPi binding site [chemical binding]; other site 985080002757 candidate oxyanion hole; other site 985080002758 catalytic triad [active] 985080002759 potential glutamine specificity residues [chemical binding]; other site 985080002760 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 985080002761 ATP Binding subdomain [chemical binding]; other site 985080002762 Ligand Binding sites [chemical binding]; other site 985080002763 Dimerization subdomain; other site 985080002764 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 985080002765 molybdopterin guanine dinucleotide-containing S/N-oxide reductases; Region: bisC_fam; TIGR00509 985080002766 molybdopterin cofactor binding site [chemical binding]; other site 985080002767 substrate binding site [chemical binding]; other site 985080002768 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 985080002769 molybdopterin cofactor binding site; other site 985080002770 Protein of unknown function (DUF3972); Region: DUF3972; pfam13118 985080002771 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 985080002772 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 985080002773 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 985080002774 catalytic residue [active] 985080002775 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 985080002776 nucleotide binding site/active site [active] 985080002777 HIT family signature motif; other site 985080002778 catalytic residue [active] 985080002779 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 985080002780 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 985080002781 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 985080002782 dimer interface [polypeptide binding]; other site 985080002783 motif 1; other site 985080002784 active site 985080002785 motif 2; other site 985080002786 motif 3; other site 985080002787 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 985080002788 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 985080002789 putative tRNA-binding site [nucleotide binding]; other site 985080002790 tRNA synthetase B5 domain; Region: B5; pfam03484 985080002791 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 985080002792 dimer interface [polypeptide binding]; other site 985080002793 motif 1; other site 985080002794 motif 3; other site 985080002795 motif 2; other site 985080002796 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 985080002797 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 985080002798 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 985080002799 hinge; other site 985080002800 active site 985080002801 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 985080002802 LytB protein; Region: LYTB; pfam02401 985080002803 ribosomal protein S1; Region: rpsA; TIGR00717 985080002804 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 985080002805 RNA binding site [nucleotide binding]; other site 985080002806 Ribosomal protein S1-like RNA-binding domain; Region: S1; smart00316 985080002807 RNA binding site [nucleotide binding]; other site 985080002808 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 985080002809 RNA binding site [nucleotide binding]; other site 985080002810 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 985080002811 RNA binding site [nucleotide binding]; other site 985080002812 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 985080002813 RNA binding site [nucleotide binding]; other site 985080002814 D-3-phosphoglycerate dehydrogenase; Region: PGDH; TIGR01327 985080002815 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_4; cd12173 985080002816 ligand binding site [chemical binding]; other site 985080002817 NAD binding site [chemical binding]; other site 985080002818 dimerization interface [polypeptide binding]; other site 985080002819 catalytic site [active] 985080002820 C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH); Region: ACT_3PGDH-xct; cd04902 985080002821 putative L-serine binding site [chemical binding]; other site 985080002822 menaquinone biosynthesis decarboxylase, SCO4490 family; Region: mena_SCO4490; TIGR03701 985080002823 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 985080002824 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 985080002825 catalytic residue [active] 985080002826 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 985080002827 putative active site [active] 985080002828 putative metal binding site [ion binding]; other site 985080002829 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 985080002830 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 985080002831 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 985080002832 active site 985080002833 phosphorylation site [posttranslational modification] 985080002834 intermolecular recognition site; other site 985080002835 dimerization interface [polypeptide binding]; other site 985080002836 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 985080002837 putative binding surface; other site 985080002838 active site 985080002839 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 985080002840 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 985080002841 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 985080002842 ATP binding site [chemical binding]; other site 985080002843 Mg2+ binding site [ion binding]; other site 985080002844 G-X-G motif; other site 985080002845 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 985080002846 Response regulator receiver domain; Region: Response_reg; pfam00072 985080002847 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 985080002848 active site 985080002849 phosphorylation site [posttranslational modification] 985080002850 intermolecular recognition site; other site 985080002851 dimerization interface [polypeptide binding]; other site 985080002852 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 985080002853 putative CheA interaction surface; other site 985080002854 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 985080002855 dimer interface [polypeptide binding]; other site 985080002856 catalytic triad [active] 985080002857 peroxidatic and resolving cysteines [active] 985080002858 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 985080002859 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 985080002860 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 985080002861 ubiE/COQ5 methyltransferase family; Region: Ubie_methyltran; pfam01209 985080002862 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 985080002863 S-adenosylmethionine binding site [chemical binding]; other site 985080002864 primosome assembly protein PriA; Validated; Region: PRK05580 985080002865 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 985080002866 ATP binding site [chemical binding]; other site 985080002867 putative Mg++ binding site [ion binding]; other site 985080002868 helicase superfamily c-terminal domain; Region: HELICc; smart00490 985080002869 Sporulation related domain; Region: SPOR; pfam05036 985080002870 Peptidase family M48; Region: Peptidase_M48; pfam01435 985080002871 HemK family putative methylases; Region: hemK_fam; TIGR00536 985080002872 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 985080002873 glutamate dehydrogenase; Provisional; Region: PRK09414 985080002874 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 985080002875 NAD(P) binding domain of glutamate dehydrogenase, subgroup 2; Region: NAD_bind_2_Glu_DH; cd05313 985080002876 NAD(P) binding site [chemical binding]; other site 985080002877 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 985080002878 cytochrome c-type biogenesis protein CcsB; Region: cytochr_II_ccsB; TIGR03144 985080002879 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 985080002880 catalytic residues [active] 985080002881 ferrochelatase; Region: hemH; TIGR00109 985080002882 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 985080002883 C-terminal domain interface [polypeptide binding]; other site 985080002884 active site 985080002885 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 985080002886 active site 985080002887 N-terminal domain interface [polypeptide binding]; other site 985080002888 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385 985080002889 RNA methyltransferase, RsmE family; Region: TIGR00046 985080002890 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 985080002891 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 985080002892 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 985080002893 trimer interface [polypeptide binding]; other site 985080002894 active site 985080002895 acetyl-CoA carboxylase, biotin carboxyl carrier protein; Region: BCCP; TIGR00531 985080002896 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 985080002897 carboxyltransferase (CT) interaction site; other site 985080002898 biotinylation site [posttranslational modification]; other site 985080002899 biotin carboxylase; Validated; Region: PRK08462 985080002900 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 985080002901 ATP-grasp domain; Region: ATP-grasp_4; cl17255 985080002902 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 985080002903 Methyltransferase domain; Region: Methyltransf_26; pfam13659 985080002904 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 985080002905 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 985080002906 inhibitor-cofactor binding pocket; inhibition site 985080002907 pyridoxal 5'-phosphate binding site [chemical binding]; other site 985080002908 catalytic residue [active] 985080002909 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 985080002910 dimer interface [polypeptide binding]; other site 985080002911 putative radical transfer pathway; other site 985080002912 diiron center [ion binding]; other site 985080002913 tyrosyl radical; other site 985080002914 protein-L-isoaspartate(D-aspartate) O-methyltransferase; Region: pimt; TIGR00080 985080002915 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 985080002916 S-adenosylmethionine binding site [chemical binding]; other site 985080002917 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 985080002918 Predicted permeases [General function prediction only]; Region: COG0795 985080002919 tRNA pseudouridine(38-40) synthase; Region: hisT_truA; TIGR00071 985080002920 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 985080002921 dimerization interface 3.5A [polypeptide binding]; other site 985080002922 active site 985080002923 UDP-glucose-4-epimerase GalE; Region: galE; TIGR01179 985080002924 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 985080002925 NAD binding site [chemical binding]; other site 985080002926 homodimer interface [polypeptide binding]; other site 985080002927 active site 985080002928 substrate binding site [chemical binding]; other site 985080002929 classical (c) SDR, subgroup 5; Region: SDR_c5; cd05346 985080002930 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 985080002931 putative NAD(P) binding site [chemical binding]; other site 985080002932 homodimer interface [polypeptide binding]; other site 985080002933 homotetramer interface [polypeptide binding]; other site 985080002934 active site 985080002935 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 985080002936 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 985080002937 binding surface 985080002938 TPR motif; other site 985080002939 Sel1-like repeats; Region: SEL1; smart00671 985080002940 Sel1-like repeats; Region: SEL1; smart00671 985080002941 Sel1-like repeats; Region: SEL1; smart00671 985080002942 Entner-Doudoroff aldolase; Region: eda; TIGR01182 985080002943 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 985080002944 active site 985080002945 intersubunit interface [polypeptide binding]; other site 985080002946 catalytic residue [active] 985080002947 phosphogluconate dehydratase; Validated; Region: PRK09054 985080002948 6-phosphogluconate dehydratase; Region: edd; TIGR01196 985080002949 Glucose-6-phosphate 1-dehydrogenase [Carbohydrate transport and metabolism]; Region: Zwf; COG0364 985080002950 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 985080002951 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 985080002952 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 985080002953 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 985080002954 putative active site [active] 985080002955 glucokinase, proteobacterial