-- dump date 20140619_113538 -- class Genbank::misc_feature -- table misc_feature_note -- id note 85963000001 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 85963000002 putative RNA binding site [nucleotide binding]; other site 85963000003 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 85963000004 homopentamer interface [polypeptide binding]; other site 85963000005 active site 85963000006 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 85963000007 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 85963000008 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 85963000009 active site clefts [active] 85963000010 zinc binding site [ion binding]; other site 85963000011 dimer interface [polypeptide binding]; other site 85963000012 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 85963000013 active site 85963000014 dimer interface [polypeptide binding]; other site 85963000015 pantoate--beta-alanine ligase; Region: panC; TIGR00018 85963000016 Pantoate-beta-alanine ligase; Region: PanC; cd00560 85963000017 active site 85963000018 ATP-binding site [chemical binding]; other site 85963000019 pantoate-binding site; other site 85963000020 HXXH motif; other site 85963000021 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963000022 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 85963000023 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 85963000024 ring oligomerisation interface [polypeptide binding]; other site 85963000025 ATP/Mg binding site [chemical binding]; other site 85963000026 stacking interactions; other site 85963000027 hinge regions; other site 85963000028 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 85963000029 oligomerisation interface [polypeptide binding]; other site 85963000030 mobile loop; other site 85963000031 roof hairpin; other site 85963000032 DNA primase, catalytic core; Region: dnaG; TIGR01391 85963000033 CHC2 zinc finger; Region: zf-CHC2; pfam01807 85963000034 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 85963000035 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 85963000036 active site 85963000037 metal binding site [ion binding]; metal-binding site 85963000038 interdomain interaction site; other site 85963000039 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 85963000040 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 85963000041 Ligand Binding Site [chemical binding]; other site 85963000042 TrbC/VIRB2 family; Region: TrbC; cl01583 85963000043 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 85963000044 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 85963000045 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 85963000046 Walker A motif; other site 85963000047 ATP binding site [chemical binding]; other site 85963000048 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 85963000049 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3014 85963000050 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 85963000051 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 85963000052 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 85963000053 active site 85963000054 phosphorylation site [posttranslational modification] 85963000055 intermolecular recognition site; other site 85963000056 dimerization interface [polypeptide binding]; other site 85963000057 carboxynorspermidine decarboxylase; Region: nspC; TIGR01047 85963000058 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Carboxynorspermidine Decarboxylase; Region: PLPDE_III_CANSDC; cd06829 85963000059 dimer interface [polypeptide binding]; other site 85963000060 active site 85963000061 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 85963000062 catalytic residues [active] 85963000063 substrate binding site [chemical binding]; other site 85963000064 lipid A 1-phosphatase; Reviewed; Region: PRK09597 85963000065 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 85963000066 active site 85963000067 lipid A phosphoethanolamine transferase; Reviewed; Region: PRK09598 85963000068 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 85963000069 Sulfatase; Region: Sulfatase; pfam00884 85963000070 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963000071 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 85963000072 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 85963000073 dimer interface [polypeptide binding]; other site 85963000074 active site 85963000075 citrylCoA binding site [chemical binding]; other site 85963000076 NADH binding [chemical binding]; other site 85963000077 cationic pore residues; other site 85963000078 oxalacetate/citrate binding site [chemical binding]; other site 85963000079 coenzyme A binding site [chemical binding]; other site 85963000080 catalytic triad [active] 85963000081 isocitrate dehydrogenase; Validated; Region: PRK07362 85963000082 isocitrate dehydrogenase; Reviewed; Region: PRK07006 85963000083 Protein of unknown function (DUF1523); Region: DUF1523; pfam07509 85963000084 Dethiobiotin synthetase [Coenzyme metabolism]; Region: BioD; COG0132 85963000085 AAA domain; Region: AAA_26; pfam13500 85963000086 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 85963000087 Ligand Binding Site [chemical binding]; other site 85963000088 Uncharacterized conserved protein [Function unknown]; Region: COG2127 85963000089 ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]; Region: clpA; COG0542 85963000090 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 85963000091 Walker A motif; other site 85963000092 ATP binding site [chemical binding]; other site 85963000093 Walker B motif; other site 85963000094 arginine finger; other site 85963000095 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 85963000096 Walker A motif; other site 85963000097 ATP binding site [chemical binding]; other site 85963000098 Walker B motif; other site 85963000099 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 85963000100 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 85963000101 tetramerization interface [polypeptide binding]; other site 85963000102 active site 85963000103 hypothetical protein; Provisional; Region: PRK03762 85963000104 PDZ domain; Region: PDZ_2; pfam13180 85963000105 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 85963000106 Type IV secretory pathway, TrbL components [Intracellular trafficking and secretion]; Region: TrbL; COG3846 85963000107 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 85963000108 Type IV secretory pathway, VirB9 components [Intracellular trafficking and secretion]; Region: VirB9; COG3504 85963000109 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 85963000110 VirB7 interaction site; other site 85963000111 Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion]; Region: VirB10; COG2948 85963000112 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 85963000113 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 85963000114 Substrate binding site; other site 85963000115 Cupin domain; Region: Cupin_2; cl17218 85963000116 GDP-mannose 4,6-dehydratase; Region: gmd; TIGR01472 85963000117 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 85963000118 NADP-binding site; other site 85963000119 homotetramer interface [polypeptide binding]; other site 85963000120 substrate binding site [chemical binding]; other site 85963000121 homodimer interface [polypeptide binding]; other site 85963000122 active site 85963000123 GDP-fucose synthetase, extended (e) SDRs; Region: GDP_FS_SDR_e; cd05239 85963000124 GDP-4-keto-6-deoxymannose-3, 5-epimerase-4-reductase; Region: PLN02725 85963000125 NADP binding site [chemical binding]; other site 85963000126 active site 85963000127 putative substrate binding site [chemical binding]; other site 85963000128 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 85963000129 dimerization interface [polypeptide binding]; other site 85963000130 hydrogenase expression/formation protein HypE; Region: hypE; TIGR02124 85963000131 ATP binding site [chemical binding]; other site 85963000132 Acylphosphatase; Region: Acylphosphatase; pfam00708 85963000133 [NiFe] hydrogenase maturation protein HypF; Region: hypF; TIGR00143 85963000134 HypF finger; Region: zf-HYPF; pfam07503 85963000135 HypF finger; Region: zf-HYPF; pfam07503 85963000136 Telomere recombination; Region: Sua5_yciO_yrdC; pfam01300 85963000137 Peptidylarginine deiminase and related enzymes [Amino acid transport and metabolism]; Region: COG2957 85963000138 Porphyromonas-type peptidyl-arginine deiminase; Region: PAD_porph; pfam04371 85963000139 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 85963000140 DNA methylase; Region: N6_N4_Mtase; pfam01555 85963000141 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 85963000142 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 85963000143 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 85963000144 DNA methylase; Region: N6_N4_Mtase; pfam01555 85963000145 Tsp45I type II restriction enzyme; Region: Tsp45I; pfam06300 85963000146 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 85963000147 Na(+)/proline cotransporter PutP and related proteins; solute binding domain; Region: SLC5sbd_PutP; cd11475 85963000148 Na binding site [ion binding]; other site 85963000149 Proline dehydrogenase; Region: Pro_dh; pfam01619 85963000150 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 85963000151 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 85963000152 Glutamate binding site [chemical binding]; other site 85963000153 NAD binding site [chemical binding]; other site 85963000154 catalytic residues [active] 85963000155 integrating conjugative element protein, PFL_4705 family; Region: conj_TIGR03752 85963000156 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 85963000157 Proteins of 100 residues with WXG; Region: WXG100; pfam06013 85963000158 A nuclease of the HNH/ENDO VII superfamily with conserved WHH; Region: WHH; pfam14414 85963000159 SMI1 / KNR4 family (SUKH-1); Region: SMI1_KNR4; pfam09346 85963000160 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 85963000161 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 85963000162 Urease accessory protein UreH [Posttranslational modification, protein turnover, chaperones]; Region: UreH; COG0829 85963000163 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cd00882 85963000164 G1 box; other site 85963000165 GTP/Mg2+ binding site [chemical binding]; other site 85963000166 G2 box; other site 85963000167 Switch I region; other site 85963000168 G3 box; other site 85963000169 Switch II region; other site 85963000170 G4 box; other site 85963000171 G5 box; other site 85963000172 Urease accessory protein UreF [Posttranslational modification, protein turnover, chaperones]; Region: UreF; COG0830 85963000173 UreF; Region: UreF; pfam01730 85963000174 urease accessory protein UreE; Provisional; Region: ureE; PRK13261 85963000175 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 85963000176 dimer interface [polypeptide binding]; other site 85963000177 catalytic residues [active] 85963000178 AmiS/UreI family transporter; Region: AmiS_UreI; pfam02293 85963000179 urease subunit beta; Provisional; Region: ureB; PRK13985 85963000180 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 85963000181 subunit interactions [polypeptide binding]; other site 85963000182 active site 85963000183 flap region; other site 85963000184 urease subunit alpha; Provisional; Region: PRK13986 85963000185 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 85963000186 alpha-gamma subunit interface [polypeptide binding]; other site 85963000187 beta-gamma subunit interface [polypeptide binding]; other site 85963000188 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 85963000189 gamma-beta subunit interface [polypeptide binding]; other site 85963000190 alpha-beta subunit interface [polypeptide binding]; other site 85963000191 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 85963000192 phosphoglucosamine mutase; Provisional; Region: glmM; PRK14324 85963000193 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 85963000194 active site 85963000195 substrate binding site [chemical binding]; other site 85963000196 metal binding site [ion binding]; metal-binding site 85963000197 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 85963000198 peptide chain release factor 1; Validated; Region: prfA; PRK00591 85963000199 This domain is found in peptide chain release factors; Region: PCRF; smart00937 85963000200 RF-1 domain; Region: RF-1; pfam00472 85963000201 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963000202 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 85963000203 dimer interface [polypeptide binding]; other site 85963000204 putative CheW interface [polypeptide binding]; other site 85963000205 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 85963000206 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 85963000207 23S rRNA interface [nucleotide binding]; other site 85963000208 L3 interface [polypeptide binding]; other site 85963000209 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl17341 85963000210 Predicted dehydrogenase [General function prediction only]; Region: COG0579 85963000211 NLPC_P60 stabilising domain, N term; Region: N_NLPC_P60; pfam12912 85963000212 SH3 domain of the SH3b1 type; Region: SH3_6; pfam12913 85963000213 SH3 domain of SH3b2 type; Region: SH3_7; pfam12914 85963000214 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 85963000215 NlpC/P60 family; Region: NLPC_P60; pfam00877 85963000216 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 85963000217 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 85963000218 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 85963000219 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 85963000220 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 85963000221 DNA binding residues [nucleotide binding] 85963000222 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Validated; Region: PRK05584 85963000223 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Region: MTA/SAH-Nsdase; TIGR01704 85963000224 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 85963000225 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 85963000226 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 85963000227 Methyltransferase domain; Region: Methyltransf_26; pfam13659 85963000228 DNA methylase; Region: N6_N4_Mtase; pfam01555 85963000229 Alpha-1,2-fucosyltransferase; Region: Fut1_Fut2_like; cd11301 85963000230 Glycosyl transferase family 11; Region: Glyco_transf_11; pfam01531 85963000231 GDP-Fucose binding site [chemical binding]; other site 85963000232 2-hydroxyacid dehydrogenase; Provisional; Region: PRK08410 85963000233 Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; Region: FDH_GDH_like; cl17240 85963000234 NAD binding site [chemical binding]; other site 85963000235 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 85963000236 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 85963000237 pyridoxal 5'-phosphate binding site [chemical binding]; other site 85963000238 catalytic residue [active] 85963000239 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 85963000240 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 85963000241 dimer interface [polypeptide binding]; other site 85963000242 putative CheW interface [polypeptide binding]; other site 85963000243 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 85963000244 Ligand Binding Site [chemical binding]; other site 85963000245 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963000246 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 85963000247 WfgS and WfeV are involved in O-antigen biosynthesis; Region: GT_2_WfgS_like; cd06433 85963000248 metal-binding site 85963000249 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 85963000250 HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain; Region: HAMP; smart00304 85963000251 dimerization interface [polypeptide binding]; other site 85963000252 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 85963000253 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 85963000254 dimer interface [polypeptide binding]; other site 85963000255 putative CheW interface [polypeptide binding]; other site 85963000256 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases [Nucleotide transport and metabolism]; Region: UshA; COG0737 85963000257 Escherichia coli CpdB and related proteins, N-terminal metallophosphatase domain; Region: MPP_CpdB_N; cd07410 85963000258 active site 85963000259 metal binding site [ion binding]; metal-binding site 85963000260 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 85963000261 S-Ribosylhomocysteinase (LuxS); Region: LuxS; pfam02664 85963000262 cystathionine gamma-synthase/cystathionine beta-lyase; Validated; Region: PRK06176 85963000263 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 85963000264 homodimer interface [polypeptide binding]; other site 85963000265 substrate-cofactor binding pocket; other site 85963000266 pyridoxal 5'-phosphate binding site [chemical binding]; other site 85963000267 catalytic residue [active] 85963000268 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 85963000269 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 85963000270 dimer interface [polypeptide binding]; other site 85963000271 pyridoxal 5'-phosphate binding site [chemical binding]; other site 85963000272 catalytic residue [active] 85963000273 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 85963000274 Nucleotide-binding domain of human HSPA9 and similar proteins; Region: HSPA9-Ssq1-like_NBD; cd10234 85963000275 nucleotide binding site [chemical binding]; other site 85963000276 NEF interaction site [polypeptide binding]; other site 85963000277 SBD interface [polypeptide binding]; other site 85963000278 GrpE; Region: GrpE; pfam01025 85963000279 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 85963000280 dimer interface [polypeptide binding]; other site 85963000281 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 85963000282 heat-inducible transcription repressor; Provisional; Region: PRK03911 85963000283 hypothetical protein; Provisional; Region: PRK05834 85963000284 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2604 85963000285 flagellin B; Provisional; Region: PRK13588 85963000286 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 85963000287 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 85963000288 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 85963000289 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 85963000290 DNA topoisomerase I; Validated; Region: PRK05582 85963000291 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 85963000292 active site 85963000293 interdomain interaction site; other site 85963000294 putative metal-binding site [ion binding]; other site 85963000295 nucleotide binding site [chemical binding]; other site 85963000296 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 85963000297 domain I; other site 85963000298 DNA binding groove [nucleotide binding] 85963000299 phosphate binding site [ion binding]; other site 85963000300 domain II; other site 85963000301 domain III; other site 85963000302 nucleotide binding site [chemical binding]; other site 85963000303 catalytic site [active] 85963000304 domain IV; other site 85963000305 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 85963000306 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 85963000307 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 85963000308 Fe-S oxidoreductases [Energy production and conversion]; Region: COG0731 85963000309 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 85963000310 FeS/SAM binding site; other site 85963000311 Helicobacter pylori protein of unknown function (DUF874); Region: DUF874; pfam05917 85963000312 phosphoenolpyruvate synthase; Validated; Region: PRK06464 85963000313 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 85963000314 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 85963000315 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 85963000316 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK12305 85963000317 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; pfam07973 85963000318 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 85963000319 active site 85963000320 dimer interface [polypeptide binding]; other site 85963000321 motif 1; other site 85963000322 motif 2; other site 85963000323 motif 3; other site 85963000324 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 85963000325 anticodon binding site; other site 85963000326 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 85963000327 translation initiation factor IF-3; Region: infC; TIGR00168 85963000328 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 85963000329 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 85963000330 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 85963000331 23S rRNA binding site [nucleotide binding]; other site 85963000332 L21 binding site [polypeptide binding]; other site 85963000333 L13 binding site [polypeptide binding]; other site 85963000334 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963000335 Protein of unknown function (DUF1104); Region: DUF1104; pfam06518 85963000336 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 85963000337 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 85963000338 Serine dehydratase alpha chain; Region: SDH_alpha; pfam03313 85963000339 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 85963000340 serine transporter; Region: stp; TIGR00814 85963000341 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase [Amino acid transport and metabolism]; Region: AroG; COG3200 85963000342 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 85963000343 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 85963000344 catalytic triad [active] 85963000345 Uncharacterized conserved protein [Function unknown]; Region: COG1556 85963000346 iron-sulfur cluster-binding protein; Region: TIGR00273 85963000347 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 85963000348 Domain of unknown function (DUF3390); Region: DUF3390; pfam11870 85963000349 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 85963000350 Cysteine-rich domain; Region: CCG; pfam02754 85963000351 Cysteine-rich domain; Region: CCG; pfam02754 85963000352 L-lactate transport; Region: lctP; TIGR00795 85963000353 L-lactate permease [Energy production and conversion]; Region: LldP; COG1620 85963000354 L-lactate permease [Energy production and conversion]; Region: LldP; COG1620 85963000355 L-lactate transport; Region: lctP; TIGR00795 85963000356 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 85963000357 DNA glycosylase MutY; Provisional; Region: PRK13910 85963000358 minor groove reading motif; other site 85963000359 helix-hairpin-helix signature motif; other site 85963000360 substrate binding pocket [chemical binding]; other site 85963000361 active site 85963000362 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 85963000363 DNA binding and oxoG recognition site [nucleotide binding] 85963000364 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 85963000365 Sodium:sulfate symporter transmembrane region; Region: Na_sulph_symp; pfam00939 85963000366 transmembrane helices; other site 85963000367 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 85963000368 Low-spin heme binding site [chemical binding]; other site 85963000369 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 85963000370 D-pathway; other site 85963000371 Putative water exit pathway; other site 85963000372 Binuclear center (active site) [active] 85963000373 K-pathway; other site 85963000374 Putative proton exit pathway; other site 85963000375 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 85963000376 cytochrome c oxidase, cbb3-type, subunit II; Region: ccoO; TIGR00781 85963000377 cytochrome c oxidase, cbb3-type, CcoQ subunit, epsilon-Proteobacterial; Region: cbb3_Q_epsi; TIGR02736 85963000378 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 85963000379 Cytochrome c; Region: Cytochrom_C; pfam00034 85963000380 Cytochrome c; Region: Cytochrom_C; pfam00034 85963000381 Family of unknown function (DUF4006); Region: DUF4006; pfam13179 85963000382 Predicted periplasmic solute-binding protein [General function prediction only]; Region: COG2107 85963000383 recombinase A; Provisional; Region: recA; PRK09354 85963000384 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 85963000385 hexamer interface [polypeptide binding]; other site 85963000386 Walker A motif; other site 85963000387 ATP binding site [chemical binding]; other site 85963000388 Walker B motif; other site 85963000389 enolase; Provisional; Region: eno; PRK00077 85963000390 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 85963000391 dimer interface [polypeptide binding]; other site 85963000392 metal binding site [ion binding]; metal-binding site 85963000393 substrate binding pocket [chemical binding]; other site 85963000394 AMIN domain; Region: AMIN; pfam11741 85963000395 Shikimate kinase [Amino acid transport and metabolism]; Region: AroK; COG0703 85963000396 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 85963000397 ADP binding site [chemical binding]; other site 85963000398 magnesium binding site [ion binding]; other site 85963000399 putative shikimate binding site; other site 85963000400 Cache domain; Region: Cache_1; pfam02743 85963000401 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 85963000402 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 85963000403 Ligand binding site; other site 85963000404 metal-binding site 85963000405 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 85963000406 Sel1-like repeats; Region: SEL1; smart00671 85963000407 Sel1-like repeats; Region: SEL1; smart00671 85963000408 Sel1-like repeats; Region: SEL1; smart00671 85963000409 Sel1 repeat; Region: Sel1; cl02723 85963000410 Sel1-like repeats; Region: SEL1; smart00671 85963000411 Sel1-like repeats; Region: SEL1; smart00671 85963000412 hypothetical protein; Provisional; Region: PRK12378 85963000413 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 85963000414 dimer interface [polypeptide binding]; other site 85963000415 active site 85963000416 Schiff base residues; other site 85963000417 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 85963000418 HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain; Region: HAMP; smart00304 85963000419 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 85963000420 dimer interface [polypeptide binding]; other site 85963000421 phosphorylation site [posttranslational modification] 85963000422 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 85963000423 ATP binding site [chemical binding]; other site 85963000424 Mg2+ binding site [ion binding]; other site 85963000425 G-X-G motif; other site 85963000426 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 85963000427 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 85963000428 active site 85963000429 phosphorylation site [posttranslational modification] 85963000430 intermolecular recognition site; other site 85963000431 dimerization interface [polypeptide binding]; other site 85963000432 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 85963000433 DNA binding site [nucleotide binding] 85963000434 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 85963000435 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 85963000436 Peptidase family U32; Region: Peptidase_U32; pfam01136 85963000437 peptide chain release factor 2; Region: prfB; TIGR00020 85963000438 This domain is found in peptide chain release factors; Region: PCRF; smart00937 85963000439 RF-1 domain; Region: RF-1; pfam00472 85963000440 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 85963000441 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 85963000442 dimer interface [polypeptide binding]; other site 85963000443 putative functional site; other site 85963000444 putative MPT binding site; other site 85963000445 Flagellar biosynthesis pathway, component FliR [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FliR; COG1684 85963000446 Etoposide-induced protein 2.4 (EI24); Region: EI24; pfam07264 85963000447 Parvulin-like peptidyl-prolyl isomerase [Posttranslational modification, protein turnover, chaperones]; Region: SurA; COG0760 85963000448 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 85963000449 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 85963000450 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 85963000451 intersubunit interface [polypeptide binding]; other site 85963000452 active site 85963000453 zinc binding site [ion binding]; other site 85963000454 Na+ binding site [ion binding]; other site 85963000455 elongation factor P; Validated; Region: PRK00529 85963000456 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 85963000457 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 85963000458 RNA binding site [nucleotide binding]; other site 85963000459 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 85963000460 RNA binding site [nucleotide binding]; other site 85963000461 GTPase subunit of restriction endonuclease [Defense mechanisms]; Region: McrB; COG1401 85963000462 AAA domain (dynein-related subfamily); Region: AAA_5; pfam07728 85963000463 Walker A motif; other site 85963000464 ATP binding site [chemical binding]; other site 85963000465 Walker B motif; other site 85963000466 LlaJI restriction endonuclease; Region: RE_LlaJI; pfam09563 85963000467 pseudaminic acid synthase; Region: PseI; TIGR03586 85963000468 NeuB family; Region: NeuB; pfam03102 85963000469 C-terminal SAF domain of sialic acid synthetase; Region: SAF_NeuB_like; cd11615 85963000470 NeuB binding interface [polypeptide binding]; other site 85963000471 putative substrate binding site [chemical binding]; other site 85963000472 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 85963000473 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 85963000474 Walker A/P-loop; other site 85963000475 ATP binding site [chemical binding]; other site 85963000476 Q-loop/lid; other site 85963000477 ABC transporter signature motif; other site 85963000478 Walker B; other site 85963000479 D-loop; other site 85963000480 H-loop/switch region; other site 85963000481 apolipoprotein N-acyltransferase; Reviewed; Region: PRK12291 85963000482 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cl11424 85963000483 active site 85963000484 catalytic triad [active] 85963000485 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 85963000486 Colicin V production protein; Region: Colicin_V; pfam02674 85963000487 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 85963000488 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 85963000489 dimer interface [polypeptide binding]; other site 85963000490 putative anticodon binding site; other site 85963000491 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 85963000492 motif 1; other site 85963000493 active site 85963000494 motif 2; other site 85963000495 motif 3; other site 85963000496 serine hydroxymethyltransferase; Reviewed; Region: PRK13034 85963000497 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 85963000498 dimer interface [polypeptide binding]; other site 85963000499 active site 85963000500 glycine-pyridoxal phosphate binding site [chemical binding]; other site 85963000501 folate binding site [chemical binding]; other site 85963000502 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 85963000503 nucleotide binding site [chemical binding]; other site 85963000504 Eukaryotic and archaeal DNA primase small subunit; Region: DNA_primase_S; pfam01896 85963000505 Sporulation related domain; Region: SPOR; cl10051 85963000506 Protein of unknown function DUF262; Region: DUF262; pfam03235 85963000507 Uncharacterized conserved protein [Function unknown]; Region: COG1479 85963000508 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 85963000509 Uncharacterized protein family, UPF0114; Region: UPF0114; cl01078 85963000510 Phosphatidylserine/phosphatidylglycerophosphate/car diolipin synthases and related enzymes [Lipid metabolism]; Region: Cls; COG1502 85963000511 Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_1; cd09111 85963000512 putative active site [active] 85963000513 catalytic site [active] 85963000514 Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_2; cd09113 85963000515 putative active site [active] 85963000516 catalytic site [active] 85963000517 fumarate reductase iron-sulfur subunit; Provisional; Region: frdB; PRK13552 85963000518 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 85963000519 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 85963000520 fumarate reductase flavoprotein subunit; Provisional; Region: PRK08626 85963000521 L-aspartate oxidase; Provisional; Region: PRK06175 85963000522 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 85963000523 fumarate reductase cytochrome b-556 subunit; Provisional; Region: PRK13553 85963000524 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 85963000525 Iron-sulfur protein interface; other site 85963000526 proximal heme binding site [chemical binding]; other site 85963000527 distal heme binding site [chemical binding]; other site 85963000528 dimer interface [polypeptide binding]; other site 85963000529 triosephosphate isomerase; Provisional; Region: PRK14567 85963000530 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 85963000531 substrate binding site [chemical binding]; other site 85963000532 dimer interface [polypeptide binding]; other site 85963000533 catalytic triad [active] 85963000534 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK08415 85963000535 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 85963000536 NAD binding site [chemical binding]; other site 85963000537 homotetramer interface [polypeptide binding]; other site 85963000538 homodimer interface [polypeptide binding]; other site 85963000539 substrate binding site [chemical binding]; other site 85963000540 active site 85963000541 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Region: lipid_A_lpxD; TIGR01853 85963000542 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 85963000543 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 85963000544 trimer interface [polypeptide binding]; other site 85963000545 active site 85963000546 UDP-GlcNAc binding site [chemical binding]; other site 85963000547 lipid binding site [chemical binding]; lipid-binding site 85963000548 S-adenosylmethionine synthetase; Validated; Region: PRK05250 85963000549 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 85963000550 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 85963000551 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 85963000552 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 85963000553 active site 85963000554 multimer interface [polypeptide binding]; other site 85963000555 Uncharacterized ACR, COG1399; Region: DUF177; cl00616 85963000556 Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]; Region: RpmF; COG0333 85963000557 fatty acid/phospholipid synthesis protein PlsX; Region: plsX; TIGR00182 85963000558 3-oxoacyl-(acyl-carrier-protein) synthase III; Region: fabH; TIGR00747 85963000559 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 85963000560 dimer interface [polypeptide binding]; other site 85963000561 active site 85963000562 CoA binding pocket [chemical binding]; other site 85963000563 AAA ATPase domain; Region: AAA_15; pfam13175 85963000564 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cd00267 85963000565 Walker B; other site 85963000566 D-loop; other site 85963000567 H-loop/switch region; other site 85963000568 antiporter inner membrane protein; Provisional; Region: PRK11670 85963000569 Domain of unknown function DUF59; Region: DUF59; pfam01883 85963000570 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 85963000571 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 85963000572 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 85963000573 Ligand binding site; other site 85963000574 metal-binding site 85963000575 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 85963000576 heat shock protein 90; Provisional; Region: PRK05218 85963000577 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 85963000578 ATP binding site [chemical binding]; other site 85963000579 Mg2+ binding site [ion binding]; other site 85963000580 G-X-G motif; other site 85963000581 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 85963000582 Sel1-like repeats; Region: SEL1; smart00671 85963000583 Sel1-like repeats; Region: SEL1; smart00671 85963000584 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 85963000585 TPR motif; other site 85963000586 binding surface 85963000587 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 85963000588 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 85963000589 metal binding site [ion binding]; metal-binding site 85963000590 dimer interface [polypeptide binding]; other site 85963000591 glucose-inhibited division protein A; Region: gidA; TIGR00136 85963000592 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 85963000593 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 85963000594 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 85963000595 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 85963000596 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 85963000597 transmembrane helices; other site 85963000598 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 85963000599 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 85963000600 1-deoxy-D-xylulose 5-phosphate reductoisomerase [Lipid metabolism]; Region: Dxr; COG0743 85963000601 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 85963000602 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 85963000603 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 85963000604 Beta-1,4-N-acetylgalactosaminyltransferase (CgtA); Region: CgtA; pfam06306 85963000605 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 85963000606 substrate binding site [chemical binding]; other site 85963000607 Helix-turn-helix domain; Region: HTH_28; pfam13518 85963000608 cysteine desulfurase, NifS family, epsilon proteobacteria type; Region: nifS_epsilon; TIGR03403 85963000609 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 85963000610 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 85963000611 catalytic residue [active] 85963000612 Fe-S cluster assembly protein NifU; Region: NifU_proper; TIGR02000 85963000613 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 85963000614 trimerization site [polypeptide binding]; other site 85963000615 active site 85963000616 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 85963000617 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 85963000618 Ribbon-helix-helix protein, copG family; Region: RHH_1; pfam01402 85963000619 DNA repair protein RadA; Region: sms; TIGR00416 85963000620 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 85963000621 Walker A motif/ATP binding site; other site 85963000622 ATP binding site [chemical binding]; other site 85963000623 Walker B motif; other site 85963000624 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 85963000625 Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: MsrA; COG0225 85963000626 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: COG0229 85963000627 SelR domain; Region: SelR; pfam01641 85963000628 Predicted permeases [General function prediction only]; Region: COG0730 85963000629 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963000630 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 85963000631 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 85963000632 Sulfate transporter family; Region: Sulfate_transp; pfam00916 85963000633 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963000634 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 85963000635 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 85963000636 Ligand binding site; other site 85963000637 oligomer interface; other site 85963000638 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 85963000639 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 85963000640 hypothetical protein; Provisional; Region: PRK04081 85963000641 Glutathionylspermidine synthase [Amino acid transport and metabolism]; Region: Gsp; COG0754 85963000642 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 85963000643 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 85963000644 binding surface 85963000645 TPR motif; other site 85963000646 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 85963000647 binding surface 85963000648 TPR motif; other site 85963000649 Sel1-like repeats; Region: SEL1; smart00671 85963000650 Sel1-like repeats; Region: SEL1; smart00671 85963000651 Cytochrome c; Region: Cytochrom_C; cl11414 85963000652 Porphobilinogen deaminase [Coenzyme metabolism]; Region: HemC; COG0181 85963000653 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 85963000654 domain interfaces; other site 85963000655 active site 85963000656 prolyl-tRNA synthetase; Provisional; Region: PRK09194 85963000657 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 85963000658 dimer interface [polypeptide binding]; other site 85963000659 motif 1; other site 85963000660 active site 85963000661 motif 2; other site 85963000662 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 85963000663 putative deacylase active site [active] 85963000664 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 85963000665 active site 85963000666 motif 3; other site 85963000667 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 85963000668 anticodon binding site; other site 85963000669 glutamyl-tRNA reductase; Region: hemA; TIGR01035 85963000670 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 85963000671 tRNA; other site 85963000672 putative tRNA binding site [nucleotide binding]; other site 85963000673 putative NADP binding site [chemical binding]; other site 85963000674 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 85963000675 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 85963000676 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 85963000677 substrate binding pocket [chemical binding]; other site 85963000678 chain length determination region; other site 85963000679 substrate-Mg2+ binding site; other site 85963000680 catalytic residues [active] 85963000681 aspartate-rich region 1; other site 85963000682 active site lid residues [active] 85963000683 aspartate-rich region 2; other site 85963000684 Domain of unknown function (DUF2018); Region: DUF2018; pfam09442 85963000685 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 85963000686 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 85963000687 dimerization interface [polypeptide binding]; other site 85963000688 DPS ferroxidase diiron center [ion binding]; other site 85963000689 ion pore; other site 85963000690 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 85963000691 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 85963000692 dimer interface [polypeptide binding]; other site 85963000693 phosphorylation site [posttranslational modification] 85963000694 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 85963000695 ATP binding site [chemical binding]; other site 85963000696 Mg2+ binding site [ion binding]; other site 85963000697 G-X-G motif; other site 85963000698 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 85963000699 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 85963000700 helicase 45; Provisional; Region: PTZ00424 85963000701 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 85963000702 ATP binding site [chemical binding]; other site 85963000703 Mg++ binding site [ion binding]; other site 85963000704 motif III; other site 85963000705 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 85963000706 nucleotide binding region [chemical binding]; other site 85963000707 ATP-binding site [chemical binding]; other site 85963000708 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 85963000709 SPFH domain / Band 7 family; Region: Band_7; pfam01145 85963000710 Protein of unknown function (DUF2393); Region: DUF2393; pfam09624 85963000711 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 85963000712 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 85963000713 Walker A/P-loop; other site 85963000714 ATP binding site [chemical binding]; other site 85963000715 Q-loop/lid; other site 85963000716 ABC transporter signature motif; other site 85963000717 Walker B; other site 85963000718 D-loop; other site 85963000719 H-loop/switch region; other site 85963000720 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 85963000721 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 85963000722 Walker A/P-loop; other site 85963000723 ATP binding site [chemical binding]; other site 85963000724 Q-loop/lid; other site 85963000725 ABC transporter signature motif; other site 85963000726 Walker B; other site 85963000727 D-loop; other site 85963000728 H-loop/switch region; other site 85963000729 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 85963000730 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4239 85963000731 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 85963000732 dimer interface [polypeptide binding]; other site 85963000733 conserved gate region; other site 85963000734 putative PBP binding loops; other site 85963000735 ABC-ATPase subunit interface; other site 85963000736 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963000737 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963000738 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 85963000739 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 85963000740 GDP-binding site [chemical binding]; other site 85963000741 ACT binding site; other site 85963000742 IMP binding site; other site 85963000743 Uncharacterized conserved protein [Function unknown]; Region: COG3334 85963000744 RIP metalloprotease RseP; Region: TIGR00054 85963000745 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 85963000746 active site 85963000747 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 85963000748 exodeoxyribonuclease VII, large subunit; Region: xseA; TIGR00237 85963000749 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 85963000750 generic binding surface II; other site 85963000751 generic binding surface I; other site 85963000752 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 85963000753 DNA methylase; Region: N6_N4_Mtase; pfam01555 85963000754 DNA methylase; Region: N6_N4_Mtase; pfam01555 85963000755 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 85963000756 DNA methylase; Region: N6_N4_Mtase; pfam01555 85963000757 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 85963000758 Clp amino terminal domain; Region: Clp_N; pfam02861 85963000759 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 85963000760 Walker A motif; other site 85963000761 ATP binding site [chemical binding]; other site 85963000762 Walker B motif; other site 85963000763 arginine finger; other site 85963000764 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 85963000765 Walker A motif; other site 85963000766 ATP binding site [chemical binding]; other site 85963000767 Walker B motif; other site 85963000768 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 85963000769 Cytochrome c biogenesis protein [Posttranslational modification, protein turnover, chaperones]; Region: CcdA; COG0785 85963000770 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; pfam02683 85963000771 Dihydroorotase and related cyclic amidohydrolases [Nucleotide transport and metabolism]; Region: PyrC; COG0044 85963000772 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 85963000773 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 85963000774 active site 85963000775 chlorohydrolase; Provisional; Region: PRK08418 85963000776 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 85963000777 active site 85963000778 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 85963000779 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14339 85963000780 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 85963000781 FeS/SAM binding site; other site 85963000782 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: DUF374; Region: LPLAT_DUF374-like; cd07983 85963000783 putative acyl-acceptor binding pocket; other site 85963000784 urocanate hydratase; Provisional; Region: PRK05414 85963000785 Predicted Fe-S-cluster oxidoreductase [General function prediction only]; Region: COG0727 85963000786 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 85963000787 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 85963000788 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 85963000789 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 85963000790 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 85963000791 putative active site [active] 85963000792 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 85963000793 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 85963000794 putative acyl-acceptor binding pocket; other site 85963000795 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 85963000796 tRNA-guanine family transglycosylase; Region: tgt_general; TIGR00449 85963000797 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3400 85963000798 TrkA-C domain; Region: TrkA_C; pfam02080 85963000799 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 85963000800 active site 85963000801 dimer interface [polypeptide binding]; other site 85963000802 metal binding site [ion binding]; metal-binding site 85963000803 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 85963000804 Mechanosensitive ion channel; Region: MS_channel; pfam00924 85963000805 radical SAM methylthiotransferase, MiaB/RimO family; Region: TIGR00089 85963000806 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 85963000807 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 85963000808 FeS/SAM binding site; other site 85963000809 ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]; Region: HflB; COG0465 85963000810 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 85963000811 Walker B motif; other site 85963000812 arginine finger; other site 85963000813 Domain of unknown function (DUF4149); Region: DUF4149; pfam13664 85963000814 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 85963000815 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 85963000816 PPE-repeat proteins [Cell motility and secretion]; Region: COG5651 85963000817 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 85963000818 Autotransporter beta-domain; Region: Autotransporter; pfam03797 85963000819 diaminopimelate decarboxylase; Region: lysA; TIGR01048 85963000820 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 85963000821 active site 85963000822 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 85963000823 substrate binding site [chemical binding]; other site 85963000824 catalytic residues [active] 85963000825 dimer interface [polypeptide binding]; other site 85963000826 Chorismate mutase [Amino acid transport and metabolism]; Region: PheA; COG1605 85963000827 Uncharacterized conserved protein [Function unknown]; Region: COG4866 85963000828 aminodeoxychorismate synthase; Provisional; Region: PRK07508 85963000829 chorismate binding enzyme; Region: Chorismate_bind; cl10555 85963000830 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 85963000831 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 85963000832 acylamide amidohydrolase; Provisional; Region: amiE; PRK13286 85963000833 aliphatic amidases (class 2 nitrilases); Region: aliphatic_amidase; cd07565 85963000834 multimer interface [polypeptide binding]; other site 85963000835 active site 85963000836 catalytic triad [active] 85963000837 dimer interface [polypeptide binding]; other site 85963000838 flagellar hook-associated protein FlgL; Validated; Region: flgL; PRK08412 85963000839 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 85963000840 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 85963000841 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 85963000842 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 85963000843 The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; Region: PBP2_DppA_like; cd08493 85963000844 peptide binding site [polypeptide binding]; other site 85963000845 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 85963000846 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 85963000847 dimer interface [polypeptide binding]; other site 85963000848 conserved gate region; other site 85963000849 putative PBP binding loops; other site 85963000850 ABC-ATPase subunit interface; other site 85963000851 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 85963000852 nickel import ATP-binding protein NikD; Region: nickel_nikD; TIGR02770 85963000853 Walker A/P-loop; other site 85963000854 ATP binding site [chemical binding]; other site 85963000855 Q-loop/lid; other site 85963000856 ABC transporter signature motif; other site 85963000857 Walker B; other site 85963000858 D-loop; other site 85963000859 H-loop/switch region; other site 85963000860 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; pfam08352 85963000861 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 85963000862 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 85963000863 Walker A/P-loop; other site 85963000864 ATP binding site [chemical binding]; other site 85963000865 Q-loop/lid; other site 85963000866 ABC transporter signature motif; other site 85963000867 Walker B; other site 85963000868 D-loop; other site 85963000869 H-loop/switch region; other site 85963000870 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; pfam08352 85963000871 GTPase CgtA; Reviewed; Region: obgE; PRK12299 85963000872 GTP1/OBG; Region: GTP1_OBG; pfam01018 85963000873 Obg GTPase; Region: Obg; cd01898 85963000874 G1 box; other site 85963000875 GTP/Mg2+ binding site [chemical binding]; other site 85963000876 Switch I region; other site 85963000877 G2 box; other site 85963000878 G3 box; other site 85963000879 Switch II region; other site 85963000880 G4 box; other site 85963000881 G5 box; other site 85963000882 Alginate lyase; Region: Alginate_lyase; pfam05426 85963000883 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 85963000884 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 85963000885 inhibitor-cofactor binding pocket; inhibition site 85963000886 pyridoxal 5'-phosphate binding site [chemical binding]; other site 85963000887 catalytic residue [active] 85963000888 Putative F0F1-ATPase subunit (ATPase_gene1); Region: ATPase_gene1; pfam09527 85963000889 Predicted amidohydrolase [General function prediction only]; Region: COG0388 85963000890 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cd07197 85963000891 active site 85963000892 catalytic triad [active] 85963000893 dimer interface [polypeptide binding]; other site 85963000894 Catalytic domain of Helicobacter pylori peptidoglycan deacetylase (HpPgdA) and similar proteins; Region: CE4_HpPgdA_like; cd10938 85963000895 active site 85963000896 catalytic site [active] 85963000897 Zn binding site [ion binding]; other site 85963000898 tetramer interface [polypeptide binding]; other site 85963000899 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 85963000900 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 85963000901 CobW/HypB/UreG, nucleotide-binding domain; Region: cobW; pfam02492 85963000902 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; pfam07683 85963000903 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 85963000904 Major Facilitator Superfamily; Region: MFS_1; pfam07690 85963000905 putative substrate translocation pore; other site 85963000906 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 85963000907 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 85963000908 Walker A/P-loop; other site 85963000909 ATP binding site [chemical binding]; other site 85963000910 Q-loop/lid; other site 85963000911 ABC transporter signature motif; other site 85963000912 Walker B; other site 85963000913 D-loop; other site 85963000914 H-loop/switch region; other site 85963000915 heme oxygenase, HugZ family; Region: heme_ox_HugZ; TIGR04109 85963000916 Protein of unknown function (DUF2470); Region: DUF2470; pfam10615 85963000917 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 85963000918 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 85963000919 arginyl-tRNA synthetase; Region: argS; TIGR00456 85963000920 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 85963000921 active site 85963000922 HIGH motif; other site 85963000923 KMSK motif region; other site 85963000924 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 85963000925 tRNA binding surface [nucleotide binding]; other site 85963000926 anticodon binding site; other site 85963000927 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 85963000928 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 85963000929 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 85963000930 catalytic site [active] 85963000931 G-X2-G-X-G-K; other site 85963000932 nuclease NucT; Provisional; Region: PRK13912 85963000933 Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6, and similar proteins; Region: PLDc_Nuc_like; cd09116 85963000934 putative active site [active] 85963000935 catalytic site [active] 85963000936 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963000937 Flagellar basal body L-ring protein [Cell motility and secretion]; Region: FlgH; COG2063 85963000938 flagellar basal body L-ring protein; Reviewed; Region: flgH; PRK00249 85963000939 pseudaminic acid biosynthesis N-acetyl transferase; Region: PseH; TIGR03585 85963000940 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 85963000941 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 85963000942 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 85963000943 NAD synthetase; Provisional; Region: PRK13980 85963000944 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 85963000945 homodimer interface [polypeptide binding]; other site 85963000946 NAD binding pocket [chemical binding]; other site 85963000947 ATP binding pocket [chemical binding]; other site 85963000948 Mg binding site [ion binding]; other site 85963000949 active-site loop [active] 85963000950 ketol-acid reductoisomerase; Provisional; Region: PRK05479 85963000951 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 85963000952 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 85963000953 Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]; Region: MinD; COG2894 85963000954 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 85963000955 Switch I; other site 85963000956 Switch II; other site 85963000957 cell division topological specificity factor MinE; Region: minE; TIGR01215 85963000958 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 85963000959 DNA protecting protein DprA; Region: dprA; TIGR00732 85963000960 Holliday junction resolvase-like protein; Reviewed; Region: PRK00109 85963000961 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 85963000962 Sel1-like repeats; Region: SEL1; smart00671 85963000963 Sel1-like repeats; Region: SEL1; smart00671 85963000964 Sel1-like repeats; Region: SEL1; smart00671 85963000965 Sel1-like repeats; Region: SEL1; smart00671 85963000966 Sel1 repeat; Region: Sel1; cl02723 85963000967 Sel1-like repeats; Region: SEL1; smart00671 85963000968 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 85963000969 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 85963000970 active site 85963000971 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 85963000972 DHH family; Region: DHH; pfam01368 85963000973 DHHA1 domain; Region: DHHA1; pfam02272 85963000974 CTP synthetase; Validated; Region: pyrG; PRK05380 85963000975 CTP synthetase (CTPs) is a two-domain protein, which consists of an N-terminal synthetase domain and C-terminal glutaminase domain. The enzymes hydrolyze the amide bond of glutamine to ammonia and glutamate at the glutaminase domains and transfer nascent...; Region: CTGs; cd03113 85963000976 Catalytic site [active] 85963000977 active site 85963000978 UTP binding site [chemical binding]; other site 85963000979 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 85963000980 active site 85963000981 putative oxyanion hole; other site 85963000982 catalytic triad [active] 85963000983 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 85963000984 flagellar basal-body M-ring protein/flagellar hook-basal body protein (fliF); Region: fliF; TIGR00206 85963000985 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; pfam01514 85963000986 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 85963000987 flagellar motor switch protein FliG; Region: fliG; TIGR00207 85963000988 FliG C-terminal domain; Region: FliG_C; pfam01706 85963000989 flagellar assembly protein H; Validated; Region: fliH; PRK06669 85963000990 Flagellar assembly protein FliH; Region: FliH; pfam02108 85963000991 1-deoxy-D-xylulose-5-phosphate synthase; Region: dxs; TIGR00204 85963000992 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 85963000993 TPP-binding site; other site 85963000994 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 