type; Region: glk; TIGR00749 985080002956 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 985080002957 nucleotide binding site [chemical binding]; other site 985080002958 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 985080002959 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD1; cd05283 985080002960 putative NAD(P) binding site [chemical binding]; other site 985080002961 putative substrate binding site [chemical binding]; other site 985080002962 catalytic Zn binding site [ion binding]; other site 985080002963 structural Zn binding site [ion binding]; other site 985080002964 dimer interface [polypeptide binding]; other site 985080002965 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 985080002966 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 985080002967 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 985080002968 active site 985080002969 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 985080002970 pyruvate flavodoxin oxidoreductase subunit gamma; Validated; Region: PRK05844 985080002971 pyruvate/ketoisovalerate ferredoxin oxidoreductase subunit gamma; Provisional; Region: PRK14029 985080002972 pyruvate flavodoxin oxidoreductase subunit delta; Reviewed; Region: porD; PRK09625 985080002973 4Fe-4S binding domain; Region: Fer4; pfam00037 985080002974 pyruvate flavodoxin oxidoreductase subunit alpha; Reviewed; Region: porA; PRK09622 985080002975 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 985080002976 dimer interface [polypeptide binding]; other site 985080002977 PYR/PP interface [polypeptide binding]; other site 985080002978 TPP binding site [chemical binding]; other site 985080002979 substrate binding site [chemical binding]; other site 985080002980 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 985080002981 pyruvate ferredoxin oxidoreductase subunit beta; Provisional; Region: PRK11865 985080002982 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 985080002983 TPP-binding site [chemical binding]; other site 985080002984 putative dimer interface [polypeptide binding]; other site 985080002985 adenylosuccinate lyase; Provisional; Region: PRK08470 985080002986 Adenylsuccinate lyase (ASL)_subgroup 1; Region: Adenylsuccinate_lyase_1; cd01360 985080002987 tetramer interface [polypeptide binding]; other site 985080002988 active site 985080002989 Adenylosuccinate lyase C-terminus; Region: ADSL_C; smart00998 985080002990 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 985080002991 excinuclease ABC subunit B; Provisional; Region: PRK05298 985080002992 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 985080002993 ATP binding site [chemical binding]; other site 985080002994 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 985080002995 putative Mg++ binding site [ion binding]; other site 985080002996 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 985080002997 nucleotide binding region [chemical binding]; other site 985080002998 ATP-binding site [chemical binding]; other site 985080002999 Ultra-violet resistance protein B; Region: UvrB; pfam12344 985080003000 UvrB/uvrC motif; Region: UVR; pfam02151 985080003001 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl17192 985080003002 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 985080003003 binding surface 985080003004 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 985080003005 TPR motif; other site 985080003006 Sel1-like repeats; Region: SEL1; smart00671 985080003007 Sel1-like repeats; Region: SEL1; smart00671 985080003008 Sel1-like repeats; Region: SEL1; smart00671 985080003009 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 985080003010 gamma-glutamyltranspeptidase; Region: g_glut_trans; TIGR00066 985080003011 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK08471 985080003012 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 985080003013 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 985080003014 DNA-methyltransferase (dcm); Region: dcm; TIGR00675 985080003015 cofactor binding site; other site 985080003016 DNA binding site [nucleotide binding] 985080003017 substrate interaction site [chemical binding]; other site 985080003018 Anti-sigma-28 factor, FlgM; Region: FlgM; cl01052 985080003019 FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]; Region: SlpA; COG1047 985080003020 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 985080003021 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 985080003022 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 985080003023 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 985080003024 ligand binding site [chemical binding]; other site 985080003025 translocation protein TolB; Provisional; Region: tolB; PRK04043 985080003026 TolB amino-terminal domain; Region: TolB_N; pfam04052 985080003027 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 985080003028 TonB C terminal; Region: TonB_2; pfam13103 985080003029 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 985080003030 TolR protein; Region: tolR; TIGR02801 985080003031 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; pfam01618 985080003032 ATP synthase, F1 epsilon subunit (delta in mitochondria); Region: ATP_synt_epsi; TIGR01216 985080003033 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 985080003034 gamma subunit interface [polypeptide binding]; other site 985080003035 epsilon subunit interface [polypeptide binding]; other site 985080003036 LBP interface [polypeptide binding]; other site 985080003037 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 985080003038 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 985080003039 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 985080003040 alpha subunit interaction interface [polypeptide binding]; other site 985080003041 Walker A motif; other site 985080003042 ATP binding site [chemical binding]; other site 985080003043 Walker B motif; other site 985080003044 inhibitor binding site; inhibition site 985080003045 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 985080003046 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 985080003047 core domain interface [polypeptide binding]; other site 985080003048 delta subunit interface [polypeptide binding]; other site 985080003049 epsilon subunit interface [polypeptide binding]; other site 985080003050 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 985080003051 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 985080003052 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 985080003053 beta subunit interaction interface [polypeptide binding]; other site 985080003054 Walker A motif; other site 985080003055 ATP binding site [chemical binding]; other site 985080003056 Walker B motif; other site 985080003057 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 985080003058 F0F1 ATP synthase subunit delta; Provisional; Region: PRK13431 985080003059 F0F1 ATP synthase subunit B; Validated; Region: PRK08475 985080003060 F0F1 ATP synthase subunit B'; Validated; Region: PRK08476 985080003061 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 985080003062 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 985080003063 ParB-like nuclease domain; Region: ParB; smart00470 985080003064 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 985080003065 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 985080003066 P-loop; other site 985080003067 Magnesium ion binding site [ion binding]; other site 985080003068 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 985080003069 Magnesium ion binding site [ion binding]; other site 985080003070 biotin--protein ligase; Provisional; Region: PRK08477 985080003071 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 985080003072 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 985080003073 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 985080003074 putative active site [active] 985080003075 substrate binding site [chemical binding]; other site 985080003076 putative cosubstrate binding site; other site 985080003077 catalytic site [active] 985080003078 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 985080003079 substrate binding site [chemical binding]; other site 985080003080 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4694 985080003081 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4487 985080003082 Uncharacterized protein conserved in bacteria (DUF2130); Region: DUF2130; pfam09903 985080003083 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 985080003084 tRNA (Guanine-1)-methyltransferase; Region: tRNA_m1G_MT; cl00407 985080003085 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK14593 985080003086 RimM N-terminal domain; Region: RimM; pfam01782 985080003087 PRC-barrel domain; Region: PRC; pfam05239 985080003088 Predicted RNA-binding protein (contains KH domain) [General function prediction only]; Region: COG1837 985080003089 KH domain; Region: KH_4; pfam13083 985080003090 G-X-X-G motif; other site 985080003091 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 985080003092 signal recognition particle protein; Provisional; Region: PRK10867 985080003093 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 985080003094 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 985080003095 P loop; other site 985080003096 GTP binding site [chemical binding]; other site 985080003097 Signal peptide binding domain; Region: SRP_SPB; pfam02978 985080003098 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 985080003099 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 985080003100 active site 985080003101 HIGH motif; other site 985080003102 nucleotide binding site [chemical binding]; other site 985080003103 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 985080003104 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 985080003105 active site 985080003106 KMSKS motif; other site 985080003107 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 985080003108 anticodon binding site; other site 985080003109 flagellar assembly protein FliW; Provisional; Region: PRK13283 985080003110 undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase; Region: murG; TIGR01133 985080003111 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 985080003112 active site 985080003113 homodimer interface [polypeptide binding]; other site 985080003114 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 985080003115 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 985080003116 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 985080003117 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 985080003118 potential frameshift: common BLAST hit: gi|15612151|ref|NP_223803.1| cAMP-induced cell filamentation protein 985080003119 Fic/DOC family; Region: Fic; cl00960 985080003120 Protein involved in cell division [Cell division and chromosome partitioning]; Region: Fic; COG2184 985080003121 metal-binding heat shock protein; Provisional; Region: PRK00016 985080003122 flavodoxin FldA; Validated; Region: PRK09267 985080003123 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 985080003124 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 985080003125 Uncharacterized protein, possibly involved in nitrogen fixation [Inorganic ion transport and metabolism]; Region: FixS; COG3197 985080003126 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 985080003127 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 985080003128 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 985080003129 potential frameshift: common BLAST hit: gi|208435059|ref|YP_002266725.1| tetracycline resistance proteintet A (P ) 985080003130 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 985080003131 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 985080003132 active site 985080003133 dimer interface [polypeptide binding]; other site 985080003134 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 985080003135 dimer interface [polypeptide binding]; other site 985080003136 active site 985080003137 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 985080003138 carbon starvation protein A; Provisional; Region: PRK15015 985080003139 Carbon starvation protein CstA; Region: CstA; pfam02554 985080003140 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 985080003141 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 985080003142 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 985080003143 dimer interface [polypeptide binding]; other site 985080003144 conserved gate region; other site 985080003145 putative PBP binding loops; other site 985080003146 ABC-ATPase subunit interface; other site 985080003147 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 985080003148 dimer interface [polypeptide binding]; other site 985080003149 conserved gate region; other site 985080003150 putative PBP binding loops; other site 985080003151 ABC-ATPase subunit interface; other site 985080003152 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 985080003153 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 985080003154 Walker A/P-loop; other site 985080003155 ATP binding site [chemical binding]; other site 985080003156 Q-loop/lid; other site 985080003157 ABC transporter signature motif; other site 985080003158 Walker B; other site 985080003159 D-loop; other site 985080003160 H-loop/switch region; other site 985080003161 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 985080003162 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 985080003163 substrate binding pocket [chemical binding]; other site 985080003164 membrane-bound complex binding site; other site 985080003165 hinge residues; other site 985080003166 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 985080003167 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 985080003168 putative substrate translocation pore; other site 985080003169 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 985080003170 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 985080003171 purine-nucleoside phosphorylase, family 1 (deoD); Region: deoD; TIGR00107 985080003172 phosphopentomutase; Provisional; Region: PRK05362 985080003173 Metalloenzyme superfamily; Region: Metalloenzyme; pfam01676 985080003174 Nucleoside permease [Nucleotide transport and metabolism]; Region: NupC; COG1972 985080003175 Na+ dependent nucleoside transporter N-terminus; Region: Nucleos_tra2_N; pfam01773 985080003176 Nucleoside recognition; Region: Gate; pfam07670 985080003177 Na+ dependent nucleoside transporter C-terminus; Region: Nucleos_tra2_C; pfam07662 985080003178 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 985080003179 Major Facilitator Superfamily; Region: MFS_1; pfam07690 985080003180 putative substrate translocation pore; other site 985080003181 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 985080003182 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 985080003183 Ligand Binding Site [chemical binding]; other site 985080003184 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 985080003185 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 985080003186 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 985080003187 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA; Region: MATE_MepA_like; cd13143 985080003188 putative arabinose transporter; Provisional; Region: PRK03545 985080003189 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 985080003190 putative substrate translocation pore; other site 985080003191 Carbonic anhydrase [Inorganic ion transport and metabolism]; Region: Cah; COG3338 985080003192 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 985080003193 active site 985080003194 zinc binding site [ion binding]; other site 985080003195 Helicobacter pylori protein of unknown function (DUF874); Region: DUF874; pfam05917 985080003196 aspartate-semialdehyde dehydrogenase (peptidoglycan organisms); Region: asd_B; TIGR01296 985080003197 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 985080003198 Histidyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: HisS; COG0124 985080003199 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 985080003200 dimer interface [polypeptide binding]; other site 985080003201 motif 1; other site 985080003202 active site 985080003203 motif 2; other site 985080003204 motif 3; other site 985080003205 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 985080003206 anticodon binding site; other site 985080003207 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 985080003208 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 985080003209 putative active site [active] 985080003210 elongation factor G; Reviewed; Region: PRK00007 985080003211 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 985080003212 G1 box; other site 985080003213 putative GEF interaction site [polypeptide binding]; other site 985080003214 GTP/Mg2+ binding site [chemical binding]; other site 985080003215 Switch I region; other site 985080003216 G2 box; other site 985080003217 G3 box; other site 985080003218 Switch II region; other site 985080003219 G4 box; other site 985080003220 G5 box; other site 985080003221 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 985080003222 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 985080003223 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 985080003224 30S ribosomal protein S7; Validated; Region: PRK05302 985080003225 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 985080003226 S17 interaction site [polypeptide binding]; other site 985080003227 S8 interaction site; other site 985080003228 16S rRNA interaction site [nucleotide binding]; other site 985080003229 streptomycin interaction site [chemical binding]; other site 985080003230 23S rRNA interaction site [nucleotide binding]; other site 985080003231 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 985080003232 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed; Region: PRK09603 985080003233 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl17585 985080003234 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 985080003235 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 985080003236 RPB11 interaction site [polypeptide binding]; other site 985080003237 RPB12 interaction site [polypeptide binding]; other site 985080003238 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 985080003239 RPB3 interaction site [polypeptide binding]; other site 985080003240 RPB1 interaction site [polypeptide binding]; other site 985080003241 RPB11 interaction site [polypeptide binding]; other site 985080003242 RPB10 interaction site [polypeptide binding]; other site 985080003243 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 985080003244 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 985080003245 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 985080003246 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 985080003247 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 985080003248 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 985080003249 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 985080003250 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 985080003251 DNA binding site [nucleotide binding] 985080003252 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 985080003253 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 985080003254 core dimer interface [polypeptide binding]; other site 985080003255 peripheral dimer interface [polypeptide binding]; other site 985080003256 L10 interface [polypeptide binding]; other site 985080003257 L11 interface [polypeptide binding]; other site 985080003258 putative EF-Tu interaction site [polypeptide binding]; other site 985080003259 putative EF-G interaction site [polypeptide binding]; other site 985080003260 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 985080003261 23S rRNA interface [nucleotide binding]; other site 985080003262 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 985080003263 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 985080003264 mRNA/rRNA interface [nucleotide binding]; other site 985080003265 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 985080003266 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 985080003267 23S rRNA interface [nucleotide binding]; other site 985080003268 L7/L12 interface [polypeptide binding]; other site 985080003269 putative thiostrepton binding site; other site 985080003270 L25 interface [polypeptide binding]; other site 985080003271 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 985080003272 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 985080003273 putative homodimer interface [polypeptide binding]; other site 985080003274 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 985080003275 heterodimer interface [polypeptide binding]; other site 985080003276 homodimer interface [polypeptide binding]; other site 985080003277 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 985080003278 elongation factor Tu; Reviewed; Region: PRK00049 985080003279 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 985080003280 G1 box; other site 985080003281 GEF interaction site [polypeptide binding]; other site 985080003282 GTP/Mg2+ binding site [chemical binding]; other site 985080003283 Switch I region; other site 985080003284 G2 box; other site 985080003285 G3 box; other site 985080003286 Switch II region; other site 985080003287 G4 box; other site 985080003288 G5 box; other site 985080003289 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 985080003290 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 985080003291 Antibiotic Binding Site [chemical binding]; other site 985080003292 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 985080003293 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 985080003294 Walker A/P-loop; other site 985080003295 ATP binding site [chemical binding]; other site 985080003296 Q-loop/lid; other site 985080003297 ABC transporter signature motif; other site 985080003298 Walker B; other site 985080003299 D-loop; other site 985080003300 H-loop/switch region; other site 985080003301 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 985080003302 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 985080003303 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG3392 985080003304 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; pfam02086 985080003305 serine O-acetyltransferase; Region: cysE; TIGR01172 985080003306 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 985080003307 trimer interface [polypeptide binding]; other site 985080003308 active site 985080003309 substrate binding site [chemical binding]; other site 985080003310 CoA binding site [chemical binding]; other site 985080003311 F0F1 ATP synthase subunit C; Validated; Region: PRK08482 985080003312 RNase PH-like 3'-5' exoribonucleases; Region: RNase_PH; cl03114 985080003313 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 985080003314 oligomer interface [polypeptide binding]; other site 985080003315 RNA binding site [nucleotide binding]; other site 985080003316 RNase PH-like 3'-5' exoribonucleases; Region: RNase_PH; cl03114 985080003317 oligomer interface [polypeptide binding]; other site 985080003318 RNA binding site [nucleotide binding]; other site 985080003319 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 985080003320 putative nucleic acid binding region [nucleotide binding]; other site 985080003321 G-X-X-G motif; other site 985080003322 Ribosomal protein S1-like RNA-binding domain; Region: S1; smart00316 985080003323 RNA binding site [nucleotide binding]; other site 985080003324 Predicted phosphoribosyltransferases [General function prediction only]; Region: COG1926 985080003325 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 985080003326 Organic solvent tolerance protein; Region: OstA_C; pfam04453 985080003327 Predicted membrane protein/domain [Function unknown]; Region: COG1714 985080003328 phosphoribosylamine--glycine ligase; Region: purD; TIGR00877 985080003329 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 985080003330 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 985080003331 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 985080003332 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 985080003333 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 985080003334 Walker A/P-loop; other site 985080003335 ATP binding site [chemical binding]; other site 985080003336 Q-loop/lid; other site 985080003337 ABC transporter signature motif; other site 985080003338 Walker B; other site 985080003339 D-loop; other site 985080003340 H-loop/switch region; other site 985080003341 Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl...; Region: CIS_IPPS; cd00475 985080003342 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 985080003343 catalytic