85963000995 PYR/PP interface [polypeptide binding]; other site 85963000996 dimer interface [polypeptide binding]; other site 85963000997 TPP binding site [chemical binding]; other site 85963000998 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 85963000999 GTP-binding protein LepA; Provisional; Region: PRK05433 85963001000 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 85963001001 G1 box; other site 85963001002 putative GEF interaction site [polypeptide binding]; other site 85963001003 GTP/Mg2+ binding site [chemical binding]; other site 85963001004 Switch I region; other site 85963001005 G2 box; other site 85963001006 G3 box; other site 85963001007 Switch II region; other site 85963001008 G4 box; other site 85963001009 G5 box; other site 85963001010 lepA_II: This subfamily represents the domain II of LepA, a GTP-binding protein localized in the cytoplasmic membrane. The N-terminal domain of LepA shares regions of homology to translation factors. In terms of interaction with the ribosome, EF-G, EF-Tu...; Region: lepA_II; cd03699 85963001011 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 85963001012 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 85963001013 Domain of unknown function (DUF3883); Region: DUF3883; pfam13020 85963001014 Flagellar basal body rod protein [Cell motility and secretion]; Region: FlgG; COG4786 85963001015 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 85963001016 alpha-ketoglutarate transporter; Provisional; Region: PRK10406 85963001017 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 85963001018 putative substrate translocation pore; other site 85963001019 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 85963001020 TspO/MBR family; Region: TspO_MBR; cl01379 85963001021 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 85963001022 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 85963001023 Inactivated superfamily I helicase [DNA replication, recombination, and repair]; Region: COG3893 85963001024 RecB family exonuclease [DNA replication, recombination, and repair]; Region: COG2887 85963001025 transketolase, bacterial and yeast; Region: tktlase_bact; TIGR00232 85963001026 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 85963001027 TPP-binding site [chemical binding]; other site 85963001028 dimer interface [polypeptide binding]; other site 85963001029 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 85963001030 PYR/PP interface [polypeptide binding]; other site 85963001031 dimer interface [polypeptide binding]; other site 85963001032 TPP binding site [chemical binding]; other site 85963001033 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 85963001034 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 85963001035 riboflavin kinase/FMN adenylyltransferase; Region: ribF; TIGR00083 85963001036 active site 85963001037 Riboflavin kinase; Region: Flavokinase; pfam01687 85963001038 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 85963001039 S4 RNA-binding domain; Region: S4; smart00363 85963001040 RNA binding surface [nucleotide binding]; other site 85963001041 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 85963001042 S-adenosylmethionine binding site [chemical binding]; other site 85963001043 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 85963001044 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 85963001045 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 85963001046 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 85963001047 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 85963001048 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 85963001049 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 85963001050 Walker A/P-loop; other site 85963001051 ATP binding site [chemical binding]; other site 85963001052 Q-loop/lid; other site 85963001053 ABC transporter signature motif; other site 85963001054 Walker B; other site 85963001055 D-loop; other site 85963001056 H-loop/switch region; other site 85963001057 Predicted endonuclease distantly related to archaeal Holliday junction resolvase and Mrr-like restriction enzymes [Defense mechanisms]; Region: COG1787 85963001058 Restriction endonuclease; Region: Mrr_cat; pfam04471 85963001059 Predicted ATPases [General function prediction only]; Region: COG1106 85963001060 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 85963001061 Walker A/P-loop; other site 85963001062 ATP binding site [chemical binding]; other site 85963001063 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 85963001064 Walker B; other site 85963001065 D-loop; other site 85963001066 H-loop/switch region; other site 85963001067 Pectinesterase/pectinesterase inhibitor; Region: PLN02313 85963001068 High-affinity nickel permease [Inorganic ion transport and metabolism]; Region: HoxN; COG3376 85963001069 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cd00596 85963001070 active site 85963001071 Zn binding site [ion binding]; other site 85963001072 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 85963001073 metal-binding site [ion binding] 85963001074 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 85963001075 metal-binding site [ion binding] 85963001076 fungal transcription factor regulatory middle homology region; Region: fungal_TF_MHR; cd12148 85963001077 copper-(or silver)-translocating P-type ATPase; Region: ATPase-IB1_Cu; TIGR01511 85963001078 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 85963001079 Soluble P-type ATPase [General function prediction only]; Region: COG4087 85963001080 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 85963001081 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 85963001082 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 85963001083 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 85963001084 Walker A motif; other site 85963001085 ATP binding site [chemical binding]; other site 85963001086 Walker B motif; other site 85963001087 arginine finger; other site 85963001088 Peptidase family M41; Region: Peptidase_M41; pfam01434 85963001089 ribosomal protein L11 methyltransferase; Region: prmA; TIGR00406 85963001090 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 85963001091 S-adenosylmethionine binding site [chemical binding]; other site 85963001092 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 85963001093 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 85963001094 active site 85963001095 phosphorylation site [posttranslational modification] 85963001096 intermolecular recognition site; other site 85963001097 dimerization interface [polypeptide binding]; other site 85963001098 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963001099 rRNA small subunit methyltransferase G; Region: GidB; pfam02527 85963001100 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 85963001101 S-adenosylmethionine binding site [chemical binding]; other site 85963001102 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 85963001103 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 85963001104 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 85963001105 sec-independent translocase; Provisional; Region: PRK04098 85963001106 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 85963001107 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 85963001108 Walker A motif; other site 85963001109 ATP binding site [chemical binding]; other site 85963001110 Walker B motif; other site 85963001111 arginine finger; other site 85963001112 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 85963001113 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 85963001114 oligomerization interface [polypeptide binding]; other site 85963001115 active site 85963001116 metal binding site [ion binding]; metal-binding site 85963001117 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963001118 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963001119 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 85963001120 septum formation inhibitor; Reviewed; Region: minC; PRK00556 85963001121 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 85963001122 UDP-3-0-acyl N-acetylglucosamine deacetylase; Region: lpxC; TIGR00325 85963001123 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 85963001124 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214 85963001125 homoserine kinase; Region: thrB; TIGR00191 85963001126 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 85963001127 Predicted nucleic-acid-binding protein implicated in transcription termination [Transcription]; Region: COG2740 85963001128 putative RNA binding cleft [nucleotide binding]; other site 85963001129 translation initiation factor IF-2; Region: IF-2; TIGR00487 85963001130 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 85963001131 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 85963001132 G1 box; other site 85963001133 putative GEF interaction site [polypeptide binding]; other site 85963001134 GTP/Mg2+ binding site [chemical binding]; other site 85963001135 Switch I region; other site 85963001136 G2 box; other site 85963001137 G3 box; other site 85963001138 Switch II region; other site 85963001139 G4 box; other site 85963001140 G5 box; other site 85963001141 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 85963001142 Translation-initiation factor 2; Region: IF-2; pfam11987 85963001143 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 85963001144 Ribosome-binding factor A; Region: RBFA; cl00542 85963001145 Uncharacterized BCR, YhbC family COG0779; Region: DUF150; pfam02576 85963001146 Sm and related proteins; Region: Sm_like; cl00259 85963001147 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 85963001148 putative oligomer interface [polypeptide binding]; other site 85963001149 putative RNA binding site [nucleotide binding]; other site 85963001150 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 85963001151 putative active site [active] 85963001152 putative metal binding site [ion binding]; other site 85963001153 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 85963001154 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 85963001155 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 85963001156 active site 85963001157 intermolecular recognition site; other site 85963001158 dimerization interface [polypeptide binding]; other site 85963001159 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 85963001160 DNA binding site [nucleotide binding] 85963001161 Predicted phosphohydrolase (DHH superfamily) [General function prediction only]; Region: COG2404 85963001162 DHH family; Region: DHH; pfam01368 85963001163 flagellar biosynthesis protein FlhA; Validated; Region: flhA; PRK06012 85963001164 FHIPEP family; Region: FHIPEP; pfam00771 85963001165 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 85963001166 16S/18S rRNA binding site [nucleotide binding]; other site 85963001167 S13e-L30e interaction site [polypeptide binding]; other site 85963001168 25S rRNA binding site [nucleotide binding]; other site 85963001169 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 85963001170 O-Antigen ligase; Region: Wzy_C; pfam04932 85963001171 Dehydroquinase class II; Region: DHquinase_II; pfam01220 85963001172 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 85963001173 trimer interface [polypeptide binding]; other site 85963001174 active site 85963001175 dimer interface [polypeptide binding]; other site 85963001176 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 85963001177 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 85963001178 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 85963001179 active site 85963001180 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 85963001181 catalytic center binding site [active] 85963001182 ATP binding site [chemical binding]; other site 85963001183 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK05703 85963001184 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 85963001185 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 85963001186 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 85963001187 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 85963001188 Protein of unknown function (DUF1018); Region: DUF1018; cl01815 85963001189 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 85963001190 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 85963001191 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 85963001192 DNA binding residues [nucleotide binding] 85963001193 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 85963001194 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 85963001195 flagellar motor switch protein FliY; Validated; Region: PRK08432 85963001196 flagellar motor switch protein FliN; Region: fliN; TIGR02480 85963001197 Beta-galactosidase, beta subunit [Carbohydrate transport and metabolism]; Region: EbgC; COG2731 85963001198 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4731 85963001199 ferric uptake regulator; Provisional; Region: fur; PRK09462 85963001200 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 85963001201 metal binding site 2 [ion binding]; metal-binding site 85963001202 putative DNA binding helix; other site 85963001203 metal binding site 1 [ion binding]; metal-binding site 85963001204 dimer interface [polypeptide binding]; other site 85963001205 structural Zn2+ binding site [ion binding]; other site 85963001206 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]; Region: MGS1; COG2256 85963001207 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 85963001208 Walker A motif; other site 85963001209 ATP binding site [chemical binding]; other site 85963001210 Walker B motif; other site 85963001211 arginine finger; other site 85963001212 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 85963001213 Helix-Turn-Helix DNA binding domain of the HspR transcription regulator; Region: HTH_HspR; cd04766 85963001214 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 85963001215 DNA binding residues [nucleotide binding] 85963001216 putative dimer interface [polypeptide binding]; other site 85963001217 chaperone protein DnaJ; Provisional; Region: PRK14299 85963001218 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 85963001219 HSP70 interaction site [polypeptide binding]; other site 85963001220 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 85963001221 substrate binding site [polypeptide binding]; other site 85963001222 dimer interface [polypeptide binding]; other site 85963001223 5'-3' exonuclease; Provisional; Region: PRK14976 85963001224 PIN (PilT N terminus) domain: Superfamily; Region: PIN_SF; cl14812 85963001225 putative active site [active] 85963001226 Helix-hairpin-helix class 2 (Pol1 family) motifs; Region: HhH2; smart00279 85963001227 DNA binding site [nucleotide binding] 85963001228 metal binding site [ion binding]; metal-binding site 85963001229 Response regulator receiver domain; Region: Response_reg; pfam00072 85963001230 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 85963001231 active site 85963001232 dimerization interface [polypeptide binding]; other site 85963001233 bifunctional 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase/2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase protein; Provisional; Region: ispDF; PRK09382 85963001234 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 85963001235 substrate binding site; other site 85963001236 dimer interface; other site 85963001237 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 85963001238 homotrimer interaction site [polypeptide binding]; other site 85963001239 zinc binding site [ion binding]; other site 85963001240 CDP-binding sites; other site 85963001241 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 85963001242 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 85963001243 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 85963001244 protein binding site [polypeptide binding]; other site 85963001245 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 85963001246 S-methylmethionine transporter; Provisional; Region: PRK11387 85963001247 CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase; Region: pgsA; TIGR00560 85963001248 7-alpha-hydroxysteroid dehydrogenase; Provisional; Region: PRK08416 85963001249 1-cyclohexenylcarbonyl_coenzyme A_reductase (ChcA)_like, classical (c) SDRs; Region: ChcA_like_SDR_c; cd05359 85963001250 putative NAD(P) binding site [chemical binding]; other site 85963001251 active site 85963001252 dihydrodipicolinate synthase; Region: dapA; TIGR00674 85963001253 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 85963001254 dimer interface [polypeptide binding]; other site 85963001255 active site 85963001256 catalytic residue [active] 85963001257 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 85963001258 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 85963001259 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 85963001260 dihydroorotate dehydrogenase, subfamily 2; Region: pyrD_sub2; TIGR01036 85963001261 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 85963001262 quinone interaction residues [chemical binding]; other site 85963001263 active site 85963001264 catalytic residues [active] 85963001265 FMN binding site [chemical binding]; other site 85963001266 substrate binding site [chemical binding]; other site 85963001267 Polyphosphate kinase [Inorganic ion transport and metabolism]; Region: Ppk; COG0855 85963001268 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 85963001269 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 85963001270 Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C1_like; cd09165 85963001271 putative domain interface [polypeptide binding]; other site 85963001272 putative active site [active] 85963001273 catalytic site [active] 85963001274 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 85963001275 putative active site [active] 85963001276 putative domain interface [polypeptide binding]; other site 85963001277 catalytic site [active] 85963001278 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 85963001279 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 85963001280 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 85963001281 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 85963001282 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 85963001283 S-adenosylmethionine binding site [chemical binding]; other site 85963001284 Eco57I restriction-modification methylase; Region: Eco57I; pfam07669 85963001285 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2604 85963001286 N-terminal tellurium resistance protein terB-like domain of heat shock DnaJ-like proteins; Region: terB_like_DjlA; cd07316 85963001287 putative metal binding site [ion binding]; other site 85963001288 CoB--CoM heterodisulfide reductase, subunit B; Region: CoB_CoM_SS_B; TIGR03288 85963001289 oligoendopeptidase, pepF/M3 family; Region: M3_fam_3; TIGR02290 85963001290 Peptidase family M3B Oligopeptidase F (PepF); Region: M3B_PepF_5; cd09610 85963001291 active site 85963001292 Zn binding site [ion binding]; other site 85963001293 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 85963001294 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 85963001295 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963001296 ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: ModA; COG0725 85963001297 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 85963001298 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 85963001299 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 85963001300 dimer interface [polypeptide binding]; other site 85963001301 conserved gate region; other site 85963001302 putative PBP binding loops; other site 85963001303 ABC-ATPase subunit interface; other site 85963001304 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 85963001305 putative bacteriocin export ABC transporter, lactococcin 972 group; Region: L_ocin_972_ABC; TIGR03608 85963001306 Walker A/P-loop; other site 85963001307 ATP binding site [chemical binding]; other site 85963001308 Q-loop/lid; other site 85963001309 ABC transporter signature motif; other site 85963001310 Walker B; other site 85963001311 D-loop; other site 85963001312 H-loop/switch region; other site 85963001313 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 85963001314 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 85963001315 active site 85963001316 HIGH motif; other site 85963001317 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 85963001318 active site 85963001319 KMSKS motif; other site 85963001320 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963001321 Helix-turn-helix domain; Region: HTH_17; pfam12728 85963001322 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0827 85963001323 Methyltransferase domain; Region: Methyltransf_26; pfam13659 85963001324 TaqI-like C-terminal specificity domain; Region: TaqI_C; pfam12950 85963001325 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 85963001326 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 85963001327 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 85963001328 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 85963001329 G1 box; other site 85963001330 putative GEF interaction site [polypeptide binding]; other site 85963001331 GTP/Mg2+ binding site [chemical binding]; other site 85963001332 Switch I region; other site 85963001333 G2 box; other site 85963001334 G3 box; other site 85963001335 Switch II region; other site 85963001336 G4 box; other site 85963001337 G5 box; other site 85963001338 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 85963001339 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 85963001340 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dam; COG0338 85963001341 Catalytic GIY-YIG domain of coliphage T4 non-specific endonuclease II, type II restriction endonuclease R.Hpy188I, and similar proteins; Region: GIY-YIG_EndoII_Hpy188I_like; cd10436 85963001342 GIY-YIG motif/motif A; other site 85963001343 DNA binding site [nucleotide binding] 85963001344 active site 85963001345 catalytic site [active] 85963001346 metal binding site [ion binding]; metal-binding site 85963001347 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 85963001348 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 85963001349 cofactor binding site; other site 85963001350 DNA binding site [nucleotide binding] 85963001351 substrate interaction site [chemical binding]; other site 85963001352 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 85963001353 Catalase-like heme-binding proteins similar to the uncharacterized srpA; Region: srpA_like; cd08153 85963001354 putative heme binding pocket [chemical binding]; other site 85963001355 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 85963001356 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 85963001357 Protein of unknown function (DUF3519); Region: DUF3519; pfam12033 85963001358 Kef-type K+ transport systems, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: Kch; COG1226 85963001359 TrkA-N domain; Region: TrkA_N; pfam02254 85963001360 TrkA-C domain; Region: TrkA_C; pfam02080 85963001361 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 85963001362 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 85963001363 phospho-N-acetylmuramoyl-pentapeptide-transferase; Region: mraY; TIGR00445 85963001364 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 85963001365 Mg++ binding site [ion binding]; other site 85963001366 putative catalytic motif [active] 85963001367 putative substrate binding site [chemical binding]; other site 85963001368 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK03815 85963001369 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 85963001370 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 85963001371 Protein of unknown function (DUF493); Region: DUF493; pfam04359 85963001372 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 85963001373 active site 85963001374 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 85963001375 Na2 binding site [ion binding]; other site 85963001376 putative substrate binding site 1 [chemical binding]; other site 85963001377 Na binding site 1 [ion binding]; other site 85963001378 putative substrate binding site 2 [chemical binding]; other site 85963001379 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 85963001380 Na2 binding site [ion binding]; other site 85963001381 putative substrate binding site 1 [chemical binding]; other site 85963001382 Na binding site 1 [ion binding]; other site 85963001383 putative substrate binding site 2 [chemical binding]; other site 85963001384 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 85963001385 dimerization interface [polypeptide binding]; other site 85963001386 substrate binding site [chemical binding]; other site 85963001387 active site 85963001388 calcium binding site [ion binding]; other site 85963001389 DNA polymerase III, beta subunit; Region: dnan; TIGR00663 85963001390 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 85963001391 putative DNA binding surface [nucleotide binding]; other site 85963001392 dimer interface [polypeptide binding]; other site 85963001393 beta-clamp/translesion DNA polymerase binding surface; other site 85963001394 beta-clamp/clamp loader binding surface; other site 85963001395 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 85963001396 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 85963001397 Mg2+ binding site [ion binding]; other site 85963001398 G-X-G motif; other site 85963001399 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 85963001400 anchoring element; other site 85963001401 dimer interface [polypeptide binding]; other site 85963001402 ATP binding site [chemical binding]; other site 85963001403 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 85963001404 active site 85963001405 putative metal-binding site [ion binding]; other site 85963001406 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 85963001407 R.Pab1 restriction endonuclease; Region: RE_R_Pab1; pfam09522 85963001408 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 85963001409 Peptidase family M23; Region: Peptidase_M23; pfam01551 85963001410 nudix-type nucleoside diphosphatase, YffH/AdpP family; Region: TIGR00052 85963001411 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 85963001412 dimer interface [polypeptide binding]; other site 85963001413 ADP-ribose binding site [chemical binding]; other site 85963001414 active site 85963001415 nudix motif; other site 85963001416 metal binding site [ion binding]; metal-binding site 85963001417 FAD binding domain; Region: FAD_binding_4; pfam01565 85963001418 glycolate oxidase, subunit GlcD; Region: glcD; TIGR00387 85963001419 Protein-interacting Bro1-like domain of mammalian Alix and related domains; Region: BRO1_Alix_like; cl14649 85963001420 dihydrodipicolinate reductase; Region: dapB; TIGR00036 85963001421 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 85963001422 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 85963001423 glutamine synthetase, type I; Region: GlnA; TIGR00653 85963001424 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 85963001425 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 85963001426 Uncharacterized conserved protein [Function unknown]; Region: COG1479 85963001427 Protein of unknown function DUF262; Region: DUF262; pfam03235 85963001428 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 85963001429 Uncharacterized conserved protein [Function unknown]; Region: COG3586 85963001430 ribosomal protein L9; Region: L9; TIGR00158 85963001431 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 85963001432 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 85963001433 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 85963001434 active site 85963001435 HslU subunit interaction site [polypeptide binding]; other site 85963001436 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 85963001437 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 85963001438 Walker A motif; other site 85963001439 ATP binding site [chemical binding]; other site 85963001440 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 85963001441 Walker B motif; other site 85963001442 arginine finger; other site 85963001443 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 85963001444 GTPase [General function prediction only]; Region: Era; COG1159 85963001445 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 85963001446 G1 box; other site 85963001447 GTP/Mg2+ binding site [chemical binding]; other site 85963001448 Switch I region; other site 85963001449 G2 box; other site 85963001450 Switch II region; other site 85963001451 G3 box; other site 85963001452 G4 box; other site 85963001453 G5 box; other site 85963001454 KH domain; Region: KH_2; pfam07650 85963001455 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3034 85963001456 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 85963001457 Sel1-like repeats; Region: SEL1; smart00671 85963001458 Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]; Region: TopA; COG0551 85963001459 Type IV secretory pathway, VirD4 components [Intracellular trafficking and secretion]; Region: VirD4; COG3505 85963001460 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 85963001461 Walker A motif; other site 85963001462 ATP binding site [chemical binding]; other site 85963001463 Walker B motif; other site 85963001464 P-type DNA transfer ATPase VirB11; Region: VirB11; TIGR02788 85963001465 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 85963001466 ATP binding site [chemical binding]; other site 85963001467 Walker A motif; other site 85963001468 hexamer interface [polypeptide binding]; other site 85963001469 Walker B motif; other site 85963001470 CagZ; Region: CagZ; pfam09053 85963001471 DC-EC Repeat; Region: CagY_M; pfam07337 85963001472 DC-EC Repeat; Region: CagY_M; pfam07337 85963001473 DC-EC Repeat; Region: CagY_M; pfam07337 85963001474 DC-EC Repeat; Region: CagY_M; pfam07337 85963001475 DC-EC Repeat; Region: CagY_M; pfam07337 85963001476 DC-EC Repeat; Region: CagY_M; pfam07337 85963001477 DC-EC Repeat; Region: CagY_M; pfam07337 85963001478 DC-EC Repeat; Region: CagY_M; pfam07337 85963001479 DC-EC Repeat; Region: CagY_M; pfam07337 85963001480 DC-EC Repeat; Region: CagY_M; pfam07337 85963001481 DC-EC Repeat; Region: CagY_M; pfam07337 85963001482 DC-EC Repeat; Region: CagY_M; pfam07337 85963001483 DC-EC Repeat; Region: CagY_M; pfam07337 85963001484 DC-EC Repeat; Region: CagY_M; pfam07337 85963001485 Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion]; Region: VirB10; COG2948 85963001486 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cl11423 85963001487 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cl11423 85963001488 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 85963001489 VirB7 interaction site; other site 85963001490 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 85963001491 Cag pathogenicity island protein Cag12; Region: Cag12; pfam13117 85963001492 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK06945 85963001493 prolyl-tRNA synthetase; Provisional; Region: PRK08661 85963001494 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 85963001495 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 85963001496 CagA exotoxin; Region: CagA; pfam03507 85963001497 CagA exotoxin; Region: CagA; pfam03507 85963001498 glutamate racemase; Region: glut_race; TIGR00067 85963001499 transcription termination factor Rho; Provisional; Region: rho; PRK09376 85963001500 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 85963001501 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 85963001502 RNA binding site [nucleotide binding]; other site 85963001503 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 85963001504 multimer interface [polypeptide binding]; other site 85963001505 Walker A motif; other site 85963001506 ATP binding site [chemical binding]; other site 85963001507 Walker B motif; other site 85963001508 Ribosomal protein L31; Region: Ribosomal_L31; pfam01197 85963001509 Predicted methyltransferases [General function prediction only]; Region: COG0313 85963001510 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 85963001511 putative SAM binding site [chemical binding]; other site 85963001512 putative homodimer interface [polypeptide binding]; other site 85963001513 rRNA methylase, putative, group 3; Region: rRNA_methyl_3; TIGR00186 85963001514 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 85963001515 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 85963001516 acetyl-CoA carboxylase, carboxyl transferase, alpha subunit; Region: accA; TIGR00513 85963001517 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 85963001518 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK08439 85963001519 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 85963001520 dimer interface [polypeptide binding]; other site 85963001521 active site 85963001522 acyl carrier protein; Provisional; Region: acpP; PRK00982 85963001523 similar to hypothetical protein; similar to H. pylori 26695 gene HP0560 85963001524 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 85963001525 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 85963001526 NAD(P) binding site [chemical binding]; other site 85963001527 active site 85963001528 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 85963001529 Predicted membrane protein [Function unknown]; Region: COG3059 85963001530 diaminopimelate epimerase; Region: DapF; TIGR00652 85963001531 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 85963001532 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 85963001533 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 85963001534 Domain of unknown function DUF20; Region: UPF0118; pfam01594 85963001535 Domain of unknown function (DUF4008); Region: DUF4008; pfam13186 85963001536 GTP-binding protein YchF; Reviewed; Region: PRK09601 85963001537 YchF GTPase; Region: YchF; cd01900 85963001538 G1 box; other site 85963001539 GTP/Mg2+ binding site [chemical binding]; other site 85963001540 Switch I region; other site 85963001541 G2 box; other site 85963001542 Switch II region; other site 85963001543 G3 box; other site 85963001544 G4 box; other site 85963001545 G5 box; other site 85963001546 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 85963001547 multifunctional aminopeptidase A; Provisional; Region: PRK00913 85963001548 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 85963001549 interface (dimer of trimers) [polypeptide binding]; other site 85963001550 Substrate-binding/catalytic site; other site 85963001551 Zn-binding sites [ion binding]; other site 85963001552 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 85963001553 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 85963001554 active site 85963001555 ribose 5-phosphate isomerase B; Region: rpiB; TIGR01120 85963001556 Peptidase family M50; Region: Peptidase_M50; pfam02163 85963001557 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 85963001558 active site 85963001559 putative substrate binding region [chemical binding]; other site 85963001560 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 85963001561 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 85963001562 Catalytic site [active] 85963001563 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 85963001564 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14191 85963001565 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 85963001566 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 85963001567 homodimer interface [polypeptide binding]; other site 85963001568 NADP binding site [chemical binding]; other site 85963001569 substrate binding site [chemical binding]; other site 85963001570 Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]; Region: MdoB; COG1368 85963001571 Sulfatase; Region: Sulfatase; pfam00884 85963001572 Predicted neuraminidase (sialidase) [Carbohydrate transport and metabolism]; Region: COG4692 85963001573 BNR repeat-like domain; Region: BNR_2; pfam13088 85963001574 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 85963001575 active site 85963001576 substrate binding pocket [chemical binding]; other site 85963001577 dimer interface [polypeptide binding]; other site 85963001578 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 85963001579 TonB family C-terminal domain; Region: tonB_Cterm; TIGR01352 85963001580 flagellar motor switch protein; Validated; Region: PRK08433 85963001581 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 85963001582 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 85963001583 minor groove reading motif; other site 85963001584 helix-hairpin-helix signature motif; other site 85963001585 substrate binding pocket [chemical binding]; other site 85963001586 active site 85963001587 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 85963001588 Fe2+ transport system protein A [Inorganic ion transport and metabolism]; Region: FeoA; COG1918 85963001589 Protein of unknown function; Region: DUF3971; pfam13116 85963001590 AsmA-like C-terminal region; Region: AsmA_1; pfam13109 85963001591 Aminodeoxychorismate lyase [Coenzyme transport and metabolism]; Region: COG1559 85963001592 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 85963001593 dimerization interface [polypeptide binding]; other site 85963001594 2-oxoglutarate-acceptor oxidoreductase subunit OorD; Reviewed; Region: oorD; PRK09626 85963001595 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 85963001596 2-oxoglutarate-acceptor oxidoreductase subunit OorA; Reviewed; Region: oorA; PRK09627 85963001597 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 85963001598 dimer interface [polypeptide binding]; other site 85963001599 PYR/PP interface [polypeptide binding]; other site 85963001600 TPP binding site [chemical binding]; other site 85963001601 substrate binding site [chemical binding]; other site 85963001602 2-oxoglutarate-acceptor oxidoreductase subunit OorB; Reviewed; Region: oorB; PRK09628 85963001603 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 85963001604 TPP-binding site [chemical binding]; other site 85963001605 2-oxoglutarate-acceptor oxidoreductase subunit OorC; Reviewed; Region: oorC; PRK08441 85963001606 2-oxoglutarate ferredoxin oxidoreductase subunit gamma; Validated; Region: PRK08537 85963001607 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 85963001608 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 85963001609 motif II; other site 85963001610 Disulfide bond formation protein DsbB [Posttranslational modification, protein turnover, chaperones]; Region: DsbB; COG1495 85963001611 tumor necrosis factor alpha-inducing protein; Reviewed; Region: PRK12303 85963001612 Transglycosylase; Region: Transgly; pfam00912 85963001613 penicillin-binding protein, 1A family; Region: PBP_1a_fam; TIGR02074 85963001614 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 85963001615 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 85963001616 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 85963001617 catalytic residue [active] 85963001618 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 85963001619 dimer interface [polypeptide binding]; other site 85963001620 putative CheW interface [polypeptide binding]; other site 85963001621 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 85963001622 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 85963001623 ATP-binding cassette domain of multidrug resistance protein-like transporters; Region: ABCC_MRP_Like; cd03228 85963001624 Walker A/P-loop; other site 85963001625 ATP binding site [chemical binding]; other site 85963001626 Q-loop/lid; other site 85963001627 ABC transporter signature motif; other site 85963001628 Walker B; other site 85963001629 D-loop; other site 85963001630 H-loop/switch region; other site 85963001631 flagellin A; Reviewed; Region: PRK12584 85963001632 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 85963001633 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 85963001634 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 85963001635 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 85963001636 3-methyladenine DNA glycosylase; Provisional; Region: PRK13913 85963001637 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 85963001638 minor groove reading motif; other site 85963001639 helix-hairpin-helix signature motif; other site 85963001640 active site 85963001641 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 85963001642 substrate binding site [chemical binding]; other site 85963001643 active site 85963001644 Outer membrane efflux protein; Region: OEP; pfam02321 85963001645 Outer membrane efflux protein; Region: OEP; pfam02321 85963001646 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 85963001647 HlyD family secretion protein; Region: HlyD_3; pfam13437 85963001648 AcrB/AcrD/AcrF family; Region: ACR_tran; pfam00873 85963001649 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963001650 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 85963001651 PPE-repeat proteins [Cell motility and secretion]; Region: COG5651 85963001652 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 85963001653 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 85963001654 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 85963001655 PPE-repeat proteins [Cell motility and secretion]; Region: COG5651 85963001656 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 85963001657 Autotransporter beta-domain; Region: Autotransporter; pfam03797 85963001658 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 85963001659 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 85963001660 nucleotide binding pocket [chemical binding]; other site 85963001661 K-X-D-G motif; other site 85963001662 catalytic site [active] 85963001663 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 85963001664 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 85963001665 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 85963001666 Dimer interface [polypeptide binding]; other site 85963001667 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 85963001668 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 85963001669 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 85963001670 active site 85963001671 phosphorylation site [posttranslational modification] 85963001672 intermolecular recognition site; other site 85963001673 dimerization interface [polypeptide binding]; other site 85963001674 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 85963001675 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 85963001676 dimer interface [polypeptide binding]; other site 85963001677 anticodon binding site; other site 85963001678 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 85963001679 homodimer interface [polypeptide binding]; other site 85963001680 motif 1; other site 85963001681 active site 85963001682 motif 2; other site 85963001683 GAD domain; Region: GAD; pfam02938 85963001684 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 85963001685 active site 85963001686 motif 3; other site 85963001687 adenylate kinase; Reviewed; Region: adk; PRK00279 85963001688 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 85963001689 AMP-binding site [chemical binding]; other site 85963001690 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 85963001691 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 85963001692 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 85963001693 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 85963001694 Glycosyltransferase involved in LPS biosynthesis [Cell envelope biogenesis, outer membrane]; Region: COG3306 85963001695 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 85963001696 dimer interface [polypeptide binding]; other site 85963001697 substrate binding site [chemical binding]; other site 85963001698 metal binding sites [ion binding]; metal-binding site 85963001699 recombination and DNA strand exchange inhibitor protein; Reviewed; Region: PRK00409 85963001700 ATPase domain of DNA mismatch repair MUTS family; Region: MUTSac; smart00534 85963001701 Walker A/P-loop; other site 85963001702 ATP binding site [chemical binding]; other site 85963001703 Q-loop/lid; other site 85963001704 ABC transporter signature motif; other site 85963001705 Walker B; other site 85963001706 D-loop; other site 85963001707 H-loop/switch region; other site 85963001708 Smr domain; Region: Smr; pfam01713 85963001709 UDP-N-acetylmuramate--alanine ligase; Region: murC; TIGR01082 85963001710 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 85963001711 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 85963001712 hypothetical protein; Provisional; Region: PRK05839 85963001713 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 85963001714 pyridoxal 5'-phosphate binding site [chemical binding]; other site 85963001715 homodimer interface [polypeptide binding]; other site 85963001716 catalytic residue [active] 85963001717 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 85963001718 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 85963001719 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 85963001720 Tetrahydrodipicolinate N-succinyltransferase [Amino acid transport and metabolism]; Region: DapD; COG2171 85963001721 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 85963001722 putative trimer interface [polypeptide binding]; other site 85963001723 putative CoA binding site [chemical binding]; other site 85963001724 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 85963001725 Sel1-like repeats; Region: SEL1; smart00671 85963001726 Sel1-like repeats; Region: SEL1; smart00671 85963001727 Sel1 repeat; Region: Sel1; cl02723 85963001728 Sel1-like repeats; Region: SEL1; smart00671 85963001729 Uncharacterized conserved protein [Function unknown]; Region: COG1479 85963001730 Protein of unknown function DUF262; Region: DUF262; pfam03235 85963001731 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 85963001732 Putative NADPH-quinone reductase (modulator of drug activity B) [General function prediction only]; Region: MdaB; COG2249 85963001733 hydrogenase (NiFe) small subunit (hydA); Region: hydA; TIGR00391 85963001734 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 85963001735 Ni,Fe-hydrogenase I large subunit [Energy production and conversion]; Region: HyaB; COG0374 85963001736 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; pfam00374 85963001737 Ni/Fe-hydrogenase, b-type cytochrome subunit; Region: CytB-hydogenase; TIGR02125 85963001738 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 85963001739 nickel binding site [ion binding]; other site 85963001740 putative substrate-binding site; other site 85963001741 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963001742 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 85963001743 Ligand Binding Site [chemical binding]; other site 85963001744 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 85963001745 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 85963001746 active site 85963001747 NTP binding site [chemical binding]; other site 85963001748 metal binding triad [ion binding]; metal-binding site 85963001749 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 85963001750 Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins; Region: SRPBCC_4; cd07822 85963001751 putative hydrophobic ligand binding site [chemical binding]; other site 85963001752 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 85963001753 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 85963001754 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 85963001755 dimer interface [polypeptide binding]; other site 85963001756 FMN binding site [chemical binding]; other site 85963001757 glutamylglutaminyl-tRNA synthetase; Provisional; Region: PRK12410 85963001758 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 85963001759 active site 85963001760 HIGH motif; other site 85963001761 nucleotide binding site [chemical binding]; other site 85963001762 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 85963001763 active site 85963001764 KMSKS motif; other site 85963001765 YGGT family; Region: YGGT; pfam02325 85963001766 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 85963001767 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 85963001768 N-acetyl-D-glucosamine binding site [chemical binding]; other site 85963001769 catalytic residue [active] 85963001770 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 85963001771 dTDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]; Region: RfbA; COG1209 85963001772 active site 85963001773 tetramer interface; other site 85963001774 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 85963001775 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 85963001776 hinge; other site 85963001777 active site 85963001778 aspartate ammonia-lyase; Provisional; Region: aspA; PRK12273 85963001779 Aspartase; Region: Aspartase; cd01357 85963001780 active sites [active] 85963001781 tetramer interface [polypeptide binding]; other site 85963001782 Uncharacterized subfamily of Uracil-DNA glycosylases; Region: UDG_like_2; cd10034 85963001783 putative uracil binding site [chemical binding]; other site 85963001784 putative active site [active] 85963001785 Glycosyltransferase family 10 (fucosyltransferase); Region: Glyco_transf_10; pfam00852 85963001786 phosphoserine phosphatase SerB; Region: serB; TIGR00338 85963001787 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 85963001788 motif II; other site 85963001789 nonheme-containing ferritins; Region: Nonheme_Ferritin; cd01055 85963001790 Ferritin-like domain; Region: Ferritin; pfam00210 85963001791 ferroxidase diiron center [ion binding]; other site 85963001792 hypothetical protein; Provisional; Region: PRK08444 85963001793 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 85963001794 FeS/SAM binding site; other site 85963001795 Outer membrane protein/protective antigen OMA87 [Cell envelope biogenesis, outer membrane]; Region: COG4775 85963001796 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 85963001797 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 85963001798 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 85963001799 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 85963001800 Surface antigen; Region: Bac_surface_Ag; pfam01103 85963001801 hypothetical protein; Provisional; Region: PRK08445 85963001802 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 85963001803 FeS/SAM binding site; other site 85963001804 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 85963001805 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 85963001806 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 85963001807 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 85963001808 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 85963001809 GatB domain; Region: GatB_Yqey; smart00845 85963001810 SurA N-terminal domain; Region: SurA_N; pfam09312 85963001811 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]; Region: COG2956 85963001812 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]; Region: COG1439 85963001813 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 85963001814 RNA/DNA hybrid binding site [nucleotide binding]; other site 85963001815 active site 85963001816 ribonuclease III; Reviewed; Region: rnc; PRK00102 85963001817 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 85963001818 dimerization interface [polypeptide binding]; other site 85963001819 active site 85963001820 metal binding site [ion binding]; metal-binding site 85963001821 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 85963001822 dsRNA binding site [nucleotide binding]; other site 85963001823 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 85963001824 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 85963001825 Tetramer interface [polypeptide binding]; other site 85963001826 active site 85963001827 FMN-binding site [chemical binding]; other site 85963001828 Protein of unknown function (DUF2603); Region: DUF2603; pfam10788 85963001829 oxygen-independent coproporphyrinogen III oxidase; Region: hemN; TIGR00538 85963001830 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 85963001831 FeS/SAM binding site; other site 85963001832 HemN C-terminal domain; Region: HemN_C; pfam06969 85963001833 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 85963001834 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 85963001835 Cysteine-rich domain; Region: CCG; pfam02754 85963001836 Cysteine-rich domain; Region: CCG; pfam02754 85963001837 Predicted helicase [General function prediction only]; Region: COG4889 85963001838 Restriction endonuclease; Region: Mrr_cat_2; pfam13156 85963001839 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 85963001840 ATP binding site [chemical binding]; other site 85963001841 putative Mg++ binding site [ion binding]; other site 85963001842 Predicted helicase [General function prediction only]; Region: COG4889 85963001843 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 85963001844 nucleotide binding region [chemical binding]; other site 85963001845 ATP-binding site [chemical binding]; other site 85963001846 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963001847 aspartate aminotransferase; Provisional; Region: PRK05764 85963001848 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 85963001849 pyridoxal 5'-phosphate binding site [chemical binding]; other site 85963001850 homodimer interface [polypeptide binding]; other site 85963001851 catalytic residue [active] 85963001852 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 85963001853 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 85963001854 active site 85963001855 DNA binding site [nucleotide binding] 85963001856 Int/Topo IB signature motif; other site 85963001857 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 85963001858 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 85963001859 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 85963001860 DNA binding site [nucleotide binding] 85963001861 active site 85963001862 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 85963001863 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 85963001864 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 85963001865 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 85963001866 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK08447 85963001867 ATP cone domain; Region: ATP-cone; pfam03477 85963001868 Class I ribonucleotide reductase; Region: RNR_I; cd01679 85963001869 active site 85963001870 dimer interface [polypeptide binding]; other site 85963001871 catalytic residues [active] 85963001872 effector binding site; other site 85963001873 R2 peptide binding site; other site 85963001874 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK14359 85963001875 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 85963001876 Substrate binding site; other site 85963001877 Mg++ binding site; other site 85963001878 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 85963001879 active site 85963001880 substrate binding site [chemical binding]; other site 85963001881 CoA binding site [chemical binding]; other site 85963001882 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK05699 85963001883 Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]; Region: FecA; COG4772 85963001884 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 85963001885 N-terminal plug; other site 85963001886 ligand-binding site [chemical binding]; other site 85963001887 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 85963001888 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 85963001889 G1 box; other site 85963001890 GTP/Mg2+ binding site [chemical binding]; other site 85963001891 Switch I region; other site 85963001892 G2 box; other site 85963001893 G3 box; other site 85963001894 Switch II region; other site 85963001895 G4 box; other site 85963001896 G5 box; other site 85963001897 Nucleoside recognition; Region: Gate; pfam07670 85963001898 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 85963001899 Nucleoside recognition; Region: Gate; pfam07670 85963001900 Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; Region: DNA_polB_like1_exo; cd05782 85963001901 active site 85963001902 catalytic site [active] 85963001903 substrate binding site [chemical binding]; other site 85963001904 Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; Region: DNA_pol_B_exo2; pfam10108 85963001905 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 85963001906 DNA methylase; Region: N6_N4_Mtase; pfam01555 85963001907 CfrBI restriction endonuclease; Region: RE_CfrBI; pfam09516 85963001908 Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcxC; COG4647 85963001909 Acetone carboxylase gamma subunit; Region: Acetone_carb_G; pfam08882 85963001910 N-methylhydantoinase B/acetone carboxylase, alpha subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuB; COG0146 85963001911 Hydantoinase B/oxoprolinase; Region: Hydantoinase_B; pfam02538 85963001912 N-methylhydantoinase A/acetone carboxylase, beta subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuA; COG0145 85963001913 Hydantoinase/oxoprolinase N-terminal region; Region: Hydant_A_N; pfam05378 85963001914 Hydantoinase/oxoprolinase; Region: Hydantoinase_A; pfam01968 85963001915 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3528 85963001916 Short chain fatty acid transporter; Region: SCFA_trans; pfam02667 85963001917 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 85963001918 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 85963001919 putative acyltransferase; Provisional; Region: PRK05790 85963001920 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 85963001921 dimer interface [polypeptide binding]; other site 85963001922 active site 85963001923 Diacylglycerol kinase [Cell envelope biogenesis, outer membrane]; Region: DgkA; COG0818 85963001924 DNA gyrase subunit A; Validated; Region: PRK05560 85963001925 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 85963001926 CAP-like domain; other site 85963001927 active site 85963001928 primary dimer interface [polypeptide binding]; other site 85963001929 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 85963001930 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 85963001931 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 85963001932 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 85963001933 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 85963001934 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 85963001935 Response regulator receiver domain; Region: Response_reg; pfam00072 85963001936 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 85963001937 active site 85963001938 phosphorylation site [posttranslational modification] 85963001939 intermolecular recognition site; other site 85963001940 dimerization interface [polypeptide binding]; other site 85963001941 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 85963001942 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 85963001943 Walker A motif; other site 85963001944 ATP binding site [chemical binding]; other site 85963001945 Walker B motif; other site 85963001946 arginine finger; other site 85963001947 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 85963001948 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 85963001949 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 85963001950 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 85963001951 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963001952 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG0275 85963001953 16S rRNA (cytosine(1402)-N(4))-methyltransferase; Region: TIGR00006 85963001954 Uncharacterized conserved protein [Function unknown]; Region: COG1912 85963001955 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963001956 Competence protein ComGF [Intracellular trafficking and secretion]; Region: ComGF; COG4940 85963001957 Predicted hydrolases of HD superfamily [General function prediction only]; Region: COG1896 85963001958 Fic family protein [Function unknown]; Region: COG3177 85963001959 Fic/DOC family; Region: Fic; pfam02661 85963001960 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 85963001961 RNA polymerase sigma-54 factor; Region: rpoN_sigma; TIGR02395 85963001962 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 85963001963 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 85963001964 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 85963001965 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 85963001966 Walker A/P-loop; other site 85963001967 ATP binding site [chemical binding]; other site 85963001968 Q-loop/lid; other site 85963001969 ABC transporter signature motif; other site 85963001970 Walker B; other site 85963001971 D-loop; other site 85963001972 H-loop/switch region; other site 85963001973 Uncharacterized P-loop hydrolase UPF0079; Region: UPF0079; cl00520 85963001974 DNA polymerase III subunits gamma and tau; Validated; Region: PRK08451 85963001975 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 