residue [active] 985080003344 putative FPP diphosphate binding site; other site 985080003345 putative FPP binding hydrophobic cleft; other site 985080003346 dimer interface [polypeptide binding]; other site 985080003347 putative IPP diphosphate binding site; other site 985080003348 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 985080003349 FAD binding domain; Region: FAD_binding_4; pfam01565 985080003350 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 985080003351 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 985080003352 active site residue [active] 985080003353 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 985080003354 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 985080003355 active site 985080003356 camphor resistance protein CrcB; Provisional; Region: PRK14204 985080003357 coproporphyrinogen III oxidase; Provisional; Region: PRK08446 985080003358 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 985080003359 FeS/SAM binding site; other site 985080003360 HemN C-terminal domain; Region: HemN_C; pfam06969 985080003361 Cytochrome c553 [Energy production and conversion]; Region: COG2863 985080003362 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 985080003363 putative active site [active] 985080003364 Ap4A binding site [chemical binding]; other site 985080003365 nudix motif; other site 985080003366 putative metal binding site [ion binding]; other site 985080003367 aspartate kinase; Reviewed; Region: PRK06635 985080003368 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 985080003369 putative nucleotide binding site [chemical binding]; other site 985080003370 putative catalytic residues [active] 985080003371 putative Mg ion binding site [ion binding]; other site 985080003372 putative aspartate binding site [chemical binding]; other site 985080003373 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 985080003374 putative allosteric regulatory site; other site 985080003375 ACT domains of the lysine-sensitive, aspartokinase (AK) isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related domains; Region: ACT_AKii-LysC-BS-like_2; cd04936 985080003376 putative allosteric regulatory residue; other site 985080003377 DNA replication regulator; Region: HobA; pfam12163 985080003378 DNA polymerase III subunit delta'; Validated; Region: PRK08485 985080003379 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 985080003380 dihydropteroate synthase; Region: DHPS; TIGR01496 985080003381 substrate binding pocket [chemical binding]; other site 985080003382 dimer interface [polypeptide binding]; other site 985080003383 inhibitor binding site; inhibition site 985080003384 The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Region: NR_LBD; cl11397 985080003385 coregulator recognition site; other site 985080003386 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 985080003387 EamA-like transporter family; Region: EamA; pfam00892 985080003388 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2952 985080003389 Carbamoylphosphate synthase small subunit [Amino acid transport and metabolism / Nucleotide transport and metabolism]; Region: CarA; COG0505 985080003390 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; pfam00988 985080003391 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 985080003392 catalytic site [active] 985080003393 subunit interface [polypeptide binding]; other site 985080003394 formamidase; Provisional; Region: amiF; PRK13287 985080003395 aliphatic amidases (class 2 nitrilases); Region: aliphatic_amidase; cd07565 985080003396 multimer interface [polypeptide binding]; other site 985080003397 active site 985080003398 catalytic triad [active] 985080003399 dimer interface [polypeptide binding]; other site 985080003400 Maf-like protein; Region: Maf; pfam02545 985080003401 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 985080003402 active site 985080003403 dimer interface [polypeptide binding]; other site 985080003404 potential frameshift: common BLAST hit: gi|254779785|ref|YP_003057891.1| alanyl-tRNA synthetase 985080003405 alanine-tRNA ligase; Region: PLN02961 985080003406 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 985080003407 DHHA1 domain; Region: DHHA1; pfam02272 985080003408 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 985080003409 motif 1; other site 985080003410 active site 985080003411 motif 2; other site 985080003412 motif 3; other site 985080003413 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2841 985080003414 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 985080003415 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 985080003416 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 985080003417 dimer interface [polypeptide binding]; other site 985080003418 ssDNA binding site [nucleotide binding]; other site 985080003419 tetramer (dimer of dimers) interface [polypeptide binding]; other site 985080003420 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 985080003421 DNA polymerase III subunit delta; Validated; Region: PRK08487 985080003422 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 985080003423 Exoribonuclease R [Transcription]; Region: VacB; COG0557 985080003424 RNB domain; Region: RNB; pfam00773 985080003425 shikimate 5-dehydrogenase; Region: aroE; TIGR00507 985080003426 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 985080003427 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 985080003428 shikimate binding site; other site 985080003429 NAD(P) binding site [chemical binding]; other site 985080003430 Bacterial SH3 domain; Region: SH3_3; pfam08239 985080003431 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4174 985080003432 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 985080003433 dimer interface [polypeptide binding]; other site 985080003434 conserved gate region; other site 985080003435 putative PBP binding loops; other site 985080003436 ABC-ATPase subunit interface; other site 985080003437 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 985080003438 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 985080003439 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 985080003440 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 985080003441 active site 985080003442 HIGH motif; other site 985080003443 dimer interface [polypeptide binding]; other site 985080003444 KMSKS motif; other site 985080003445 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 985080003446 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 985080003447 S-adenosylmethionine binding site [chemical binding]; other site 985080003448 Preprotein translocase subunit SecG [Intracellular trafficking and secretion]; Region: SecG; COG1314 985080003449 ribosome recycling factor; Reviewed; Region: frr; PRK00083 985080003450 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 985080003451 hinge region; other site 985080003452 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 985080003453 active site 985080003454 RDD family; Region: RDD; pfam06271 985080003455 NAD-dependent protein deacetylases, SIR2 family [Transcription]; Region: SIR2; COG0846 985080003456 SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which...; Region: SIRT5_Af1_CobB; cd01412 985080003457 NAD+ binding site [chemical binding]; other site 985080003458 substrate binding site [chemical binding]; other site 985080003459 Zn binding site [ion binding]; other site 985080003460 NADH dehydrogenase subunit A; Validated; Region: PRK08489 985080003461 NADH dehydrogenase subunit B; Validated; Region: PRK06411 985080003462 NADH dehydrogenase subunit C; Provisional; Region: PRK08491 985080003463 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 985080003464 NADH dehydrogenase subunit D; Validated; Region: PRK06075 985080003465 NADH dehydrogenase I, D subunit; Region: NuoD; TIGR01962 985080003466 NADH dehydrogenase subunit G; Validated; Region: PRK08493 985080003467 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 985080003468 catalytic loop [active] 985080003469 iron binding site [ion binding]; other site 985080003470 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 985080003471 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 985080003472 molybdopterin cofactor binding site; other site 985080003473 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; cd00368 985080003474 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 985080003475 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 985080003476 NADH-quinone oxidoreductase, chain I; Region: NuoI; TIGR01971 985080003477 4Fe-4S binding domain; Region: Fer4; cl02805 985080003478 4Fe-4S binding domain; Region: Fer4; pfam00037 985080003479 NADH:ubiquinone oxidoreductase subunit 6 (chain J) [Energy production and conversion]; Region: NuoJ; COG0839 985080003480 NADH dehydrogenase subunit J; Provisional; Region: PRK06433 985080003481 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 985080003482 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 985080003483 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 985080003484 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 985080003485 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 985080003486 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 985080003487 proton-translocating NADH-quinone oxidoreductase, chain N; Region: NDH_I_N; TIGR01770 985080003488 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 985080003489 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 985080003490 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 985080003491 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 985080003492 active site 985080003493 substrate binding site [chemical binding]; other site 985080003494 metal binding site [ion binding]; metal-binding site 985080003495 Protein of unknown function (DUF4065); Region: DUF4065; pfam13274 985080003496 tryptophan synthase alpha subunit; Provisional; Region: trpA; CHL00200 985080003497 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 985080003498 substrate binding site [chemical binding]; other site 985080003499 active site 985080003500 catalytic residues [active] 985080003501 heterodimer interface [polypeptide binding]; other site 985080003502 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 985080003503 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 985080003504 pyridoxal 5'-phosphate binding site [chemical binding]; other site 985080003505 catalytic residue [active] 985080003506 bifunctional indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase; Provisional; Region: PRK09427 985080003507 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 985080003508 active site 985080003509 ribulose/triose binding site [chemical binding]; other site 985080003510 phosphate binding site [ion binding]; other site 985080003511 substrate (anthranilate) binding pocket [chemical binding]; other site 985080003512 product (indole) binding pocket [chemical binding]; other site 985080003513 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 985080003514 active site 985080003515 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 985080003516 anthranilate phosphoribosyltransferase; Region: trpD; TIGR01245 985080003517 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 985080003518 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 985080003519 Glutamine amidotransferase class-I; Region: GATase; pfam00117 985080003520 glutamine binding [chemical binding]; other site 985080003521 catalytic triad [active] 985080003522 anthranilate synthase component I; Provisional; Region: PRK13564 985080003523 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 985080003524 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 985080003525 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 985080003526 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 985080003527 putative active site [active] 985080003528 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 985080003529 active site 985080003530 motif I; other site 985080003531 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 985080003532 motif II; other site 985080003533 Uncharacterized conserved protein [Function unknown]; Region: COG2353 985080003534 thiaminase II; Region: salvage_TenA; TIGR04306 985080003535 Nicotinamide mononucleotide transporter [Coenzyme metabolism]; Region: PnuC; COG3201 985080003536 Thiamine