85963001976 Walker A motif; other site 85963001977 ATP binding site [chemical binding]; other site 85963001978 Walker B motif; other site 85963001979 arginine finger; other site 85963001980 L-lysine exporter; Region: 2a75; TIGR00948 85963001981 Protein of unknown function (DUF1104); Region: DUF1104; pfam06518 85963001982 Protein of unknown function (DUF1104); Region: DUF1104; pfam06518 85963001983 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963001984 anaerobic c4-dicarboxylate membrane transporter family protein; Region: Dcu; TIGR00770 85963001985 Anaerobic C4-dicarboxylate transporter [General function prediction only]; Region: DcuB; COG2704 85963001986 Type II (periplasmic) bacterial L-asparaginase; Region: L-asparaginase_II; cd08964 85963001987 active site 85963001988 homotetramer interface [polypeptide binding]; other site 85963001989 homodimer interface [polypeptide binding]; other site 85963001990 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963001991 tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; Region: COG0042 85963001992 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 85963001993 FMN binding site [chemical binding]; other site 85963001994 active site 85963001995 catalytic residues [active] 85963001996 substrate binding site [chemical binding]; other site 85963001997 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 85963001998 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 85963001999 Ligand Binding Site [chemical binding]; other site 85963002000 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 85963002001 G1 box; other site 85963002002 GTP/Mg2+ binding site [chemical binding]; other site 85963002003 G2 box; other site 85963002004 Switch I region; other site 85963002005 G3 box; other site 85963002006 Switch II region; other site 85963002007 G4 box; other site 85963002008 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 85963002009 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 85963002010 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 85963002011 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 85963002012 FeS/SAM binding site; other site 85963002013 Predicted phosphoribosyltransferases [General function prediction only]; Region: COG2236 85963002014 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 85963002015 active site 85963002016 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]; Region: COG0075 85963002017 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 85963002018 catalytic residue [active] 85963002019 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 85963002020 tetramer interfaces [polypeptide binding]; other site 85963002021 binuclear metal-binding site [ion binding]; other site 85963002022 D-alanyl-alanine synthetase A; Reviewed; Region: ddl; PRK01966 85963002023 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 85963002024 ATP-grasp domain; Region: ATP-grasp_4; cl17255 85963002025 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 85963002026 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 85963002027 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 85963002028 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 85963002029 nucleotide binding site/active site [active] 85963002030 HIT family signature motif; other site 85963002031 catalytic residue [active] 85963002032 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 85963002033 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 85963002034 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 85963002035 active site 85963002036 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 85963002037 Predicted GTPase [General function prediction only]; Region: COG3596 85963002038 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cd00882 85963002039 G1 box; other site 85963002040 GTP/Mg2+ binding site [chemical binding]; other site 85963002041 G2 box; other site 85963002042 Switch I region; other site 85963002043 G3 box; other site 85963002044 Switch II region; other site 85963002045 G4 box; other site 85963002046 Uncharacterized protein/domain associated with GTPases [Function unknown]; Region: COG3597 85963002047 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 85963002048 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 85963002049 RNA binding surface [nucleotide binding]; other site 85963002050 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 85963002051 active site 85963002052 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 85963002053 Fibronectin type 3 domain-containing protein [General function prediction only]; Region: COG3401 85963002054 Interdomain contacts; other site 85963002055 Cytokine receptor motif; other site 85963002056 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 85963002057 Interdomain contacts; other site 85963002058 Cytokine receptor motif; other site 85963002059 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 85963002060 Interdomain contacts; other site 85963002061 Cytokine receptor motif; other site 85963002062 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 85963002063 S-adenosylmethionine binding site [chemical binding]; other site 85963002064 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 85963002065 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 85963002066 Walker A/P-loop; other site 85963002067 ATP binding site [chemical binding]; other site 85963002068 Q-loop/lid; other site 85963002069 ABC transporter signature motif; other site 85963002070 Walker B; other site 85963002071 D-loop; other site 85963002072 H-loop/switch region; other site 85963002073 putative protein insertion permease FtsX; Region: ftsX; TIGR00439 85963002074 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 85963002075 Peptidase family M23; Region: Peptidase_M23; pfam01551 85963002076 flagellar protein FlaG; Provisional; Region: PRK08452 85963002077 flagellar capping protein; Validated; Region: fliD; PRK08453 85963002078 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 85963002079 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 85963002080 flagellar biosynthetic protein FliS; Region: fliS; TIGR00208 85963002081 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 85963002082 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 85963002083 putative ATP binding site [chemical binding]; other site 85963002084 putative substrate interface [chemical binding]; other site 85963002085 N-carbamoylputrescine amidohydrolase (CPA) (class 11 nitrilases); Region: CPA; cd07573 85963002086 N-carbamoylputrescine amidase; Region: agmatine_aguB; TIGR03381 85963002087 putative active site; other site 85963002088 catalytic triad [active] 85963002089 putative dimer interface [polypeptide binding]; other site 85963002090 Predicted permease [General function prediction only]; Region: COG2056 85963002091 Na+-H+ antiporter family; Region: Na_H_antiport_2; pfam13726 85963002092 Predicted membrane protein [Function unknown]; Region: COG1288; cl17886 85963002093 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Thermotoga marina NorM; Region: MATE_NorM_like; cd13137 85963002094 putative efflux protein, MATE family; Region: matE; TIGR00797 85963002095 phosphodiesterase; Provisional; Region: PRK12704 85963002096 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 85963002097 nucleic acid binding region [nucleotide binding]; other site 85963002098 G-X-X-G motif; other site 85963002099 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 85963002100 Zn2+ binding site [ion binding]; other site 85963002101 Mg2+ binding site [ion binding]; other site 85963002102 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212 85963002103 signal recognition particle-docking protein FtsY; Region: ftsY; TIGR00064 85963002104 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 85963002105 Predicted Fe-S-cluster oxidoreductase [General function prediction only]; Region: COG0727 85963002106 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 85963002107 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 85963002108 FeS/SAM binding site; other site 85963002109 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 85963002110 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 85963002111 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 85963002112 GTP binding site; other site 85963002113 flagellar biosynthetic protein FlhB; Region: flhB; TIGR00328 85963002114 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 85963002115 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 85963002116 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 85963002117 active site 85963002118 metal binding site [ion binding]; metal-binding site 85963002119 Nitronate monooxygenase; Region: NMO; pfam03060 85963002120 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 85963002121 FMN binding site [chemical binding]; other site 85963002122 substrate binding site [chemical binding]; other site 85963002123 putative catalytic residue [active] 85963002124 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 85963002125 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 85963002126 active site 85963002127 HIGH motif; other site 85963002128 dimer interface [polypeptide binding]; other site 85963002129 KMSKS motif; other site 85963002130 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 85963002131 RNA binding surface [nucleotide binding]; other site 85963002132 (p)ppGpp synthetase, RelA/SpoT family; Region: spoT_relA; TIGR00691 85963002133 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 85963002134 Zn2+ binding site [ion binding]; other site 85963002135 Mg2+ binding site [ion binding]; other site 85963002136 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 85963002137 synthetase active site [active] 85963002138 NTP binding site [chemical binding]; other site 85963002139 metal binding site [ion binding]; metal-binding site 85963002140 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 85963002141 DNA-directed RNA polymerase, subunit K/omega [Transcription]; Region: RpoZ; COG1758 85963002142 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 85963002143 putative nucleotide binding site [chemical binding]; other site 85963002144 uridine monophosphate binding site [chemical binding]; other site 85963002145 homohexameric interface [polypeptide binding]; other site 85963002146 Predicted periplasmic solute-binding protein [General function prediction only]; Region: COG1427 85963002147 aconitate hydratase 2; Region: acnB; TIGR00117 85963002148 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 85963002149 substrate binding site [chemical binding]; other site 85963002150 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 85963002151 substrate binding site [chemical binding]; other site 85963002152 ligand binding site [chemical binding]; other site 85963002153 FOG: Transposase [DNA replication, recombination, and repair]; Region: COG5659 85963002154 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 85963002155 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 85963002156 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 85963002157 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 85963002158 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 85963002159 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 85963002160 nucleotide binding region [chemical binding]; other site 85963002161 ATP-binding site [chemical binding]; other site 85963002162 SEC-C motif; Region: SEC-C; pfam02810 85963002163 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 85963002164 FtsX-like permease family; Region: FtsX; pfam02687 85963002165 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 85963002166 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 85963002167 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 85963002168 metal-binding site [ion binding] 85963002169 heavy metal-(Cd/Co/Hg/Pb/Zn)-translocating P-type ATPase; Region: ATPase-IB2_Cd; TIGR01512 85963002170 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 85963002171 Soluble P-type ATPase [General function prediction only]; Region: COG4087 85963002172 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 85963002173 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 85963002174 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 85963002175 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 85963002176 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 85963002177 active site 85963002178 catalytic residues [active] 85963002179 metal binding site [ion binding]; metal-binding site 85963002180 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 85963002181 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 85963002182 oligomer interface [polypeptide binding]; other site 85963002183 active site residues [active] 85963002184 trigger factor; Provisional; Region: tig; PRK01490 85963002185 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 85963002186 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 85963002187 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963002188 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 85963002189 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 85963002190 trimer interface [polypeptide binding]; other site 85963002191 dimer interface [polypeptide binding]; other site 85963002192 putative active site [active] 85963002193 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 85963002194 MPT binding site; other site 85963002195 trimer interface [polypeptide binding]; other site 85963002196 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 85963002197 MoaE homodimer interface [polypeptide binding]; other site 85963002198 MoaD interaction [polypeptide binding]; other site 85963002199 active site residues [active] 85963002200 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 85963002201 MoaE interaction surface [polypeptide binding]; other site 85963002202 MoeB interaction surface [polypeptide binding]; other site 85963002203 thiocarboxylated glycine; other site 85963002204 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 85963002205 dimerization interface [polypeptide binding]; other site 85963002206 active site 85963002207 Domain of unknown function (DUF3943); Region: DUF3943; pfam13084 85963002208 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional; Region: PRK09314 85963002209 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: ribB; TIGR00506 85963002210 GTP cyclohydrolase II [Coenzyme metabolism]; Region: RibA; COG0807 85963002211 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 85963002212 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG1451 85963002213 Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]; Region: FecA; COG4772 85963002214 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 85963002215 N-terminal plug; other site 85963002216 ligand-binding site [chemical binding]; other site 85963002217 holo-[acyl-carrier-protein] synthase; Region: acpS; TIGR00516 85963002218 flagellar basal body-associated protein FliL; Reviewed; Region: fliL; PRK08455 85963002219 RNA methyltransferase, RsmD family; Region: TIGR00095 85963002220 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 85963002221 Uncharacterized conserved protein [Function unknown]; Region: COG1565 85963002222 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 85963002223 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 2 [Coenzyme metabolism]; Region: ThiF; COG0476 85963002224 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 85963002225 ATP binding site [chemical binding]; other site 85963002226 substrate interface [chemical binding]; other site 85963002227 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 85963002228 flagellar motor protein MotA; Validated; Region: PRK08456 85963002229 flagellar motor protein MotB; Reviewed; Region: motB; PRK08457 85963002230 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 85963002231 ligand binding site [chemical binding]; other site 85963002232 ABC-type proline/glycine betaine transport systems, permease component [Amino acid transport and metabolism]; Region: OpuBB; COG1174 85963002233 Recombination endonuclease VII; Region: Endonuclease_7; pfam02945 85963002234 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 85963002235 DNA methylase; Region: N6_N4_Mtase; pfam01555 85963002236 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 85963002237 dimer interface [polypeptide binding]; other site 85963002238 conserved gate region; other site 85963002239 ABC-ATPase subunit interface; other site 85963002240 Periplasmic glycine betaine/choline-binding (lipo)protein of an ABC-type transport system (osmoprotectant binding protein) [Cell envelope biogenesis, outer membrane]; Region: OpuBC; COG1732 85963002241 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 85963002242 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 85963002243 Walker A/P-loop; other site 85963002244 ATP binding site [chemical binding]; other site 85963002245 Q-loop/lid; other site 85963002246 ABC transporter signature motif; other site 85963002247 Walker B; other site 85963002248 D-loop; other site 85963002249 H-loop/switch region; other site 85963002250 excinuclease ABC, C subunit; Region: uvrC; TIGR00194 85963002251 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 85963002252 GIY-YIG motif/motif A; other site 85963002253 active site 85963002254 catalytic site [active] 85963002255 putative DNA binding site [nucleotide binding]; other site 85963002256 metal binding site [ion binding]; metal-binding site 85963002257 UvrB/uvrC motif; Region: UVR; pfam02151 85963002258 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 85963002259 homoserine dehydrogenase; Provisional; Region: PRK06349 85963002260 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 85963002261 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 85963002262 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 85963002263 Uncharacterized protein family UPF0102; Region: UPF0102; pfam02021 85963002264 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 85963002265 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 85963002266 catalytic residues [active] 85963002267 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 85963002268 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 85963002269 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 85963002270 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 85963002271 RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins; Region: RRM_HP0827_like; cd12399 85963002272 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 85963002273 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 85963002274 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 85963002275 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 85963002276 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 85963002277 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 85963002278 active site 85963002279 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 85963002280 indole acetimide hydrolase; Validated; Region: PRK07488 85963002281 dephospho-CoA kinase; Region: TIGR00152 85963002282 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 85963002283 CoA-binding site [chemical binding]; other site 85963002284 ATP-binding [chemical binding]; other site 85963002285 spermidine synthase; Provisional; Region: speE; PRK00536 85963002286 spermidine synthase; Provisional; Region: PRK00811 85963002287 GTP-binding protein Der; Reviewed; Region: PRK00093 85963002288 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 85963002289 G1 box; other site 85963002290 GTP/Mg2+ binding site [chemical binding]; other site 85963002291 Switch I region; other site 85963002292 G2 box; other site 85963002293 Switch II region; other site 85963002294 G3 box; other site 85963002295 G4 box; other site 85963002296 G5 box; other site 85963002297 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 85963002298 G1 box; other site 85963002299 GTP/Mg2+ binding site [chemical binding]; other site 85963002300 Switch I region; other site 85963002301 G2 box; other site 85963002302 G3 box; other site 85963002303 Switch II region; other site 85963002304 G4 box; other site 85963002305 G5 box; other site 85963002306 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 85963002307 IHF dimer interface [polypeptide binding]; other site 85963002308 IHF - DNA interface [nucleotide binding]; other site 85963002309 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3018 85963002310 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3018 85963002311 Long-chain fatty acid transport protein [Lipid metabolism]; Region: FadL; COG2067 85963002312 UDP-N-acetylglucosamine 4,6-dehydratase; Region: PseB; TIGR03589 85963002313 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 85963002314 NAD(P) binding site [chemical binding]; other site 85963002315 homodimer interface [polypeptide binding]; other site 85963002316 substrate binding site [chemical binding]; other site 85963002317 active site 85963002318 phosphopantothenoylcysteine decarboxylase / phosphopantothenate--cysteine ligase; Region: coaBC_dfp; TIGR00521 85963002319 Flavoprotein; Region: Flavoprotein; pfam02441 85963002320 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 85963002321 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 85963002322 thiamine phosphate binding site [chemical binding]; other site 85963002323 active site 85963002324 pyrophosphate binding site [ion binding]; other site 85963002325 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 85963002326 dimer interface [polypeptide binding]; other site 85963002327 substrate binding site [chemical binding]; other site 85963002328 ATP binding site [chemical binding]; other site 85963002329 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 85963002330 substrate binding site [chemical binding]; other site 85963002331 multimerization interface [polypeptide binding]; other site 85963002332 ATP binding site [chemical binding]; other site 85963002333 type I site-specific deoxyribonuclease, HsdR family; Region: hsdR; TIGR00348 85963002334 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 85963002335 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 85963002336 ATP binding site [chemical binding]; other site 85963002337 putative Mg++ binding site [ion binding]; other site 85963002338 Type I restriction and modification enzyme - subunit R C terminal; Region: EcoR124_C; pfam12008 85963002339 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 85963002340 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 85963002341 type I restriction system adenine methylase (hsdM); Region: hsdM; TIGR00497 85963002342 HsdM N-terminal domain; Region: HsdM_N; pfam12161 85963002343 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 85963002344 S-adenosylmethionine binding site [chemical binding]; other site 85963002345 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 85963002346 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 85963002347 active site 85963002348 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2958 85963002349 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 85963002350 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 85963002351 Walker A/P-loop; other site 85963002352 ATP binding site [chemical binding]; other site 85963002353 Q-loop/lid; other site 85963002354 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 85963002355 ABC transporter; Region: ABC_tran_2; pfam12848 85963002356 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 85963002357 guanosine 5'-monophosphate oxidoreductase; Provisional; Region: PRK05458 85963002358 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 85963002359 active site 85963002360 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 85963002361 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 85963002362 dimer interface [polypeptide binding]; other site 85963002363 active site 85963002364 ADP-heptose synthase, bifunctional sugar kinase/adenylyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaE; COG2870 85963002365 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 85963002366 putative ribose interaction site [chemical binding]; other site 85963002367 putative ADP binding site [chemical binding]; other site 85963002368 rfaE bifunctional protein, domain II; Region: rfaE_dom_II; TIGR02199 85963002369 active site 85963002370 nucleotide binding site [chemical binding]; other site 85963002371 HIGH motif; other site 85963002372 KMSKS motif; other site 85963002373 ADP-L-glycero-D-mannoheptose 6-epimerase (GME), extended (e) SDRs; Region: ADP_GME_SDR_e; cd05248 85963002374 ADP-L-glycero-D-manno-heptose-6-epimerase; Region: heptose_epim; TIGR02197 85963002375 NADP binding site [chemical binding]; other site 85963002376 homopentamer interface [polypeptide binding]; other site 85963002377 substrate binding site [chemical binding]; other site 85963002378 active site 85963002379 D,D-heptose 1,7-bisphosphate phosphatase; Region: GmhB_yaeD; TIGR00213 85963002380 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 85963002381 active site 85963002382 motif I; other site 85963002383 motif II; other site 85963002384 Uncharacterized conserved protein [Function unknown]; Region: COG2836 85963002385 pantothenate kinase; Reviewed; Region: PRK13333 85963002386 PQQ-like domain; Region: PQQ_2; pfam13360 85963002387 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 85963002388 trimer interface [polypeptide binding]; other site 85963002389 active site 85963002390 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 85963002391 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 85963002392 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 85963002393 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 85963002394 lipid-A-disaccharide synthase; Region: lpxB; TIGR00215 85963002395 hydrogenase nickel incorporation protein; Provisional; Region: hypA; PRK00564 85963002396 Hydrogenase expression/synthesis hypA family; Region: HypA; pfam01155 85963002397 flagellar hook protein FlgE; Validated; Region: flgE; PRK08425 85963002398 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 85963002399 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 85963002400 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 85963002401 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 85963002402 CDP-diacylglycerol pyrophosphatase, bacterial type; Region: cdh; TIGR00672 85963002403 alkylphosphonate utilization operon protein PhnA; Region: phnA; TIGR00686 85963002404 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; pfam08274 85963002405 PhnA protein; Region: PhnA; pfam03831 85963002406 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 85963002407 Clade 3 of the heme-binding enzyme catalase; Region: catalase_clade_3; cd08156 85963002408 tetramer interface [polypeptide binding]; other site 85963002409 heme binding pocket [chemical binding]; other site 85963002410 NADPH binding site [chemical binding]; other site 85963002411 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 85963002412 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 85963002413 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 85963002414 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 85963002415 active site 85963002416 putative DNA-binding cleft [nucleotide binding]; other site 85963002417 dimer interface [polypeptide binding]; other site 85963002418 Uncharacterized conserved protein [Function unknown]; Region: COG1432 85963002419 LabA_like proteins; Region: LabA_like; cd06167 85963002420 putative metal binding site [ion binding]; other site 85963002421 Protein of unknown function (DUF3519); Region: DUF3519; pfam12033 85963002422 Protein of unknown function (DUF3519); Region: DUF3519; pfam12033 85963002423 Holliday junction DNA helicase, RuvA subunit; Region: ruvA; TIGR00084 85963002424 RuvA N terminal domain; Region: RuvA_N; pfam01330 85963002425 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 85963002426 MviN-like protein; Region: MVIN; pfam03023 85963002427 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 85963002428 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 85963002429 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 85963002430 active site 85963002431 HIGH motif; other site 85963002432 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 85963002433 KMSKS motif; other site 85963002434 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 85963002435 tRNA binding surface [nucleotide binding]; other site 85963002436 anticodon binding site; other site 85963002437 Vacuolating cyotoxin; Region: VacA; pfam02691 85963002438 Autotransporter beta-domain; Region: Autotransporter; pfam03797 85963002439 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 85963002440 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 85963002441 Ligand binding site; other site 85963002442 metal-binding site 85963002443 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 85963002444 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 85963002445 Walker A/P-loop; other site 85963002446 ATP binding site [chemical binding]; other site 85963002447 Q-loop/lid; other site 85963002448 ABC transporter signature motif; other site 85963002449 Walker B; other site 85963002450 D-loop; other site 85963002451 H-loop/switch region; other site 85963002452 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 85963002453 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 85963002454 ABC-ATPase subunit interface; other site 85963002455 dimer interface [polypeptide binding]; other site 85963002456 putative PBP binding regions; other site 85963002457 short chain dehydrogenase; Validated; Region: PRK06182 85963002458 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 85963002459 NADP binding site [chemical binding]; other site 85963002460 active site 85963002461 steroid binding site; other site 85963002462 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 85963002463 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3041 85963002464 Helix-turn-helix domain; Region: HTH_OrfB_IS605; pfam12323 85963002465 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 85963002466 Probable transposase; Region: OrfB_IS605; pfam01385 85963002467 transposase, IS605 OrfB family, central region; Region: tspaseT_teng_C; TIGR01766 85963002468 Transposase IS200 like; Region: Y1_Tnp; pfam01797 85963002469 Uncharacterized virulence-associated protein D [Function unknown]; Region: VapD; COG3309 85963002470 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3041 85963002471 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963002472 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypD; COG0409 85963002473 hydrogenase expression/formation protein HypD; Region: hypD; TIGR00075 85963002474 hydrogenase isoenzymes formation protein HypD; Provisional; Region: PRK15062 85963002475 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypC; COG0298 85963002476 hydrogenase accessory protein HypB; Region: hypB; TIGR00073 85963002477 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 85963002478 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 85963002479 acetate kinase A/propionate kinase 2; Reviewed; Region: PRK00180 85963002480 propionate/acetate kinase; Provisional; Region: PRK12379 85963002481 BioD-like N-terminal domain of phosphotransacetylase [General function prediction only]; Region: Pta; COG0857 85963002482 phosphotransacetylase; Reviewed; Region: eutD; PRK09653 85963002483 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 85963002484 flagellar basal body rod modification protein; Reviewed; Region: flgD; PRK05842 85963002485 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 85963002486 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 85963002487 flagellar hook protein FlgE; Validated; Region: flgE; PRK05841 85963002488 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 85963002489 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0827 85963002490 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 85963002491 S-adenosylmethionine binding site [chemical binding]; other site 85963002492 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 85963002493 Part of AAA domain; Region: AAA_19; pfam13245 85963002494 Family description; Region: UvrD_C_2; pfam13538 85963002495 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963002496 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963002497 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 85963002498 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 85963002499 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 85963002500 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 85963002501 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 85963002502 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 85963002503 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 85963002504 ATP-grasp domain; Region: ATP-grasp_4; cl17255 85963002505 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 85963002506 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 85963002507 ATP-grasp domain; Region: ATP-grasp_4; cl17255 85963002508 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 85963002509 IMP binding site; other site 85963002510 dimer interface [polypeptide binding]; other site 85963002511 interdomain contacts; other site 85963002512 partial ornithine binding site; other site 85963002513 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 85963002514 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 85963002515 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; pfam00044 85963002516 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 85963002517 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 85963002518 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 85963002519 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 85963002520 PPE-repeat proteins [Cell motility and secretion]; Region: COG5651 85963002521 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 85963002522 Autotransporter beta-domain; Region: Autotransporter; pfam03797 85963002523 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963002524 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 85963002525 active site 1 [active] 85963002526 dimer interface [polypeptide binding]; other site 85963002527 hexamer interface [polypeptide binding]; other site 85963002528 active site 2 [active] 85963002529 recombination protein RecR; Region: recR; TIGR00615 85963002530 RecR protein; Region: RecR; pfam02132 85963002531 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 85963002532 putative active site [active] 85963002533 putative metal-binding site [ion binding]; other site 85963002534 tetramer interface [polypeptide binding]; other site 85963002535 tRNA pseudouridine synthase, TruD family; Region: tRNA_TruD_broad; TIGR00094 85963002536 Pseudouridine synthase, similar to Escherichia coli TruD; Region: PseudoU_synth_EcTruD; cd02575 85963002537 Permutation of conserved domain; other site 85963002538 active site 85963002539 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 85963002540 heat shock protein HtpX; Provisional; Region: PRK02870 85963002541 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 85963002542 GTP cyclohydrolase I; Region: folE; TIGR00063 85963002543 GTP cyclohydrolase I; Provisional; Region: PLN03044 85963002544 active site 85963002545 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 85963002546 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 85963002547 substrate binding pocket [chemical binding]; other site 85963002548 chain length determination region; other site 85963002549 substrate-Mg2+ binding site; other site 85963002550 catalytic residues [active] 85963002551 aspartate-rich region 1; other site 85963002552 active site lid residues [active] 85963002553 aspartate-rich region 2; other site 85963002554 Predicted acid phosphatase [General function prediction only]; Region: SurE; COG0496 85963002555 6-pyruvoyl-tetrahydropterin synthase [Coenzyme metabolism]; Region: COG0720 85963002556 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 85963002557 putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE; Region: rSAM_QueE_Ecoli; TIGR04322 85963002558 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 85963002559 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 85963002560 Coenzyme A binding pocket [chemical binding]; other site 85963002561 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963002562 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 85963002563 metabolite-proton symporter; Region: 2A0106; TIGR00883 85963002564 putative substrate translocation pore; other site 85963002565 Uncharacterized conserved protein [Function unknown]; Region: COG1479 85963002566 Uncharacterized conserved protein [Function unknown]; Region: COG1479 85963002567 Protein of unknown function DUF262; Region: DUF262; pfam03235 85963002568 Protein of unknown function DUF262; Region: DUF262; pfam03235 85963002569 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 85963002570 dimer interface [polypeptide binding]; other site 85963002571 conserved gate region; other site 85963002572 putative PBP binding loops; other site 85963002573 ABC-ATPase subunit interface; other site 85963002574 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 85963002575 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 85963002576 substrate binding pocket [chemical binding]; other site 85963002577 membrane-bound complex binding site; other site 85963002578 hinge residues; other site 85963002579 alanine racemase; Region: alr; TIGR00492 85963002580 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 85963002581 active site 85963002582 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 85963002583 dimer interface [polypeptide binding]; other site 85963002584 substrate binding site [chemical binding]; other site 85963002585 catalytic residues [active] 85963002586 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 85963002587 amino acid carrier protein; Region: agcS; TIGR00835 85963002588 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 85963002589 Streptococcal 67 kDa myosin-cross-reactive antigen like family; Region: Strep_67kDa_ant; cl17487 85963002590 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 85963002591 homotrimer interaction site [polypeptide binding]; other site 85963002592 putative active site [active] 85963002593 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 85963002594 TIGR01210 family protein; Region: TIGR01210 85963002595 Uncharacterized conserved protein [Function unknown]; Region: COG1576 85963002596 acetyl-CoA carboxylase, carboxyl transferase, beta subunit; Region: accD; TIGR00515 85963002597 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 85963002598 putative recombination protein RecO; Provisional; Region: PRK13908 85963002599 competence/damage-inducible protein CinA C-terminal domain; Region: cinA_cterm; TIGR00199 85963002600 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 85963002601 dimer interface [polypeptide binding]; other site 85963002602 FMN binding site [chemical binding]; other site 85963002603 prolipoprotein diacylglyceryl transferase; Region: lgt; TIGR00544 85963002604 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 85963002605 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 85963002606 active site 85963002607 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 85963002608 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 85963002609 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]; Region: COG1579 85963002610 Putative zinc ribbon domain; Region: DUF164; pfam02591 85963002611 dinuclear metal center protein, YbgI/SA1388 family; Region: YbgI_SA1388; TIGR00486 85963002612 Uncharacterized conserved protein [Function unknown]; Region: COG0327 85963002613 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 85963002614 dimer interface [polypeptide binding]; other site 85963002615 motif 1; other site 85963002616 active site 85963002617 motif 2; other site 85963002618 motif 3; other site 85963002619 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 85963002620 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 85963002621 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 85963002622 Predicted GTPases (dynamin-related) [General function prediction only]; Region: COG0699 85963002623 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 85963002624 G1 box; other site 85963002625 GTP/Mg2+ binding site [chemical binding]; other site 85963002626 G2 box; other site 85963002627 Switch I region; other site 85963002628 Predicted GTPases (dynamin-related) [General function prediction only]; Region: COG0699 85963002629 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 85963002630 G1 box; other site 85963002631 GTP/Mg2+ binding site [chemical binding]; other site 85963002632 G2 box; other site 85963002633 Switch I region; other site 85963002634 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 85963002635 G3 box; other site 85963002636 Switch II region; other site 85963002637 G4 box; other site 85963002638 Predicted GTPases (dynamin-related) [General function prediction only]; Region: COG0699 85963002639 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 85963002640 G1 box; other site 85963002641 GTP/Mg2+ binding site [chemical binding]; other site 85963002642 G2 box; other site 85963002643 Switch I region; other site 85963002644 G3 box; other site 85963002645 Switch II region; other site 85963002646 Protein of unknown function (DUF3240); Region: DUF3240; pfam11582 85963002647 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 85963002648 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 85963002649 HlyD family secretion protein; Region: HlyD_3; pfam13437 85963002650 Outer membrane efflux protein; Region: OEP; pfam02321 85963002651 glycyl-tRNA synthetase, tetrameric type, beta subunit; Region: glyS; TIGR00211 85963002652 phosphoglyceromutase; Provisional; Region: PRK05434 85963002653 2,3-bisphosphoglycerate-independent phosphoglycerate mutase; Region: pgm_bpd_ind; TIGR01307 85963002654 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C subunit; Region: gatC; TIGR00135 85963002655 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK05964 85963002656 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 85963002657 inhibitor-cofactor binding pocket; inhibition site 85963002658 pyridoxal 5'-phosphate binding site [chemical binding]; other site 85963002659 catalytic residue [active] 85963002660 SurA N-terminal domain; Region: SurA_N_3; cl07813 85963002661 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 85963002662 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 85963002663 cell division protein FtsA; Region: ftsA; TIGR01174 85963002664 Cell division protein FtsA; Region: FtsA; smart00842 85963002665 Cell division protein FtsA; Region: FtsA; pfam14450 85963002666 cell division protein FtsZ; Validated; Region: PRK09330 85963002667 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 85963002668 nucleotide binding site [chemical binding]; other site 85963002669 SulA interaction site; other site 85963002670 Mechanosensitive ion channel; Region: MS_channel; pfam00924 85963002671 Type IV secretory pathway, VirB4 components [Intracellular trafficking and secretion]; Region: VirB4; COG3451 85963002672 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 85963002673 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 85963002674 Type IV secretory pathway, VirB4 components [Intracellular trafficking and secretion]; Region: VirB4; COG3451 85963002675 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 85963002676 Topoisomerase IA [DNA replication, recombination, and repair]; Region: TopA; COG0550 85963002677 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 85963002678 active site 85963002679 interdomain interaction site; other site 85963002680 putative metal-binding site [ion binding]; other site 85963002681 nucleotide binding site [chemical binding]; other site 85963002682 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 85963002683 domain I; other site 85963002684 DNA binding groove [nucleotide binding] 85963002685 phosphate binding site [ion binding]; other site 85963002686 domain II; other site 85963002687 domain III; other site 85963002688 nucleotide binding site [chemical binding]; other site 85963002689 catalytic site [active] 85963002690 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 85963002691 Type IV secretory pathway, VirB9 components [Intracellular trafficking and secretion]; Region: VirB9; COG3504 85963002692 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 85963002693 VirB7 interaction site; other site 85963002694 Domain of unknown function (DUF1738); Region: DUF1738; pfam08401 85963002695 Methyltransferase domain; Region: Methyltransf_26; pfam13659 85963002696 DNA methylase [Transcription / DNA replication, recombination, and repair]; Region: COG4646 85963002697 DEAD-like helicases superfamily; Region: DEXDc; smart00487 85963002698 DEAD/DEAH box helicase; Region: DEAD; pfam00270 85963002699 DNA methylase [Transcription / DNA replication, recombination, and repair]; Region: COG4646 85963002700 helicase superfamily c-terminal domain; Region: HELICc; smart00490 85963002701 nucleotide binding region [chemical binding]; other site 85963002702 ATP-binding site [chemical binding]; other site 85963002703 Topoisomerase IA [DNA replication, recombination, and repair]; Region: TopA; COG0550 85963002704 Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from...; Region: TOPRIM; cl00718 85963002705 active site 85963002706 metal binding site [ion binding]; metal-binding site 85963002707 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 85963002708 domain I; other site 85963002709 DNA binding groove [nucleotide binding] 85963002710 phosphate binding site [ion binding]; other site 85963002711 domain II; other site 85963002712 domain III; other site 85963002713 nucleotide binding site [chemical binding]; other site 85963002714 catalytic site [active] 85963002715 domain IV; other site 85963002716 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 85963002717 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 85963002718 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 85963002719 Magnesium ion binding site [ion binding]; other site 85963002720 Toprim-like; Region: Toprim_2; pfam13155 85963002721 Type IV secretory pathway, TrbL components [Intracellular trafficking and secretion]; Region: TrbL; COG3846 85963002722 HipA-like C-terminal domain; Region: HipA_C; pfam07804 85963002723 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 85963002724 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 85963002725 active site 85963002726 catalytic residues [active] 85963002727 DNA binding site [nucleotide binding] 85963002728 Int/Topo IB signature motif; other site 85963002729 Type IV secretory pathway, VirD2 components (relaxase) [Intracellular trafficking and secretion]; Region: VirD2; COG3843 85963002730 Type IV secretory pathway, TrbL components [Intracellular trafficking and secretion]; Region: TrbL; COG3846 85963002731 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 85963002732 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 85963002733 active site 85963002734 catalytic residues [active] 85963002735 DNA binding site [nucleotide binding] 85963002736 Int/Topo IB signature motif; other site 85963002737 Uncharacterized conserved protein [Function unknown]; Region: COG1479 85963002738 Protein of unknown function DUF262; Region: DUF262; pfam03235 85963002739 Protein of unknown function DUF262; Region: DUF262; pfam03235 85963002740 Uncharacterized conserved protein [Function unknown]; Region: COG1479 85963002741 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 85963002742 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: COG1598 85963002743 Predicted RNA binding protein (dsRBD-like fold), HicA family [General function prediction only]; Region: COG1724 85963002744 Arginine decarboxylase (spermidine biosynthesis) [Amino acid transport and metabolism]; Region: SpeA; COG1166 85963002745 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase; Region: PLPDE_III_ADC; cd06830 85963002746 active site 85963002747 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 85963002748 catalytic residues [active] 85963002749 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 85963002750 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 85963002751 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 85963002752 putative ADP-binding pocket [chemical binding]; other site 85963002753 HGG motif-containing thioesterase, possibly involved in aromatic compounds catabolism [Secondary metabolites biosynthesis, transport, and catabolism]; Region: PaaI; COG2050 85963002754 Methyltransferase domain; Region: Methyltransf_23; pfam13489 85963002755 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 85963002756 S-adenosylmethionine binding site [chemical binding]; other site 85963002757 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 85963002758 methionyl-tRNA synthetase; Reviewed; Region: PRK12267 85963002759 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 85963002760 active site 85963002761 HIGH motif; other site 85963002762 KMSKS motif; other site 85963002763 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 85963002764 anticodon binding site; other site 85963002765 tRNA binding surface [nucleotide binding]; other site 85963002766 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 85963002767 dimer interface [polypeptide binding]; other site 85963002768 putative tRNA-binding site [nucleotide binding]; other site 85963002769 Mycolic acid cyclopropane synthetase; Region: CMAS; pfam02353 85963002770 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 85963002771 S-adenosylmethionine binding site [chemical binding]; other site 85963002772 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 85963002773 Mechanosensitive ion channel; Region: MS_channel; pfam00924 85963002774 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 85963002775 GMP synthase; Reviewed; Region: guaA; PRK00074 85963002776 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 85963002777 AMP/PPi binding site [chemical binding]; other site 85963002778 candidate oxyanion hole; other site 85963002779 catalytic triad [active] 85963002780 potential glutamine specificity residues [chemical binding]; other site 85963002781 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 85963002782 ATP Binding subdomain [chemical binding]; other site 85963002783 Ligand Binding sites [chemical binding]; other site 85963002784 Dimerization subdomain; other site 85963002785 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 85963002786 molybdopterin guanine dinucleotide-containing S/N-oxide reductases; Region: bisC_fam; TIGR00509 85963002787 molybdopterin cofactor binding site [chemical binding]; other site 85963002788 substrate binding site [chemical binding]; other site 85963002789 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 85963002790 molybdopterin cofactor binding site; other site 85963002791 Protein of unknown function (DUF3972); Region: DUF3972; pfam13118 85963002792 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 85963002793 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 85963002794 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 85963002795 catalytic residue [active] 85963002796 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 85963002797 nucleotide binding site/active site [active] 85963002798 HIT family signature motif; other site 85963002799 catalytic residue [active] 85963002800 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 85963002801 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 85963002802 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 85963002803 dimer interface [polypeptide binding]; other site 85963002804 motif 1; other site 85963002805 active site 85963002806 motif 2; other site 85963002807 motif 3; other site 85963002808 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 85963002809 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 85963002810 putative tRNA-binding site [nucleotide binding]; other site 85963002811 tRNA synthetase B5 domain; Region: B5; pfam03484 85963002812 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 85963002813 dimer interface [polypeptide binding]; other site 85963002814 motif 1; other site 85963002815 motif 3; other site 85963002816 motif 2; other site 85963002817 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 85963002818 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 85963002819 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 85963002820 hinge; other site 85963002821 active site 85963002822 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 85963002823 LytB protein; Region: LYTB; pfam02401 85963002824 ribosomal protein S1; Region: rpsA; TIGR00717 85963002825 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 85963002826 RNA binding site [nucleotide binding]; other site 85963002827 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 85963002828 RNA binding site [nucleotide binding]; other site 85963002829 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 85963002830 RNA binding site [nucleotide binding]; other site 85963002831 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 85963002832 RNA binding site [nucleotide binding]; other site 85963002833 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 85963002834 RNA binding site [nucleotide binding]; other site 85963002835 D-3-phosphoglycerate dehydrogenase; Region: PGDH; TIGR01327 85963002836 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_4; cd12173 85963002837 ligand binding site [chemical binding]; other site 85963002838 NAD binding site [chemical binding]; other site 85963002839 dimerization interface [polypeptide binding]; other site 85963002840 catalytic site [active] 85963002841 C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH); Region: ACT_3PGDH-xct; cd04902 85963002842 putative L-serine binding site [chemical binding]; other site 85963002843 menaquinone biosynthesis decarboxylase, SCO4490 family; Region: mena_SCO4490; TIGR03701 85963002844 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 85963002845 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 85963002846 catalytic residue [active] 85963002847 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 85963002848 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 85963002849 putative active site [active] 85963002850 putative metal binding site [ion binding]; other site 85963002851 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 85963002852 putative CheA interaction surface; other site 85963002853 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 85963002854 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 85963002855 active site 85963002856 phosphorylation site [posttranslational modification] 85963002857 intermolecular recognition site; other site 85963002858 dimerization interface [polypeptide binding]; other site 85963002859 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 85963002860 putative binding surface; other site 85963002861 active site 85963002862 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 85963002863 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 85963002864 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 85963002865 ATP binding site [chemical binding]; other site 85963002866 Mg2+ binding site [ion binding]; other site 85963002867 G-X-G motif; other site 85963002868 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 85963002869 Response regulator receiver domain; Region: Response_reg; pfam00072 85963002870 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 85963002871 active site 85963002872 phosphorylation site [posttranslational modification] 85963002873 intermolecular recognition site; other site 85963002874 dimerization interface [polypeptide binding]; other site 85963002875 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 85963002876 putative CheA interaction surface; other site 85963002877 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 85963002878 dimer interface [polypeptide binding]; other site 85963002879 catalytic triad [active] 85963002880 peroxidatic and resolving cysteines [active] 85963002881 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 85963002882 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 85963002883 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 85963002884 ubiE/COQ5 methyltransferase family; Region: Ubie_methyltran; pfam01209 85963002885 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 85963002886 S-adenosylmethionine binding site [chemical binding]; other site 85963002887 primosome assembly protein PriA; Validated; Region: PRK05580 85963002888 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 85963002889 ATP binding site [chemical binding]; other site 85963002890 putative Mg++ binding site [ion binding]; other site 85963002891 helicase superfamily c-terminal domain; Region: HELICc; smart00490 85963002892 Sporulation related domain; Region: SPOR; pfam05036 85963002893 Peptidase family M48; Region: Peptidase_M48; pfam01435 85963002894 HemK family putative methylases; Region: hemK_fam; TIGR00536 85963002895 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 85963002896 glutamate dehydrogenase; Provisional; Region: PRK09414 85963002897 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 85963002898 NAD(P) binding domain of glutamate dehydrogenase, subgroup 2; Region: NAD_bind_2_Glu_DH; cd05313 85963002899 NAD(P) binding site [chemical binding]; other site 85963002900 Glycosyltransferase family 10 (fucosyltransferase); Region: Glyco_transf_10; pfam00852 85963002901 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 85963002902 cytochrome c-type biogenesis protein CcsB; Region: cytochr_II_ccsB; TIGR03144 85963002903 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 85963002904 catalytic residues [active] 85963002905 ferrochelatase; Region: hemH; TIGR00109 85963002906 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 85963002907 C-terminal domain interface [polypeptide binding]; other site 85963002908 active site 85963002909 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 85963002910 active site 85963002911 N-terminal domain interface [polypeptide binding]; other site 85963002912 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385 85963002913 RNA methyltransferase, RsmE family; Region: TIGR00046 85963002914 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963002915 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 85963002916 trimer interface [polypeptide binding]; other site 85963002917 active site 85963002918 acetyl-CoA carboxylase, biotin carboxyl carrier protein; Region: BCCP; TIGR00531 85963002919 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 85963002920 carboxyltransferase (CT) interaction site; other site 85963002921 biotinylation site [posttranslational modification]; other site 85963002922 biotin carboxylase; Validated; Region: PRK08462 85963002923 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 85963002924 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 85963002925 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 85963002926 Methyltransferase domain; Region: Methyltransf_26; pfam13659 85963002927 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 85963002928 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 85963002929 inhibitor-cofactor binding pocket; inhibition site 85963002930 pyridoxal 5'-phosphate binding site [chemical binding]; other site 85963002931 catalytic residue [active] 85963002932 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 85963002933 dimer interface [polypeptide binding]; other site 85963002934 putative radical transfer pathway; other site 85963002935 diiron center [ion binding]; other site 85963002936 tyrosyl radical; other site 85963002937 protein-L-isoaspartate(D-aspartate) O-methyltransferase; Region: pimt; TIGR00080 85963002938 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 85963002939 S-adenosylmethionine binding site [chemical binding]; other site 85963002940 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 85963002941 Predicted permeases [General function prediction only]; Region: COG0795 85963002942 tRNA pseudouridine(38-40) synthase; Region: hisT_truA; TIGR00071 85963002943 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 85963002944 dimerization interface 3.5A [polypeptide binding]; other site 85963002945 active site 85963002946 UDP-glucose-4-epimerase GalE; Region: galE; TIGR01179 85963002947 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 85963002948 NAD binding site [chemical binding]; other site 85963002949 homodimer interface [polypeptide binding]; other site 85963002950 active site 85963002951 substrate binding site [chemical binding]; other site 85963002952 classical (c) SDR, subgroup 5; Region: SDR_c5; cd05346 85963002953 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 85963002954 putative NAD(P) binding site [chemical binding]; other site 85963002955 homodimer interface [polypeptide binding]; other site 85963002956 homotetramer interface [polypeptide binding]; other site 85963002957 active site 85963002958 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 85963002959 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 85963002960 binding surface 85963002961 TPR motif; other site 85963002962 Sel1-like repeats; Region: SEL1; smart00671 85963002963 Sel1-like repeats; Region: SEL1; smart00671 85963002964 Sel1-like repeats; Region: SEL1; smart00671 85963002965 Entner-Doudoroff aldolase; Region: eda; TIGR01182 85963002966 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 85963002967 active site 85963002968 intersubunit interface [polypeptide binding]; other site 85963002969 catalytic residue [active] 85963002970 phosphogluconate dehydratase; Validated; Region: PRK09054 85963002971 6-phosphogluconate dehydratase; Region: edd; TIGR01196 85963002972 Glucose-6-phosphate 1-dehydrogenase [Carbohydrate transport and metabolism]; Region: Zwf; COG0364 85963002973 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 85963002974 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 85963002975 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 85963002976 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 85963002977 putative active site [active] 85963002978 glucokinase, proteobacterial type; Region: glk; TIGR00749 85963002979 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 85963002980 nucleotide binding site [chemical binding]; other site 85963002981 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 85963002982 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD1; cd05283 85963002983 putative NAD(P) binding site [chemical binding]; other site 85963002984 putative substrate binding site [chemical binding]; other site 85963002985 catalytic Zn binding site [ion binding]; other site 85963002986 structural Zn binding site [ion binding]; other site 85963002987 dimer interface [polypeptide binding]; other site 85963002988 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 85963002989 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 85963002990 active site 85963002991 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 85963002992 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 85963002993 active site 85963002994 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963002995 pyruvate flavodoxin oxidoreductase subunit gamma; Validated; Region: PRK05844 85963002996 pyruvate/ketoisovalerate ferredoxin oxidoreductase subunit gamma; Provisional; Region: PRK14029 85963002997 pyruvate flavodoxin oxidoreductase subunit delta; Reviewed; Region: porD; PRK09625 85963002998 4Fe-4S binding domain; Region: Fer4; pfam00037 85963002999 pyruvate flavodoxin oxidoreductase subunit alpha; Reviewed; Region: porA; PRK09622 85963003000 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 85963003001 dimer interface [polypeptide binding]; other site 85963003002 PYR/PP interface [polypeptide binding]; other site 85963003003 TPP binding site [chemical binding]; other site 85963003004 substrate binding site [chemical binding]; other site 85963003005 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 85963003006 pyruvate ferredoxin oxidoreductase subunit beta; Provisional; Region: PRK11865 85963003007 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 85963003008 TPP-binding site [chemical binding]; other site 85963003009 putative dimer interface [polypeptide binding]; other site 85963003010 adenylosuccinate lyase; Provisional; Region: PRK08470 85963003011 Adenylsuccinate lyase (ASL)_subgroup 1; Region: Adenylsuccinate_lyase_1; cd01360 85963003012 tetramer interface [polypeptide binding]; other site 85963003013 active site 85963003014 Adenylosuccinate lyase C-terminus; Region: ADSL_C; smart00998 85963003015 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963003016 excinuclease ABC subunit B; Provisional; Region: PRK05298 85963003017 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 85963003018 ATP binding site [chemical binding]; other site 85963003019 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 85963003020 putative Mg++ binding site [ion binding]; other site 85963003021 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 85963003022 nucleotide binding region [chemical binding]; other site 85963003023 ATP-binding site [chemical binding]; other site 85963003024 Ultra-violet resistance protein B; Region: UvrB; pfam12344 85963003025 UvrB/uvrC motif; Region: UVR; pfam02151 85963003026 AAA domain; Region: AAA_13; pfam13166 85963003027 Protein of unknown function (DUF3519); Region: DUF3519; pfam12033 85963003028 Protein of unknown function (DUF3519); Region: DUF3519; pfam12033 85963003029 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 85963003030 binding surface 85963003031 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 85963003032 TPR motif; other site 85963003033 Sel1-like repeats; Region: SEL1; smart00671 85963003034 Sel1-like repeats; Region: SEL1; smart00671 85963003035 Sel1-like repeats; Region: SEL1; smart00671 85963003036 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 85963003037 gamma-glutamyltranspeptidase; Region: g_glut_trans; TIGR00066 85963003038 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK08471 85963003039 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 85963003040 R.HinP1I restriction endonuclease; Region: R-HINP1I; pfam11463 85963003041 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 85963003042 DNA-methyltransferase (dcm); Region: dcm; TIGR00675 85963003043 cofactor binding site; other site 85963003044 DNA binding site [nucleotide binding] 85963003045 substrate interaction site [chemical binding]; other site 85963003046 Anti-sigma-28 factor, FlgM; Region: FlgM; cl01052 85963003047 FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]; Region: SlpA; COG1047 85963003048 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 85963003049 SH3 domain protein; Region: SH3_and_anchor; TIGR04211 85963003050 Tetratricopeptide repeat; Region: TPR_16; pfam13432 85963003051 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 85963003052 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 85963003053 ligand binding site [chemical binding]; other site 85963003054 translocation protein TolB; Provisional; Region: tolB; PRK04043 85963003055 TolB amino-terminal domain; Region: TolB_N; pfam04052 85963003056 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 85963003057 TonB C terminal; Region: TonB_2; pfam13103 85963003058 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 85963003059 TolR protein; Region: tolR; TIGR02801 85963003060 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; pfam01618 85963003061 ATP synthase, F1 epsilon subunit (delta in mitochondria); Region: ATP_synt_epsi; TIGR01216 85963003062 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 85963003063 gamma subunit interface [polypeptide binding]; other site 85963003064 epsilon subunit interface [polypeptide binding]; other site 85963003065 LBP interface [polypeptide binding]; other site 85963003066 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 85963003067 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 85963003068 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 85963003069 alpha subunit interaction interface [polypeptide binding]; other site 85963003070 Walker A motif; other site 85963003071 ATP binding site [chemical binding]; other site 85963003072 Walker B motif; other site 85963003073 inhibitor binding site; inhibition site 85963003074 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 85963003075 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 85963003076 core domain interface [polypeptide binding]; other site 85963003077 delta subunit interface [polypeptide binding]; other site 85963003078 epsilon subunit interface [polypeptide binding]; other site 85963003079 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 85963003080 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 85963003081 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 85963003082 beta subunit interaction interface [polypeptide binding]; other site 85963003083 Walker A motif; other site 85963003084 ATP binding site [chemical binding]; other site 85963003085 Walker B motif; other site 85963003086 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 85963003087 F0F1 ATP synthase subunit delta; Provisional; Region: PRK13431 85963003088 F0F1 ATP synthase subunit B; Validated; Region: PRK08475 85963003089 F0F1 ATP synthase subunit B'; Validated; Region: PRK08476 85963003090 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 85963003091 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 85963003092 ParB-like nuclease domain; Region: ParB; smart00470 85963003093 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 85963003094 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 85963003095 P-loop; other site 85963003096 Magnesium ion binding site [ion binding]; other site 85963003097 biotin--protein ligase; Provisional; Region: PRK08477 85963003098 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 85963003099 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 85963003100 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 85963003101 putative active site [active] 85963003102 substrate binding site [chemical binding]; other site 85963003103 putative cosubstrate binding site; other site 85963003104 catalytic site [active] 85963003105 Formyl transferase, C-terminal domain; Region: Formyl_trans_C; pfam02911 85963003106 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4694 85963003107 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4487 85963003108 Uncharacterized protein conserved in bacteria (DUF2130); Region: DUF2130; pfam09903 85963003109 Uncharacterized conserved protein [Function unknown]; Region: COG1432 85963003110 LabA_like proteins; Region: LabA_like; cd06167 85963003111 putative metal binding site [ion binding]; other site 85963003112 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 85963003113 tRNA (Guanine-1)-methyltransferase; Region: tRNA_m1G_MT; cl00407 85963003114 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK14593 85963003115 RimM N-terminal domain; Region: RimM; pfam01782 85963003116 PRC-barrel domain; Region: PRC; pfam05239 85963003117 Predicted RNA-binding protein (contains KH domain) [General function prediction only]; Region: COG1837 85963003118 KH domain; Region: KH_4; pfam13083 85963003119 G-X-X-G motif; other site 85963003120 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 85963003121 signal recognition particle protein; Provisional; Region: PRK10867 85963003122 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 85963003123 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 85963003124 P loop; other site 85963003125 GTP binding site [chemical binding]; other site 85963003126 Signal peptide binding domain; Region: SRP_SPB; pfam02978 85963003127 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 85963003128 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 85963003129 active site 85963003130 HIGH motif; other site 85963003131 nucleotide binding site [chemical binding]; other site 85963003132 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 85963003133 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 85963003134 active site 85963003135 KMSKS motif; other site 85963003136 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 85963003137 anticodon binding site; other site 85963003138 flagellar assembly protein FliW; Provisional; Region: PRK13283 85963003139 undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase; Region: murG; TIGR01133 85963003140 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 85963003141 active site 85963003142 homodimer interface [polypeptide binding]; other site 85963003143 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963003144 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963003145 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 85963003146 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 85963003147 Protein involved in cell division [Cell division and chromosome partitioning]; Region: Fic; COG2184 85963003148 Fic/DOC family; Region: Fic; cl00960 85963003149 metal-binding heat shock protein; Provisional; Region: PRK00016 85963003150 flavodoxin FldA; Validated; Region: PRK09267 85963003151 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 85963003152 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 85963003153 Uncharacterized protein, possibly involved in nitrogen fixation [Inorganic ion transport and metabolism]; Region: FixS; COG3197 85963003154 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 85963003155 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 85963003156 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 85963003157 Major Facilitator Superfamily; Region: MFS_1; pfam07690 85963003158 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 85963003159 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 85963003160 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 85963003161 active site 85963003162 dimer interface [polypeptide binding]; other site 85963003163 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 85963003164 dimer interface [polypeptide binding]; other site 85963003165 active site 85963003166 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 85963003167 carbon starvation protein A; Provisional; Region: PRK15015 85963003168 Carbon starvation protein CstA; Region: CstA; pfam02554 85963003169 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 85963003170 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 85963003171 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 85963003172 dimer interface [polypeptide binding]; other site 85963003173 conserved gate region; other site 85963003174 putative PBP binding loops; other site 85963003175 ABC-ATPase subunit interface; other site 85963003176 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 85963003177 dimer interface [polypeptide binding]; other site 85963003178 conserved gate region; other site 85963003179 putative PBP binding loops; other site 85963003180 ABC-ATPase subunit interface; other site 85963003181 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 85963003182 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 85963003183 Walker A/P-loop; other site 85963003184 ATP binding site [chemical binding]; other site 85963003185 Q-loop/lid; other site 85963003186 ABC transporter signature motif; other site 85963003187 Walker B; other site 85963003188 D-loop; other site 85963003189 H-loop/switch region; other site 85963003190 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 85963003191 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 85963003192 substrate binding pocket [chemical binding]; other site 85963003193 membrane-bound complex binding site; other site 85963003194 hinge residues; other site 85963003195 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 85963003196 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 85963003197 putative substrate translocation pore; other site 85963003198 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 85963003199 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963003200 purine-nucleoside phosphorylase, family 1 (deoD); Region: deoD; TIGR00107 85963003201 phosphopentomutase; Provisional; Region: PRK05362 85963003202 Metalloenzyme superfamily; Region: Metalloenzyme; pfam01676 85963003203 Nucleoside permease [Nucleotide transport and metabolism]; Region: NupC; COG1972 85963003204 Na+ dependent nucleoside transporter N-terminus; Region: Nucleos_tra2_N; pfam01773 85963003205 Nucleoside recognition; Region: Gate; pfam07670 85963003206 Na+ dependent nucleoside transporter C-terminus; Region: Nucleos_tra2_C; pfam07662 85963003207 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 85963003208 Major Facilitator Superfamily; Region: MFS_1; pfam07690 85963003209 putative substrate translocation pore; other site 85963003210 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 85963003211 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 85963003212 Ligand Binding Site [chemical binding]; other site 85963003213 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 85963003214 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 85963003215 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 85963003216 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA; Region: MATE_MepA_like; cd13143 85963003217 putative arabinose transporter; Provisional; Region: PRK03545 85963003218 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 85963003219 putative substrate translocation pore; other site 85963003220 Carbonic anhydrase [Inorganic ion transport and metabolism]; Region: Cah; COG3338 85963003221 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 85963003222 active site 85963003223 zinc binding site [ion binding]; other site 85963003224 Helicobacter pylori protein of unknown function (DUF874); Region: DUF874; pfam05917 85963003225 aspartate-semialdehyde dehydrogenase (peptidoglycan organisms); Region: asd_B; TIGR01296 85963003226 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 85963003227 Histidyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: HisS; COG0124 85963003228 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 85963003229 dimer interface [polypeptide binding]; other site 85963003230 motif 1; other site 85963003231 active site 85963003232 motif 2; other site 85963003233 motif 3; other site 85963003234 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 85963003235 anticodon binding site; other site 85963003236 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 85963003237 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 85963003238 putative active site [active] 85963003239 elongation factor G; Reviewed; Region: PRK00007 85963003240 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 85963003241 G1 box; other site 85963003242 putative GEF interaction site [polypeptide binding]; other site 85963003243 GTP/Mg2+ binding site [chemical binding]; other site 85963003244 Switch I region; other site 85963003245 G2 box; other site 85963003246 G3 box; other site 85963003247 Switch II region; other site 85963003248 G4 box; other site 85963003249 G5 box; other site 85963003250 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 85963003251 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 85963003252 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 85963003253 30S ribosomal protein S7; Validated; Region: PRK05302 85963003254 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 85963003255 S17 interaction site [polypeptide binding]; other site 85963003256 S8 interaction site; other site 85963003257 16S rRNA interaction site [nucleotide binding]; other site 85963003258 streptomycin interaction site [chemical binding]; other site 85963003259 23S rRNA interaction site [nucleotide binding]; other site 85963003260 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 85963003261 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed; Region: PRK09603 85963003262 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 85963003263 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 85963003264 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 85963003265 RPB11 interaction site [polypeptide binding]; other site 85963003266 RPB12 interaction site [polypeptide binding]; other site 85963003267 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 85963003268 RPB3 interaction site [polypeptide binding]; other site 85963003269 RPB1 interaction site [polypeptide binding]; other site 85963003270 RPB11 interaction site [polypeptide binding]; other site 85963003271 RPB10 interaction site [polypeptide binding]; other site 85963003272 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 85963003273 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 85963003274 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 85963003275 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 85963003276 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 85963003277 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 85963003278 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 85963003279 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 85963003280 DNA binding site [nucleotide binding] 85963003281 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 85963003282 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 85963003283 core dimer interface [polypeptide binding]; other site 85963003284 peripheral dimer interface [polypeptide binding]; other site 85963003285 L10 interface [polypeptide binding]; other site 85963003286 L11 interface [polypeptide binding]; other site 85963003287 putative EF-Tu interaction site [polypeptide binding]; other site 85963003288 putative EF-G interaction site [polypeptide binding]; other site 85963003289 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 85963003290 23S rRNA interface [nucleotide binding]; other site 85963003291 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 85963003292 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 85963003293 mRNA/rRNA interface [nucleotide binding]; other site 85963003294 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 85963003295 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 85963003296 23S rRNA interface [nucleotide binding]; other site 85963003297 L7/L12 interface [polypeptide binding]; other site 85963003298 putative thiostrepton binding site; other site 85963003299 L25 interface [polypeptide binding]; other site 85963003300 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 85963003301 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 85963003302 putative homodimer interface [polypeptide binding]; other site 85963003303 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 85963003304 heterodimer interface [polypeptide binding]; other site 85963003305 homodimer interface [polypeptide binding]; other site 85963003306 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 85963003307 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 85963003308 elongation factor Tu; Reviewed; Region: PRK00049 85963003309 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 85963003310 G1 box; other site 85963003311 GEF interaction site [polypeptide binding]; other site 85963003312 GTP/Mg2+ binding site [chemical binding]; other site 85963003313 Switch I region; other site 85963003314 G2 box; other site 85963003315 G3 box; other site 85963003316 Switch II region; other site 85963003317 G4 box; other site 85963003318 G5 box; other site 85963003319 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 85963003320 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 85963003321 Antibiotic Binding Site [chemical binding]; other site 85963003322 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 85963003323 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 85963003324 Walker A/P-loop; other site 85963003325 ATP binding site [chemical binding]; other site 85963003326 Q-loop/lid; other site 85963003327 ABC transporter signature motif; other site 85963003328 Walker B; other site 85963003329 D-loop; other site 85963003330 H-loop/switch region; other site 85963003331 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 85963003332 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 85963003333 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG3392 85963003334 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; pfam02086 85963003335 Helicobacter pylori IceA2 protein; Region: IceA2; pfam05862 85963003336 serine O-acetyltransferase; Region: cysE; TIGR01172 85963003337 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 85963003338 trimer interface [polypeptide binding]; other site 85963003339 active site 85963003340 substrate binding site [chemical binding]; other site 85963003341 CoA binding site [chemical binding]; other site 85963003342 F0F1 ATP synthase subunit C; Validated; Region: PRK08482 85963003343 RNase PH-like 3'-5' exoribonucleases; Region: RNase_PH; cl03114 85963003344 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 85963003345 oligomer interface [polypeptide binding]; other site 85963003346 RNA binding site [nucleotide binding]; other site 85963003347 RNase PH-like 3'-5' exoribonucleases; Region: RNase_PH; cl03114 85963003348 oligomer interface [polypeptide binding]; other site 85963003349 RNA binding site [nucleotide binding]; other site 85963003350 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 85963003351 putative nucleic acid binding region [nucleotide binding]; other site 85963003352 G-X-X-G motif; other site 85963003353 Ribosomal protein S1-like RNA-binding domain; Region: S1; smart00316 85963003354 RNA binding site [nucleotide binding]; other site 85963003355 Predicted phosphoribosyltransferases [General function prediction only]; Region: COG1926 85963003356 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 85963003357 Organic solvent tolerance protein; Region: OstA_C; pfam04453 85963003358 Predicted membrane protein/domain [Function unknown]; Region: COG1714 85963003359 phosphoribosylamine--glycine ligase; Region: purD; TIGR00877 85963003360 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 85963003361 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 85963003362 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 85963003363 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 85963003364 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 85963003365 Walker A/P-loop; other site 85963003366 ATP binding site [chemical binding]; other site 85963003367 Q-loop/lid; other site 85963003368 ABC transporter signature motif; other site 85963003369 Walker B; other site 85963003370 D-loop; other site 85963003371 H-loop/switch region; other site 85963003372 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 85963003373 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 85963003374 catalytic residue [active] 85963003375 putative FPP diphosphate binding site; other site 85963003376 putative FPP binding hydrophobic cleft; other site 85963003377 dimer interface [polypeptide binding]; other site 85963003378 putative IPP diphosphate binding site; other site 85963003379 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 85963003380 FAD binding domain; Region: FAD_binding_4; pfam01565 85963003381 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 85963003382 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 85963003383 active site residue [active] 85963003384 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 85963003385 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 85963003386 active site 85963003387 camphor resistance protein CrcB; Provisional; Region: PRK14204 85963003388 coproporphyrinogen III oxidase; Provisional; Region: PRK08446 85963003389 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 85963003390 FeS/SAM binding site; other site 85963003391 Cytochrome c553 [Energy production and conversion]; Region: COG2863 85963003392 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 85963003393 putative active site [active] 85963003394 Ap4A binding site [chemical binding]; other site 85963003395 nudix motif; other site 85963003396 putative metal binding site [ion binding]; other site 85963003397 aspartate kinase; Reviewed; Region: PRK06635 85963003398 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 85963003399 putative nucleotide binding site [chemical binding]; other site 85963003400 putative catalytic residues [active] 85963003401 putative Mg ion binding site [ion binding]; other site 85963003402 putative aspartate binding site [chemical binding]; other site 85963003403 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 85963003404 putative allosteric regulatory site; other site 85963003405 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 85963003406 putative allosteric regulatory residue; other site 85963003407 DNA replication regulator; Region: HobA; pfam12163 85963003408 DNA polymerase III subunit delta'; Validated; Region: PRK08485 85963003409 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 85963003410 dihydropteroate synthase; Region: DHPS; TIGR01496 85963003411 substrate binding pocket [chemical binding]; other site 85963003412 dimer interface [polypeptide binding]; other site 85963003413 inhibitor binding site; inhibition site 85963003414 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 85963003415 EamA-like transporter family; Region: EamA; pfam00892 85963003416 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl17364 85963003417 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2952 85963003418 Carbamoylphosphate synthase small subunit [Amino acid transport and metabolism / Nucleotide transport and metabolism]; Region: CarA; COG0505 85963003419 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; pfam00988 85963003420 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 85963003421 catalytic site [active] 85963003422 subunit interface [polypeptide binding]; other site 85963003423 formamidase; Provisional; Region: amiF; PRK13287 85963003424 aliphatic amidases (class 2 nitrilases); Region: aliphatic_amidase; cd07565 85963003425 multimer interface [polypeptide binding]; other site 85963003426 active site 85963003427 catalytic triad [active] 85963003428 dimer interface [polypeptide binding]; other site 85963003429 Maf-like protein; Region: Maf; pfam02545 85963003430 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 85963003431 active site 85963003432 dimer interface [polypeptide binding]; other site 85963003433 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 85963003434 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 85963003435 motif 1; other site 85963003436 active site 85963003437 motif 2; other site 85963003438 motif 3; other site 85963003439 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 85963003440 DHHA1 domain; Region: DHHA1; pfam02272 85963003441 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2841 85963003442 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963003443 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 85963003444 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 85963003445 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 85963003446 dimer interface [polypeptide binding]; other