pyrophosphokinase; Region: TPK; cd07995 985080003537 thiamine pyrophosphokinase; Region: thi_PPkinase; TIGR01378 985080003538 active site 985080003539 dimerization interface [polypeptide binding]; other site 985080003540 thiamine binding site [chemical binding]; other site 985080003541 Ribosomal protein L17 [Translation, ribosomal structure and biogenesis]; Region: RplQ; COG0203 985080003542 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 985080003543 alphaNTD homodimer interface [polypeptide binding]; other site 985080003544 DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type; Region: rpoA; TIGR02027 985080003545 alphaNTD - beta interaction site [polypeptide binding]; other site 985080003546 alphaNTD - beta' interaction site [polypeptide binding]; other site 985080003547 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 985080003548 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 985080003549 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 985080003550 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 985080003551 RNA binding surface [nucleotide binding]; other site 985080003552 30S ribosomal protein S11; Validated; Region: PRK05309 985080003553 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 985080003554 30S ribosomal protein S13; Region: bact_S13; TIGR03631 985080003555 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 985080003556 rRNA binding site [nucleotide binding]; other site 985080003557 predicted 30S ribosome binding site; other site 985080003558 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 985080003559 active site 985080003560 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 985080003561 SecY translocase; Region: SecY; pfam00344 985080003562 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 985080003563 ribosomal protein S5, bacterial/organelle type; Region: rpsE_bact; TIGR01021 985080003564 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 985080003565 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 985080003566 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 985080003567 23S rRNA interface [nucleotide binding]; other site 985080003568 5S rRNA interface [nucleotide binding]; other site 985080003569 L27 interface [polypeptide binding]; other site 985080003570 L5 interface [polypeptide binding]; other site 985080003571 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 985080003572 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 985080003573 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 985080003574 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08061 985080003575 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 985080003576 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 985080003577 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 985080003578 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 985080003579 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 985080003580 RNA binding site [nucleotide binding]; other site 985080003581 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 985080003582 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 985080003583 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 985080003584 L23 interface [polypeptide binding]; other site 985080003585 trigger factor interaction site; other site 985080003586 23S rRNA interface [nucleotide binding]; other site 985080003587 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 985080003588 23S rRNA interface [nucleotide binding]; other site 985080003589 5S rRNA interface [nucleotide binding]; other site 985080003590 putative antibiotic binding site [chemical binding]; other site 985080003591 L25 interface [polypeptide binding]; other site 985080003592 L27 interface [polypeptide binding]; other site 985080003593 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 985080003594 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 985080003595 G-X-X-G motif; other site 985080003596 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 985080003597 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 985080003598 putative translocon binding site; other site 985080003599 protein-rRNA interface [nucleotide binding]; other site 985080003600 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 985080003601 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 985080003602 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 985080003603 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 985080003604 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 985080003605 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 985080003606 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 985080003607 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 985080003608 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 985080003609 AAA domain; Region: AAA_14; pfam13173 985080003610 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 985080003611 RNA/DNA hybrid binding site [nucleotide binding]; other site 985080003612 active site 985080003613 fumarate hydratase; Reviewed; Region: fumC; PRK00485 985080003614 Class II fumarases; Region: Fumarase_classII; cd01362 985080003615 active site 985080003616 tetramer interface [polypeptide binding]; other site 985080003617 YtkA-like; Region: YtkA; pfam13115 985080003618 Outer membrane efflux protein; Region: OEP; pfam02321 985080003619 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 985080003620 HlyD family secretion protein; Region: HlyD_3; pfam13437 985080003621 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 985080003622 Predicted branched-chain amino acid permeases (azaleucine resistance) [Amino acid transport and metabolism]; Region: AzlD; COG1687 985080003623 AzlC protein; Region: AzlC; cl00570 985080003624 chaperone protein DnaJ; Provisional; Region: PRK14288 985080003625 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 985080003626 HSP70 interaction site [polypeptide binding]; other site 985080003627 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 985080003628 substrate binding site [polypeptide binding]; other site 985080003629 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 985080003630 Zn binding sites [ion binding]; other site 985080003631 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 985080003632 dimer interface [polypeptide binding]; other site 985080003633 tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase; Region: trmU; TIGR00420 985080003634 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 985080003635 Ligand Binding Site [chemical binding]; other site 985080003636 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 985080003637 HSP70 interaction site [polypeptide binding]; other site 985080003638 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 985080003639 Cytidylyltransferase; Region: CTP_transf_2; pfam01467 985080003640 active site 985080003641 (T/H)XGH motif; other site 985080003642 nickel responsive regulator; Provisional; Region: PRK00630 985080003643 Ribbon-helix-helix protein, copG family; Region: RHH_1; pfam01402 985080003644 NikR C terminal nickel binding domain; Region: NikR_C; pfam08753 985080003645 tonB-system energizer ExbB, group 2; Region: exbB2; TIGR02805 985080003646 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 985080003647 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 985080003648 potential frameshift: common BLAST hit: gi|298735634|ref|YP_003728159.1| periplasmic protein TonB 985080003649 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 985080003650 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 985080003651 Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]; Region: TerC; COG0861 985080003652 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 985080003653 Mg2+ transporter Helicobacter pylori CorA-like subgroup; Region: HpCorA-like; cd12836 985080003654 Cl binding site [ion binding]; other site 985080003655 oligomer interface [polypeptide binding]; other site 985080003656 phosphoglycerate kinase; Provisional; Region: pgk; PRK00073 985080003657 Phosphoglycerate kinase; Region: PGK; pfam00162 985080003658 substrate binding site [chemical binding]; other site 985080003659 hinge regions; other site 985080003660 ADP binding site [chemical binding]; other site 985080003661 catalytic site [active] 985080003662 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; pfam00044 985080003663 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 985080003664 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 985080003665 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 985080003666 ligand binding site [chemical binding]; other site 985080003667 active site 985080003668 UGI interface [polypeptide binding]; other site 985080003669 catalytic site [active] 985080003670 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 985080003671 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 985080003672 putative acyl-acceptor binding pocket; other site 985080003673 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 985080003674 C-terminal peptidase (prc); Region: prc; TIGR00225 985080003675 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 985080003676 protein binding site [polypeptide binding]; other site 985080003677 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 985080003678 Catalytic dyad [active] 985080003679 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 985080003680 DNA methylase; Region: N6_N4_Mtase; pfam01555 985080003681 Predicted helicase [General function prediction only]; Region: COG4889 985080003682 nicotinate-nucleotide pyrophosphorylase; Provisional; Region: PRK05848 985080003683 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 985080003684 dimerization interface [polypeptide binding]; other site 985080003685 active site 985080003686 quinolinate synthetase complex, A subunit; Region: nadA; TIGR00550 985080003687 phosphatidylserine decarboxylase; Provisional; Region: PRK03934 985080003688 prenyltransferase; Reviewed; Region: ubiA; PRK12874 985080003689 UbiA prenyltransferase family; Region: UbiA; pfam01040 985080003690 Predicted membrane metal-binding protein [General function prediction only]; Region: ComEC; COG0658 985080003691 Competence protein; Region: Competence; pfam03772 985080003692 replicative DNA helicase; Provisional; Region: PRK08506 985080003693 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 985080003694 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 985080003695 Walker A motif; other site 985080003696 ATP binding site [chemical binding]; other site 985080003697 Walker B motif; other site 985080003698 DNA binding loops [nucleotide binding] 985080003699 yjeF N-terminal region; Region: yjeF_nterm; TIGR00197 985080003700 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 985080003701 putative substrate binding site [chemical binding]; other site 985080003702 putative ATP binding site [chemical binding]; other site 985080003703 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 985080003704 His Kinase A (phospho-acceptor) domain; Region: HisKA; pfam00512 985080003705 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 985080003706 ATP binding site [chemical binding]; other site 985080003707 Mg2+ binding site [ion binding]; other site 985080003708 G-X-G motif; other site 985080003709 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 985080003710 DNA methylase; Region: N6_N4_Mtase; pfam01555 985080003711 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 985080003712 DNA methylase; Region: N6_N4_Mtase; pfam01555 985080003713 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 985080003714 DNA methylase; Region: N6_N4_Mtase; pfam01555 985080003715 DNA methylase; Region: N6_N4_Mtase; pfam01555 985080003716 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 985080003717 DEAD-like helicases superfamily; Region: DEXDc; smart00487 985080003718 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 985080003719 ATP binding site [chemical binding]; other site 985080003720 putative Mg++ binding site [ion binding]; other site 985080003721 Cell shape-determining protein [Cell envelope biogenesis, outer membrane]; Region: MreC; COG1792 985080003722 rod shape-determining protein MreC; Region: MreC; pfam04085 985080003723 rod shape-determining protein MreB; Provisional; Region: PRK13927 985080003724 MreB and similar proteins; Region: MreB_like; cd10225 985080003725 nucleotide binding site [chemical binding]; other site 985080003726 Mg binding site [ion binding]; other site 985080003727 putative protofilament interaction site [polypeptide binding]; other site 985080003728 RodZ interaction site [polypeptide binding]; other site 985080003729 endopeptidase Clp ATP-binding regulatory subunit (clpX); Region: clpX; TIGR00382 985080003730 ClpX C4-type zinc finger; Region: zf-C4_ClpX; smart00994 985080003731 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 985080003732 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 985080003733 Walker A motif; other site 985080003734 ATP binding site [chemical binding]; other site 985080003735 Walker B motif; other site 985080003736 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 985080003737 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 985080003738 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 985080003739 active site 985080003740 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 985080003741 flagellar assembly protein FliW; Provisional; Region: PRK13282 985080003742 DNA uptake lipoprotein [General function prediction only]; Region: ComL; COG4105 985080003743 ATP-dependent protease La; Region: lon; TIGR00763 985080003744 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 985080003745 Walker A motif; other site 985080003746 ATP binding site [chemical binding]; other site 985080003747 Walker B motif; other site 985080003748 arginine finger; other site 985080003749 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 985080003750 prephenate dehydrogenase; Validated; Region: PRK08507 985080003751 Prephenate dehydrogenase; Region: PDH; pfam02153 985080003752 DNA/RNA endonuclease G, NUC1 [Nucleotide transport and metabolism]; Region: NUC1; COG1864 985080003753 DNA/RNA non-specific endonuclease; Region: Endonuclease_NS; smart00892 985080003754 active site 985080003755 substrate binding site [chemical binding]; other site 985080003756 Mg2+ binding site [ion binding]; other site 985080003757 Type III restriction/modification enzyme methylation subunit; Region: TypeIII_RM_meth; pfam12564 985080003758 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 985080003759 DNA methylase; Region: N6_N4_Mtase; pfam01555 985080003760 DNA methylase; Region: N6_N4_Mtase; pfam01555 985080003761 potential frameshift: common BLAST hit: gi|15612362|ref|NP_224015.1| type III restriction enzyme 985080003762 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3421 985080003763 Type III restriction enzyme, res subunit; Region: ResIII; pfam04851 985080003764 ATP binding site [chemical binding]; other site 985080003765 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 985080003766 putative Mg++ binding site [ion binding]; other site 985080003767 biotin synthase; Provisional; Region: PRK08508 985080003768 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 985080003769 FeS/SAM binding site; other site 985080003770 Biotin and Thiamin Synthesis associated domain; Region: BATS; pfam06968 985080003771 YihY family inner membrane protein; Region: yihY_not_rbn; TIGR00765 985080003772 Uncharacterized conserved protein [Function unknown]; Region: COG1479 985080003773 Protein of unknown function DUF262; Region: DUF262; pfam03235 985080003774 Protein of unknown function DUF262; Region: DUF262; pfam03235 985080003775 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 985080003776 Single-stranded DNA-specific exonuclease [DNA replication, recombination, and repair]; Region: RecJ; COG0608 985080003777 DHH family; Region: DHH; pfam01368 985080003778 7-cyano-7-deazaguanine reductase; Region: QueF-II; TIGR03139 985080003779 Uncharacterized homolog of plant Iojap protein [Function unknown]; Region: COG0799 985080003780 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 985080003781 IPP transferase; Region: IPPT; pfam01715 985080003782 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 985080003783 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 985080003784 Ligand binding site; other site 985080003785 metal-binding site 985080003786 Adenine-specific methyltransferase EcoRI; Region: EcoRI_methylase; pfam13651 985080003787 Restriction endonuclease EcoRI; Region: EcoRI; pfam02963 985080003788 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13904 985080003789 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 985080003790 flagellar biosynthesis protein FliQ; Validated; Region: fliQ; PRK05700 985080003791 flagellum-specific ATP synthase; Validated; Region: fliI; PRK08472 985080003792 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 985080003793 Walker A motif/ATP binding site; other site 985080003794 Walker B motif; other site 985080003795 Type IV secretory pathway, VirB11 components, and related ATPases involved in archaeal flagella biosynthesis [Cell motility and secretion / Intracellular trafficking and secretion]; Region: VirB11; COG0630 985080003796 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 985080003797 ATP binding site [chemical binding]; other site 985080003798 Walker A motif; other site 985080003799 hexamer interface [polypeptide binding]; other site 985080003800 Walker B motif; other site 985080003801 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 985080003802 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 985080003803 active site 985080003804 HIGH motif; other site 985080003805 nucleotide binding site [chemical binding]; other site 985080003806 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 985080003807 active site 985080003808 KMSKS motif; other site 985080003809 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 985080003810 tRNA binding surface [nucleotide binding]; other site 985080003811 anticodon binding site; other site 985080003812 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 985080003813 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 985080003814 RNA binding surface [nucleotide binding]; other site 985080003815 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 985080003816 dimethyladenosine transferase; Region: ksgA; TIGR00755 985080003817 S-adenosylmethionine binding site [chemical binding]; other site 985080003818 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 985080003819 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 985080003820 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 985080003821 KpsF/GutQ family protein; Region: kpsF; TIGR00393 985080003822 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 985080003823 putative active site [active] 985080003824 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 985080003825 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK14462 985080003826 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 985080003827 FeS/SAM binding site; other site 985080003828 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 985080003829 active site 985080003830 carbon storage regulator; Provisional; Region: PRK00568 985080003831 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: PRK04181 985080003832 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 985080003833 SmpB-tmRNA interface; other site 985080003834 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; pfam01618 985080003835 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 985080003836 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 985080003837 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 985080003838 ribonuclease P protein component, eubacterial; Region: rnpA; TIGR00188 985080003839 hypothetical protein; Provisional; Region: PRK14374 985080003840 membrane protein insertase; Provisional; Region: PRK01318 985080003841 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 985080003842 Predicted RNA-binding protein [General function prediction only]; Region: Jag; COG1847 985080003843 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 985080003844 tRNA modification GTPase TrmE; Region: mnmE_trmE_thdF; TIGR00450 985080003845 Circularly permuted YlqF-related GTPases; Region: YlqF_related_GTPase; cl17249 985080003846 GTP/Mg2+ binding site [chemical binding]; other site 985080003847 G4 box; other site 985080003848 G5 box; other site 985080003849 trmE is a tRNA modification GTPase; Region: trmE; cd04164 985080003850 G1 box; other site 985080003851 G1 box; other site 985080003852 GTP/Mg2+ binding site [chemical binding]; other site 985080003853 Switch I region; other site 985080003854 Switch I region; other site 985080003855 G2 box; other site 985080003856 G2 box; other site 985080003857 Switch II region; other site 985080003858 G3 box; other site 985080003859 G3 box; other site 985080003860 Switch II region; other site 985080003861 G4 box; other site 985080003862 G5 box; other site 985080003863 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 985080003864 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 985080003865 LPP20 lipoprotein; Region: LPP20; pfam02169 985080003866 Collagen-binding surface adhesin SpaP (antigen I/II family) [General function prediction only]; Region: FlgN; COG3417 985080003867 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 985080003868 catalytic residues [active] 985080003869 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 985080003870 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 985080003871 RNA binding surface [nucleotide binding]; other site 985080003872 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 985080003873 active site 985080003874 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE3; Region: PHP_PolIIIA_DnaE3; cd12113 985080003875 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 985080003876 active site 985080003877 PHP Thumb interface [polypeptide binding]; other site 985080003878 metal binding site [ion binding]; metal-binding site 985080003879 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 985080003880 generic binding surface I; other site 985080003881 generic binding surface II; other site 985080003882 Cytochrome c peroxidase [Inorganic ion transport and metabolism]; Region: MauG; COG1858 985080003883 Heat shock protein [Posttranslational modification, protein turnover, chaperones]; Region: HslJ; COG3187 985080003884 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 985080003885 mce related protein; Region: MCE; pfam02470 985080003886 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 985080003887 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 985080003888 Walker A/P-loop; other site 985080003889 ATP binding site [chemical binding]; other site 985080003890 Q-loop/lid; other site 985080003891 ABC transporter signature motif; other site 985080003892 Walker B; other site 985080003893 D-loop; other site 985080003894 H-loop/switch region; other site 985080003895 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 985080003896 conserved hypothetical integral membrane protein; Region: TIGR00056 985080003897 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 985080003898 branched-chain amino acid aminotransferase; Provisional; Region: PRK13357 985080003899 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 985080003900 homodimer interface [polypeptide binding]; other site 985080003901 substrate-cofactor binding pocket; other site 985080003902 catalytic residue [active] 985080003903 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 985080003904 DNA polymerase I; Region: pola; TIGR00593 985080003905 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 985080003906 active site 985080003907 metal binding site 1 [ion binding]; metal-binding site 985080003908 putative 5' ssDNA interaction site; other site 985080003909 metal binding site 3; metal-binding site 985080003910 metal binding site 2 [ion binding]; metal-binding site 985080003911 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 985080003912 putative DNA binding site [nucleotide binding]; other site 985080003913 putative metal binding site [ion binding]; other site 985080003914 3'-5' exonuclease; Region: 35EXOc; smart00474 985080003915 active site 985080003916 substrate binding site [chemical binding]; other site 985080003917 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 985080003918 active site 985080003919 DNA binding site [nucleotide binding] 985080003920 catalytic site [active] 985080003921 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 985080003922 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 985080003923 potential frameshift: common BLAST hit: gi|15612430|ref|NP_224083.1| type II DNA modification enzyme 985080003924 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 985080003925 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 985080003926 thymidylate kinase; Validated; Region: tmk; PRK00698 985080003927 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 985080003928 TMP-binding site; other site 985080003929 ATP-binding site [chemical binding]; other site 985080003930 Phosphopantetheine adenylyltransferase [Coenzyme metabolism]; Region: CoaD; COG0669 985080003931 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 985080003932 active site 985080003933 (T/H)XGH motif; other site 985080003934 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Provisional; Region: PRK06029 985080003935 Flavoprotein; Region: Flavoprotein; pfam02441 985080003936 flagellar basal body P-ring biosynthesis protein FlgA; Reviewed; Region: flgA; PRK08515 985080003937 flagella basal body P-ring formation protein FlgA; Region: flgA_cterm; TIGR03170 985080003938 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 985080003939 Part of AAA domain; Region: AAA_19; pfam13245 985080003940 Family description; Region: UvrD_C_2; pfam13538 985080003941 TPR repeat; Region: TPR_11; pfam13414 985080003942 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 985080003943 TPR motif; other site 985080003944 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 985080003945 binding surface 985080003946 TPR motif; other site 985080003947 seryl-tRNA synthetase; Provisional; Region: PRK05431 985080003948 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 985080003949 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 985080003950 dimer interface [polypeptide binding]; other site 985080003951 active site 985080003952 motif 1; other site 985080003953 motif 2; other site 985080003954 motif 3; other site 985080003955 Predicted amidohydrolase [General function prediction only]; Region: COG0388 985080003956 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cd07197 985080003957 active site 985080003958 catalytic triad [active] 985080003959 dimer interface [polypeptide binding]; other site 985080003960 Exonuclease VII small subunit; Region: Exonuc_VII_S; cl00750 985080003961 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 985080003962 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 985080003963 S-adenosylmethionine binding site [chemical binding]; other site 985080003964 Uncharacterized protein family (UPF0093); Region: UPF0093; cl00863 985080003965 uncharacterized protein, YigZ family; Region: IMPACT_YIGZ; TIGR00257 985080003966 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 985080003967 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 985080003968 ABC-2 type transporter; Region: ABC2_membrane; cl17235 985080003969 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 985080003970 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 985080003971 HlyD family secretion protein; Region: HlyD_3; pfam13437 985080003972 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 985080003973 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 985080003974 Domain of unknown function DUF21; Region: DUF21; pfam01595 985080003975 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 985080003976 Transporter associated domain; Region: CorC_HlyC; smart01091 985080003977 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 985080003978 Phosphate transporter family; Region: PHO4; pfam01384 985080003979 NifU-like domain; Region: NifU; pfam01106 985080003980 UDP-N-acetylmuramyl-tripeptide synthetase; Region: murE; TIGR01085 985080003981 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 985080003982 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 985080003983 Transaldolase-like proteins from plants and bacteria; Region: Transaldolase_like; cd00955 985080003984 putative active site [active] 985080003985 transaldolase; Provisional; Region: PRK03903 985080003986 catalytic residue [active] 985080003987 ribosomal protein L25, Ctc-form; Region: ctc_TL5; TIGR00731 985080003988 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 985080003989 5S rRNA interface [nucleotide binding]; other site 985080003990 CTC domain interface [polypeptide binding]; other site 985080003991 L16 interface [polypeptide binding]; other site 985080003992 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 985080003993 putative active site [active] 985080003994 catalytic residue [active] 985080003995 Predicted permeases [General function prediction only]; Region: COG0795 985080003996 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 985080003997 Catalytic domain of type II restriction endonucleases BfiI and NgoFVII, and uncharacterized proteins with a DEAD domain; Region: PLDc_Bfil_DEXD_like; cd09117 985080003998 PLD-like domain; Region: PLDc_2; pfam13091 985080003999 homodimer interface [polypeptide binding]; other site 985080004000 putative active site [active] 985080004001 catalytic site [active] 985080004002 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 985080004003 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3399 985080004004 Putative metal-binding domain of cation transport ATPase; Region: ATPase-cat_bd; pfam12156 985080004005 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 985080004006 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 985080004007 metal-binding site [ion binding] 985080004008 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 985080004009 Soluble P-type ATPase [General function prediction only]; Region: COG4087 985080004010 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 985080004011 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 985080004012 S-adenosylmethionine binding site [chemical binding]; other site 985080004013 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 985080004014 catalytic motif [active] 985080004015 Zn binding site [ion binding]; other site 985080004016 Pyrimidine reductase, riboflavin biosynthesis [Coenzyme metabolism]; Region: RibD; COG1985 985080004017 RibD C-terminal domain; Region: RibD_C; cl17279 985080004018 sodium--glutamate symport carrier (gltS); Region: gltS; TIGR00210 985080004019 Saccharopine dehydrogenase and related proteins [Amino acid transport and metabolism]; Region: LYS9; COG1748 985080004020 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 985080004021 4Fe-4S binding domain; Region: Fer4_5; pfam12801 985080004022 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 985080004023 acyl-phosphate glycerol 3-phosphate acyltransferase; Region: TIGR00023 985080004024 FolB domain; Region: folB_dom; TIGR00526 985080004025 active site 985080004026 TonB-dependent Receptor Plug Domain; Region: Plug; cl08461 985080004027 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 985080004028 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 985080004029 Selenocysteine synthase [seryl-tRNASer selenium transferase] [Amino acid transport and metabolism]; Region: SelA; COG1921 985080004030 L-seryl-tRNA selenium transferase; Region: SelA; pfam03841 985080004031 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 985080004032 transcription elongation factor NusA; Provisional; Region: nusA; PRK12328 985080004033 NusA N-terminal domain; Region: NusA_N; pfam08529 985080004034 S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three...; Region: S1_NusA; cd04455 985080004035 RNA binding site [nucleotide binding]; other site 985080004036 homodimer interface [polypeptide binding]; other site 985080004037 NusA-like KH domain; Region: KH_5; pfam13184 985080004038 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 985080004039 G-X-X-G motif; other site 985080004040 Type II restriction enzyme, methylase subunits [Defense mechanisms]; Region: COG1002 985080004041 Eco57I restriction-modification methylase; Region: Eco57I; pfam07669 985080004042 TaqI-like C-terminal specificity domain; Region: TaqI_C; pfam12950 985080004043 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 985080004044 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 985080004045 DNA methylase; Region: N6_N4_Mtase; pfam01555 985080004046 ATP-dependent DNA helicase RecG; Region: recG; TIGR00643 985080004047 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 985080004048 ssDNA binding site; other site 985080004049 generic binding surface II; other site 985080004050 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 985080004051 ATP binding site [chemical binding]; other site 985080004052 putative Mg++ binding site [ion binding]; other site 985080004053 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 985080004054 nucleotide binding region [chemical binding]; other site 985080004055 ATP-binding site [chemical binding]; other site 985080004056 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 985080004057 Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Ape1-like_AP-endo; cd09087 985080004058 active site 985080004059 putative catalytic site [active] 985080004060 DNA binding site [nucleotide binding] 985080004061 putative phosphate binding site [ion binding]; other site 985080004062 metal binding site A [ion binding]; metal-binding site 985080004063 AP binding site [nucleotide binding]; other site 985080004064 metal binding site B [ion binding]; metal-binding site 985080004065 chromosomal replication initiator protein DnaA; Region: DnaA; TIGR00362 985080004066 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 985080004067 Walker A motif; other site 985080004068 ATP binding site [chemical binding]; other site 985080004069 Walker B motif; other site 985080004070 arginine finger; other site 985080004071 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 985080004072 DnaA box-binding interface [nucleotide binding]; other site 985080004073 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 985080004074 Protein of unknown function (DUF2443); Region: DUF2443; pfam10398 985080004075 glucosamine--fructose-6-phosphate aminotransferase (isomerizing); Region: glmS; TIGR01135 985080004076 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 985080004077 glutaminase active site [active] 985080004078 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 985080004079 dimer interface [polypeptide binding]; other site 985080004080 active site 985080004081 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 985080004082 dimer interface [polypeptide binding]; other site 985080004083 active site 985080004084 Predicted alternative thymidylate synthase [Nucleotide transport and metabolism]; Region: THY1; COG1351 985080004085 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 985080004086 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 985080004087 potential frameshift: common BLAST hit: gi|254780040|ref|YP_003058147.1| type I restriction-modification enzyme subunit M 985080004088 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 985080004089 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 985080004090 HsdM N-terminal domain; Region: HsdM_N; pfam12161 985080004091 type I site-specific deoxyribonuclease, HsdR family; Region: hsdR; TIGR00348 985080004092 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 985080004093 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 985080004094 ATP binding site [chemical binding]; other site 985080004095 putative Mg++ binding site [ion binding]; other site 985080004096 Protein of unknown function DUF45; Region: DUF45; pfam01863 985080004097 Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]; Region: FecA; COG4772 985080004098 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 985080004099 N-terminal plug; other site 985080004100 ligand-binding site [chemical binding]; other site 985080004101 Arginase family; Region: Arginase; cd09989 985080004102 active site 985080004103 Mn binding site [ion binding]; other site 985080004104 oligomer interface [polypeptide binding]; other site 985080004105 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 985080004106 Alanine dehydrogenase NAD-binding and catalytic domains; Region: L-AlaDH; cd05305 985080004107 hexamer interface [polypeptide binding]; other site 985080004108 ligand binding site [chemical binding]; other site 985080004109 putative active site [active] 985080004110 NAD(P) binding site [chemical binding]; other site 985080004111 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 985080004112 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD1; cd05283 985080004113 putative NAD(P) binding site [chemical binding]; other site 985080004114 putative substrate binding site [chemical binding]; other site 985080004115 catalytic Zn binding site [ion binding]; other site 985080004116 structural Zn binding site [ion binding]; other site 985080004117 dimer interface [polypeptide binding]; other site 985080004118 Protein of unknown function DUF262; Region: DUF262; pfam03235 985080004119 Uncharacterized conserved protein [Function unknown]; Region: COG1479 985080004120 Protein of unknown function DUF262; Region: DUF262; pfam03235 985080004121 Uncharacterized conserved protein [Function unknown]; Region: COG1479 985080004122 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 985080004123 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 985080004124 NAD kinase [Coenzyme metabolism]; Region: nadF; COG0061 985080004125 ATP-NAD kinase; Region: NAD_kinase; pfam01513 985080004126 Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]; Region: COG1293 985080004127 Domain of unknown function (DUF814); Region: DUF814; pfam05670 985080004128 Transposase IS200 like; Region: Y1_Tnp; pfam01797 985080004129 potential frameshift: common BLAST hit: gi|15611893|ref|NP_223544.1| IS606 transposase 985080004130 Helix-turn-helix domain; Region: HTH_OrfB_IS605; pfam12323 985080004131 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 985080004132 Probable transposase; Region: OrfB_IS605; pfam01385 985080004133 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 985080004134 DNA polymerase III subunit epsilon; Provisional; Region: PRK08517 985080004135 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 985080004136 active site 985080004137 catalytic site [active] 985080004138 substrate binding site [chemical binding]; other site 985080004139 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 985080004140 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 985080004141 substrate binding site [chemical binding]; other site 985080004142 hexamer interface [polypeptide binding]; other site 985080004143 metal binding site [ion binding]; metal-binding site 985080004144 FIG, FBPase/IMPase/glpX-like domain. A superfamily of metal-dependent phosphatases with various substrates. Fructose-1,6-bisphospatase (both the major and the glpX-encoded variant) hydrolyze fructose-1,6,-bisphosphate to fructose-6-phosphate in...; Region: FIG; cl00289 985080004145 active site 985080004146 Methyltransferase domain; Region: Methyltransf_26; pfam13659 985080004147 Response regulator receiver domain; Region: Response_reg; pfam00072 985080004148 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 985080004149 active site 985080004150 phosphorylation site [posttranslational modification] 985080004151 intermolecular recognition site; other site 985080004152 dimerization interface [polypeptide binding]; other site 985080004153 Transcriptional regulatory protein, C terminal; Region: Trans_reg_C; pfam00486 985080004154 DNA binding site [nucleotide binding] 985080004155 elongation factor Ts; Provisional; Region: tsf; PRK09377 985080004156 UBA/TS-N domain; Region: UBA; pfam00627 985080004157 Elongation factor TS; Region: EF_TS; pfam00889 985080004158 Elongation factor TS; Region: EF_TS; pfam00889 985080004159 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 985080004160 rRNA interaction site [nucleotide binding]; other site 985080004161 S8 interaction site; other site 985080004162 putative laminin-1 binding site; other site 985080004163 putative recombination protein RecB; Provisional; Region: PRK13909 985080004164 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 985080004165 pH-dependent sodium/proton antiporter; Provisional; Region: nhaA; PRK14856 985080004166 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 985080004167 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 985080004168 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 985080004169 protein-export membrane protein SecF; Region: 3a0501s07; TIGR00966 985080004170 Protein export membrane protein; Region: SecD_SecF; pfam02355 985080004171 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 985080004172 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 985080004173 HIGH motif; other site 985080004174 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 985080004175 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 985080004176 active site 985080004177 KMSKS motif; other site 985080004178 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 985080004179 tRNA binding surface [nucleotide binding]; other site 985080004180 anticodon binding site; other site 985080004181 Lipopolysaccharide-assembly; Region: LptE; pfam04390 985080004182 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 985080004183 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 985080004184 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 985080004185 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 985080004186 Peptidase family M23; Region: Peptidase_M23; pfam01551 985080004187 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 985080004188 Peptidase family M23; Region: Peptidase_M23; pfam01551 985080004189 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 985080004190 transcription-repair coupling factor (mfd); Region: mfd; TIGR00580 985080004191 CarD-like/TRCF domain; Region: CarD_CdnL_TRCF; pfam02559 985080004192 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 985080004193 ATP binding site [chemical binding]; other site 985080004194 putative Mg++ binding site [ion binding]; other site 985080004195 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 985080004196 nucleotide binding region [chemical binding]; other site 985080004197 ATP-binding site [chemical binding]; other site 985080004198 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 985080004199 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 985080004200 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 985080004201 [2Fe-2S] cluster binding site [ion binding]; other site 985080004202 Cytochrome b subunit of the bc complex [Energy production and conversion]; Region: QcrB; COG1290 985080004203 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 985080004204 intrachain domain interface; other site 985080004205 interchain domain interface [polypeptide binding]; other site 985080004206 heme bH binding site [chemical binding]; other site 985080004207 Qi binding site; other site 985080004208 heme bL binding site [chemical binding]; other site 985080004209 Qo binding site; other site 985080004210 interchain domain interface [polypeptide binding]; other site 985080004211 intrachain domain interface; other site 985080004212 Qi binding site; other site 985080004213 Cytochrome b(C-terminal)/b6/petD; Region: Cytochrom_B_C; pfam00032 985080004214 Qo binding site; other site 985080004215 Cytochrome c1 [Energy production and conversion]; Region: CYT1; COG2857 985080004216 Cytochrome c; Region: Cytochrom_C; pfam00034 985080004217 Cytochrome c; Region: Cytochrom_C; cl11414 985080004218 potential frameshift: common BLAST hit: gi|315454048|ref|YP_004074318.1| sulfatase 985080004219 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 985080004220 Sulfatase; Region: Sulfatase; cl17466 985080004221 Sulfatase; Region: Sulfatase; cl17466 985080004222 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 985080004223 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 985080004224 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 985080004225 flagellar hook-basal body protein FliE; Reviewed; Region: fliE; PRK03907 985080004226 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 985080004227 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 985080004228 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK05680 985080004229 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK07182 985080004230 Cell cycle protein; Region: FTSW_RODA_SPOVE; pfam01098 985080004231 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 985080004232 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 985080004233 intersubunit interface [polypeptide binding]; other site 985080004234 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 985080004235 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 985080004236 intersubunit interface [polypeptide binding]; other site 985080004237 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 985080004238 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 985080004239 dimer interface [polypeptide binding]; other site 985080004240 decamer (pentamer of dimers) interface [polypeptide binding]; other site 985080004241 catalytic triad [active] 985080004242 peroxidatic and resolving cysteines [active] 985080004243 ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]; Region: NlpA; COG1464 985080004244 NLPA lipoprotein; Region: Lipoprotein_9; pfam03180 985080004245 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 985080004246 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 985080004247 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 985080004248 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 985080004249 G1 box; other site 985080004250 GTP/Mg2+ binding site [chemical binding]; other site 985080004251 Switch I region; other site 985080004252 G2 box; other site 985080004253 G3 box; other site 985080004254 Switch II region; other site 985080004255 G4 box; other site 985080004256 G5 box; other site 985080004257 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1934 985080004258 OstA-like protein; Region: OstA; pfam03968 985080004259 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 985080004260 motif II; other site 985080004261 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 985080004262 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 985080004263 Sporulation related domain; Region: SPOR; pfam05036 985080004264 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 985080004265 N-acetyl-D-glucosamine binding site [chemical binding]; other site 985080004266 catalytic residue [active] 985080004267 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 985080004268 Predicted metal-dependent hydrolases with the TIM-barrel fold [General function prediction only]; Region: COG1099 985080004269 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 985080004270 active site 985080004271 riboflavin synthase, alpha subunit; Region: ribE; TIGR00187 985080004272 Lumazine binding domain; Region: Lum_binding; pfam00677 985080004273 Lumazine binding domain; Region: Lum_binding; pfam00677 985080004274 flhB C-terminus-related protein; Region: flhB_rel; TIGR00789 985080004275 ABC-type metal ion transport system, permease component [Inorganic ion transport and metabolism]; Region: AbcD; COG2011 985080004276 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 985080004277 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 985080004278 active site 985080004279 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 985080004280 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 985080004281 Mg++ binding site [ion binding]; other site 985080004282 putative catalytic motif [active] 985080004283 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 985080004284 active site 985080004285 hydrophilic channel; other site 985080004286 dimerization interface [polypeptide binding]; other site 985080004287 catalytic residues [active] 985080004288 active site lid [active] 985080004289 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 985080004290 4-hydroxythreonine-4-phosphate dehydrogenase; Provisional; Region: pdxA; PRK03946 985080004291 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 985080004292 metallohydrolase, glycoprotease/Kae1 family; Region: gcp_kae1; TIGR00329 985080004293 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 985080004294 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 985080004295 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 985080004296 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4735 985080004297 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4735 985080004298 Domain of unknown function (DUF3944); Region: DUF3944; pfam13099 985080004299 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4735