site 85963003447 ssDNA binding site [nucleotide binding]; other site 85963003448 tetramer (dimer of dimers) interface [polypeptide binding]; other site 85963003449 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 85963003450 DNA polymerase III subunit delta; Validated; Region: PRK08487 85963003451 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 85963003452 Exoribonuclease R [Transcription]; Region: VacB; COG0557 85963003453 RNB domain; Region: RNB; pfam00773 85963003454 shikimate 5-dehydrogenase; Region: aroE; TIGR00507 85963003455 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 85963003456 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 85963003457 shikimate binding site; other site 85963003458 NAD(P) binding site [chemical binding]; other site 85963003459 Bacterial SH3 domain; Region: SH3_3; pfam08239 85963003460 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4174 85963003461 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 85963003462 dimer interface [polypeptide binding]; other site 85963003463 conserved gate region; other site 85963003464 putative PBP binding loops; other site 85963003465 ABC-ATPase subunit interface; other site 85963003466 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 85963003467 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 85963003468 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 85963003469 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 85963003470 active site 85963003471 HIGH motif; other site 85963003472 dimer interface [polypeptide binding]; other site 85963003473 KMSKS motif; other site 85963003474 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 85963003475 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 85963003476 S-adenosylmethionine binding site [chemical binding]; other site 85963003477 Preprotein translocase subunit SecG [Intracellular trafficking and secretion]; Region: SecG; COG1314 85963003478 ribosome recycling factor; Reviewed; Region: frr; PRK00083 85963003479 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 85963003480 hinge region; other site 85963003481 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 85963003482 active site 85963003483 RDD family; Region: RDD; pfam06271 85963003484 NAD-dependent protein deacetylases, SIR2 family [Transcription]; Region: SIR2; COG0846 85963003485 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 85963003486 NAD+ binding site [chemical binding]; other site 85963003487 substrate binding site [chemical binding]; other site 85963003488 Zn binding site [ion binding]; other site 85963003489 NADH dehydrogenase subunit A; Validated; Region: PRK08489 85963003490 NADH dehydrogenase subunit B; Validated; Region: PRK06411 85963003491 NADH dehydrogenase subunit C; Provisional; Region: PRK08491 85963003492 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 85963003493 NADH dehydrogenase subunit D; Validated; Region: PRK06075 85963003494 NADH dehydrogenase I, D subunit; Region: NuoD; TIGR01962 85963003495 NADH dehydrogenase subunit G; Validated; Region: PRK08493 85963003496 NADH dehydrogenase subunit G; Validated; Region: PRK08493 85963003497 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 85963003498 catalytic loop [active] 85963003499 iron binding site [ion binding]; other site 85963003500 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 85963003501 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 85963003502 molybdopterin cofactor binding site; other site 85963003503 Domain of unknown function (DUF4350); Region: DUF4350; pfam14258 85963003504 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 85963003505 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 85963003506 NADH-quinone oxidoreductase, chain I; Region: NuoI; TIGR01971 85963003507 4Fe-4S binding domain; Region: Fer4; cl02805 85963003508 4Fe-4S binding domain; Region: Fer4; pfam00037 85963003509 NADH:ubiquinone oxidoreductase subunit 6 (chain J) [Energy production and conversion]; Region: NuoJ; COG0839 85963003510 NADH dehydrogenase subunit J; Provisional; Region: PRK06433 85963003511 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 85963003512 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 85963003513 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 85963003514 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 85963003515 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 85963003516 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 85963003517 proton-translocating NADH-quinone oxidoreductase, chain N; Region: NDH_I_N; TIGR01770 85963003518 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 85963003519 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 85963003520 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 85963003521 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 85963003522 active site 85963003523 substrate binding site [chemical binding]; other site 85963003524 metal binding site [ion binding]; metal-binding site 85963003525 tryptophan synthase alpha subunit; Provisional; Region: trpA; CHL00200 85963003526 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 85963003527 substrate binding site [chemical binding]; other site 85963003528 active site 85963003529 catalytic residues [active] 85963003530 heterodimer interface [polypeptide binding]; other site 85963003531 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 85963003532 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 85963003533 pyridoxal 5'-phosphate binding site [chemical binding]; other site 85963003534 catalytic residue [active] 85963003535 bifunctional indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase; Provisional; Region: PRK09427 85963003536 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 85963003537 active site 85963003538 ribulose/triose binding site [chemical binding]; other site 85963003539 phosphate binding site [ion binding]; other site 85963003540 substrate (anthranilate) binding pocket [chemical binding]; other site 85963003541 product (indole) binding pocket [chemical binding]; other site 85963003542 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 85963003543 active site 85963003544 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 85963003545 anthranilate phosphoribosyltransferase; Region: trpD; TIGR01245 85963003546 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 85963003547 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 85963003548 Glutamine amidotransferase class-I; Region: GATase; pfam00117 85963003549 glutamine binding [chemical binding]; other site 85963003550 catalytic triad [active] 85963003551 anthranilate synthase component I; Provisional; Region: PRK13564 85963003552 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 85963003553 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 85963003554 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 85963003555 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 85963003556 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 85963003557 active site 85963003558 motif I; other site 85963003559 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 85963003560 motif II; other site 85963003561 Uncharacterized conserved protein [Function unknown]; Region: COG2353 85963003562 thiaminase II; Region: salvage_TenA; TIGR04306 85963003563 Nicotinamide mononucleotide transporter [Coenzyme metabolism]; Region: PnuC; COG3201 85963003564 Thiamine pyrophosphokinase [Coenzyme metabolism]; Region: THI80; COG1564 85963003565 Thiamine pyrophosphokinase; Region: TPK; cd07995 85963003566 active site 85963003567 dimerization interface [polypeptide binding]; other site 85963003568 thiamine binding site [chemical binding]; other site 85963003569 Ribosomal protein L17 [Translation, ribosomal structure and biogenesis]; Region: RplQ; COG0203 85963003570 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 85963003571 alphaNTD homodimer interface [polypeptide binding]; other site 85963003572 DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type; Region: rpoA; TIGR02027 85963003573 alphaNTD - beta interaction site [polypeptide binding]; other site 85963003574 alphaNTD - beta' interaction site [polypeptide binding]; other site 85963003575 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 85963003576 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 85963003577 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 85963003578 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 85963003579 RNA binding surface [nucleotide binding]; other site 85963003580 30S ribosomal protein S11; Validated; Region: PRK05309 85963003581 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 85963003582 30S ribosomal protein S13; Region: bact_S13; TIGR03631 85963003583 Ribosomal protein L36; Region: Ribosomal_L36; cl00380 85963003584 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 85963003585 rRNA binding site [nucleotide binding]; other site 85963003586 predicted 30S ribosome binding site; other site 85963003587 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 85963003588 active site 85963003589 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 85963003590 SecY translocase; Region: SecY; pfam00344 85963003591 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 85963003592 ribosomal protein S5, bacterial/organelle type; Region: rpsE_bact; TIGR01021 85963003593 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 85963003594 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 85963003595 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 85963003596 23S rRNA interface [nucleotide binding]; other site 85963003597 5S rRNA interface [nucleotide binding]; other site 85963003598 L27 interface [polypeptide binding]; other site 85963003599 L5 interface [polypeptide binding]; other site 85963003600 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 85963003601 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 85963003602 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 85963003603 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08061 85963003604 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 85963003605 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 85963003606 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 85963003607 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 85963003608 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 85963003609 RNA binding site [nucleotide binding]; other site 85963003610 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 85963003611 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 85963003612 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 85963003613 putative translocon interaction site; other site 85963003614 23S rRNA interface [nucleotide binding]; other site 85963003615 signal recognition particle (SRP54) interaction site; other site 85963003616 L23 interface [polypeptide binding]; other site 85963003617 trigger factor interaction site; other site 85963003618 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 85963003619 23S rRNA interface [nucleotide binding]; other site 85963003620 5S rRNA interface [nucleotide binding]; other site 85963003621 putative antibiotic binding site [chemical binding]; other site 85963003622 L25 interface [polypeptide binding]; other site 85963003623 L27 interface [polypeptide binding]; other site 85963003624 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 85963003625 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 85963003626 G-X-X-G motif; other site 85963003627 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 85963003628 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 85963003629 putative translocon binding site; other site 85963003630 protein-rRNA interface [nucleotide binding]; other site 85963003631 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 85963003632 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 85963003633 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 85963003634 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 85963003635 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 85963003636 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 85963003637 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 85963003638 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 85963003639 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 85963003640 AAA domain; Region: AAA_14; pfam13173 85963003641 Helix-turn-helix domain; Region: HTH_36; pfam13730 85963003642 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 85963003643 RNA/DNA hybrid binding site [nucleotide binding]; other site 85963003644 active site 85963003645 fumarate hydratase; Reviewed; Region: fumC; PRK00485 85963003646 Class II fumarases; Region: Fumarase_classII; cd01362 85963003647 active site 85963003648 tetramer interface [polypeptide binding]; other site 85963003649 YtkA-like; Region: YtkA; pfam13115 85963003650 Outer membrane efflux protein; Region: OEP; pfam02321 85963003651 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 85963003652 HlyD family secretion protein; Region: HlyD_3; pfam13437 85963003653 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 85963003654 Predicted branched-chain amino acid permeases (azaleucine resistance) [Amino acid transport and metabolism]; Region: AzlD; COG1687 85963003655 AzlC protein; Region: AzlC; cl00570 85963003656 chaperone protein DnaJ; Provisional; Region: PRK14288 85963003657 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 85963003658 HSP70 interaction site [polypeptide binding]; other site 85963003659 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 85963003660 Zn binding sites [ion binding]; other site 85963003661 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 85963003662 dimer interface [polypeptide binding]; other site 85963003663 tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase; Region: trmU; TIGR00420 85963003664 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 85963003665 Ligand Binding Site [chemical binding]; other site 85963003666 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 85963003667 HSP70 interaction site [polypeptide binding]; other site 85963003668 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 85963003669 Cytidylyltransferase; Region: CTP_transf_2; pfam01467 85963003670 active site 85963003671 (T/H)XGH motif; other site 85963003672 nickel responsive regulator; Provisional; Region: PRK00630 85963003673 Ribbon-helix-helix protein, copG family; Region: RHH_1; pfam01402 85963003674 NikR C terminal nickel binding domain; Region: NikR_C; pfam08753 85963003675 tonB-system energizer ExbB, group 2; Region: exbB2; TIGR02805 85963003676 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 85963003677 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 85963003678 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 85963003679 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 85963003680 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963003681 Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]; Region: TerC; COG0861 85963003682 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 85963003683 Mg2+ transporter Helicobacter pylori CorA-like subgroup; Region: HpCorA-like; cd12836 85963003684 Cl binding site [ion binding]; other site 85963003685 oligomer interface [polypeptide binding]; other site 85963003686 phosphoglycerate kinase; Provisional; Region: pgk; PRK00073 85963003687 Phosphoglycerate kinase; Region: PGK; pfam00162 85963003688 substrate binding site [chemical binding]; other site 85963003689 hinge regions; other site 85963003690 ADP binding site [chemical binding]; other site 85963003691 catalytic site [active] 85963003692 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; pfam00044 85963003693 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 85963003694 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 85963003695 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 85963003696 ligand binding site [chemical binding]; other site 85963003697 active site 85963003698 UGI interface [polypeptide binding]; other site 85963003699 catalytic site [active] 85963003700 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 85963003701 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 85963003702 putative acyl-acceptor binding pocket; other site 85963003703 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 85963003704 C-terminal peptidase (prc); Region: prc; TIGR00225 85963003705 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 85963003706 protein binding site [polypeptide binding]; other site 85963003707 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 85963003708 Catalytic dyad [active] 85963003709 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 85963003710 DNA methylase; Region: N6_N4_Mtase; pfam01555 85963003711 Predicted helicase [General function prediction only]; Region: COG4889 85963003712 nicotinate-nucleotide pyrophosphorylase; Provisional; Region: PRK05848 85963003713 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 85963003714 dimerization interface [polypeptide binding]; other site 85963003715 active site 85963003716 quinolinate synthetase complex, A subunit; Region: nadA; TIGR00550 85963003717 phosphatidylserine decarboxylase; Provisional; Region: PRK03934 85963003718 prenyltransferase; Reviewed; Region: ubiA; PRK12874 85963003719 UbiA prenyltransferase family; Region: UbiA; pfam01040 85963003720 Predicted membrane metal-binding protein [General function prediction only]; Region: ComEC; COG0658 85963003721 Competence protein; Region: Competence; pfam03772 85963003722 replicative DNA helicase; Provisional; Region: PRK08506 85963003723 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 85963003724 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 85963003725 Walker A motif; other site 85963003726 ATP binding site [chemical binding]; other site 85963003727 Walker B motif; other site 85963003728 DNA binding loops [nucleotide binding] 85963003729 YjeF-related protein N-terminus; Region: YjeF_N; cl00318 85963003730 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 85963003731 putative substrate binding site [chemical binding]; other site 85963003732 putative ATP binding site [chemical binding]; other site 85963003733 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 85963003734 His Kinase A (phospho-acceptor) domain; Region: HisKA; pfam00512 85963003735 dimer interface [polypeptide binding]; other site 85963003736 phosphorylation site [posttranslational modification] 85963003737 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 85963003738 ATP binding site [chemical binding]; other site 85963003739 Mg2+ binding site [ion binding]; other site 85963003740 G-X-G motif; other site 85963003741 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 85963003742 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 85963003743 active site 85963003744 phosphorylation site [posttranslational modification] 85963003745 intermolecular recognition site; other site 85963003746 dimerization interface [polypeptide binding]; other site 85963003747 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 85963003748 DNA binding site [nucleotide binding] 85963003749 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 85963003750 DNA methylase; Region: N6_N4_Mtase; pfam01555 85963003751 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 85963003752 DEAD-like helicases superfamily; Region: DEXDc; smart00487 85963003753 Cell shape-determining protein [Cell envelope biogenesis, outer membrane]; Region: MreC; COG1792 85963003754 rod shape-determining protein MreC; Region: MreC; pfam04085 85963003755 rod shape-determining protein MreB; Provisional; Region: PRK13927 85963003756 MreB and similar proteins; Region: MreB_like; cd10225 85963003757 nucleotide binding site [chemical binding]; other site 85963003758 Mg binding site [ion binding]; other site 85963003759 putative protofilament interaction site [polypeptide binding]; other site 85963003760 RodZ interaction site [polypeptide binding]; other site 85963003761 endopeptidase Clp ATP-binding regulatory subunit (clpX); Region: clpX; TIGR00382 85963003762 ClpX C4-type zinc finger; Region: zf-C4_ClpX; smart00994 85963003763 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 85963003764 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 85963003765 Walker A motif; other site 85963003766 ATP binding site [chemical binding]; other site 85963003767 Walker B motif; other site 85963003768 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 85963003769 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 85963003770 acyl-[acyl-carrier-protein]--UDP-N- acetylglucosamine O-acyltransferase; Region: lipid_A_lpxA; TIGR01852 85963003771 active site 85963003772 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 85963003773 flagellar assembly protein FliW; Provisional; Region: PRK13282 85963003774 DNA uptake lipoprotein [General function prediction only]; Region: ComL; COG4105 85963003775 ATP-dependent protease La; Region: lon; TIGR00763 85963003776 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 85963003777 Walker A motif; other site 85963003778 ATP binding site [chemical binding]; other site 85963003779 Walker B motif; other site 85963003780 arginine finger; other site 85963003781 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 85963003782 prephenate dehydrogenase; Validated; Region: PRK08507 85963003783 Prephenate dehydrogenase; Region: PDH; pfam02153 85963003784 DNA/RNA endonuclease G, NUC1 [Nucleotide transport and metabolism]; Region: NUC1; COG1864 85963003785 DNA/RNA non-specific endonuclease; Region: Endonuclease_NS; smart00892 85963003786 active site 85963003787 substrate binding site [chemical binding]; other site 85963003788 Mg2+ binding site [ion binding]; other site 85963003789 Type III restriction/modification enzyme methylation subunit; Region: TypeIII_RM_meth; pfam12564 85963003790 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 85963003791 DNA methylase; Region: N6_N4_Mtase; pfam01555 85963003792 DNA methylase; Region: N6_N4_Mtase; pfam01555 85963003793 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3421 85963003794 Type III restriction enzyme, res subunit; Region: ResIII; pfam04851 85963003795 ATP binding site [chemical binding]; other site 85963003796 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 85963003797 putative Mg++ binding site [ion binding]; other site 85963003798 biotin synthase; Provisional; Region: PRK08508 85963003799 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 85963003800 FeS/SAM binding site; other site 85963003801 Biotin and Thiamin Synthesis associated domain; Region: BATS; pfam06968 85963003802 YihY family inner membrane protein; Region: yihY_not_rbn; TIGR00765 85963003803 Uncharacterized conserved protein [Function unknown]; Region: COG1479 85963003804 Protein of unknown function DUF262; Region: DUF262; pfam03235 85963003805 Protein of unknown function DUF262; Region: DUF262; pfam03235 85963003806 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 85963003807 Single-stranded DNA-specific exonuclease [DNA replication, recombination, and repair]; Region: RecJ; COG0608 85963003808 DHH family; Region: DHH; pfam01368 85963003809 7-cyano-7-deazaguanine reductase; Region: QueF-II; TIGR03139 85963003810 Uncharacterized homolog of plant Iojap protein [Function unknown]; Region: COG0799 85963003811 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 85963003812 tRNA dimethylallyltransferase; Region: miaA; TIGR00174 85963003813 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 85963003814 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 85963003815 Ligand binding site; other site 85963003816 metal-binding site 85963003817 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 85963003818 Sulfatase; Region: Sulfatase; pfam00884 85963003819 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13904 85963003820 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 85963003821 flagellar biosynthesis protein FliQ; Validated; Region: fliQ; PRK05700 85963003822 flagellum-specific ATP synthase; Validated; Region: fliI; PRK08472 85963003823 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 85963003824 Walker A motif/ATP binding site; other site 85963003825 Walker B motif; other site 85963003826 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 85963003827 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 85963003828 ATP binding site [chemical binding]; other site 85963003829 Walker A motif; other site 85963003830 hexamer interface [polypeptide binding]; other site 85963003831 Walker B motif; other site 85963003832 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 85963003833 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 85963003834 active site 85963003835 HIGH motif; other site 85963003836 nucleotide binding site [chemical binding]; other site 85963003837 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 85963003838 active site 85963003839 KMSKS motif; other site 85963003840 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 85963003841 tRNA binding surface [nucleotide binding]; other site 85963003842 anticodon binding site; other site 85963003843 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 85963003844 RNA binding surface [nucleotide binding]; other site 85963003845 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 85963003846 dimethyladenosine transferase; Region: ksgA; TIGR00755 85963003847 S-adenosylmethionine binding site [chemical binding]; other site 85963003848 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 85963003849 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 85963003850 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 85963003851 KpsF/GutQ family protein; Region: kpsF; TIGR00393 85963003852 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 85963003853 putative active site [active] 85963003854 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 85963003855 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK14462 85963003856 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 85963003857 FeS/SAM binding site; other site 85963003858 formyltetrahydrofolate deformylase; Region: PurU; TIGR00655 85963003859 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 85963003860 Formyltransferase, catalytic core domain; Region: FMT_core; cl00395 85963003861 active site 85963003862 substrate binding site [chemical binding]; other site 85963003863 cosubstrate binding site; other site 85963003864 catalytic site [active] 85963003865 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 85963003866 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 85963003867 tandem repeat interface [polypeptide binding]; other site 85963003868 oligomer interface [polypeptide binding]; other site 85963003869 active site residues [active] 85963003870 TIR domain; Region: TIR_2; cl17458 85963003871 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 85963003872 active site 85963003873 carbon storage regulator; Provisional; Region: PRK00568 85963003874 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: PRK04181 85963003875 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 85963003876 SmpB-tmRNA interface; other site 85963003877 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; pfam01618 85963003878 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 85963003879 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 85963003880 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 85963003881 ribonuclease P protein component, eubacterial; Region: rnpA; TIGR00188 85963003882 hypothetical protein; Provisional; Region: PRK14374 85963003883 membrane protein insertase; Provisional; Region: PRK01318 85963003884 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 85963003885 Predicted RNA-binding protein [General function prediction only]; Region: Jag; COG1847 85963003886 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 85963003887 tRNA modification GTPase TrmE; Region: mnmE_trmE_thdF; TIGR00450 85963003888 Circularly permuted YlqF-related GTPases; Region: YlqF_related_GTPase; cl17249 85963003889 GTP/Mg2+ binding site [chemical binding]; other site 85963003890 G5 box; other site 85963003891 trmE is a tRNA modification GTPase; Region: trmE; cd04164 85963003892 G1 box; other site 85963003893 G1 box; other site 85963003894 GTP/Mg2+ binding site [chemical binding]; other site 85963003895 Switch I region; other site 85963003896 Switch I region; other site 85963003897 G2 box; other site 85963003898 G2 box; other site 85963003899 Switch II region; other site 85963003900 G3 box; other site 85963003901 G3 box; other site 85963003902 Switch II region; other site 85963003903 G4 box; other site 85963003904 G5 box; other site 85963003905 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 85963003906 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963003907 LPP20 lipoprotein; Region: LPP20; pfam02169 85963003908 Collagen-binding surface adhesin SpaP (antigen I/II family) [General function prediction only]; Region: FlgN; COG3417 85963003909 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 85963003910 catalytic residues [active] 85963003911 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 85963003912 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 85963003913 RNA binding surface [nucleotide binding]; other site 85963003914 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 85963003915 active site 85963003916 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE3; Region: PHP_PolIIIA_DnaE3; cd12113 85963003917 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 85963003918 active site 85963003919 PHP Thumb interface [polypeptide binding]; other site 85963003920 metal binding site [ion binding]; metal-binding site 85963003921 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 85963003922 generic binding surface I; other site 85963003923 generic binding surface II; other site 85963003924 Cytochrome c peroxidase [Inorganic ion transport and metabolism]; Region: MauG; COG1858 85963003925 Heat shock protein [Posttranslational modification, protein turnover, chaperones]; Region: HslJ; COG3187 85963003926 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 85963003927 mce related protein; Region: MCE; pfam02470 85963003928 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 85963003929 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 85963003930 Walker A/P-loop; other site 85963003931 ATP binding site [chemical binding]; other site 85963003932 Q-loop/lid; other site 85963003933 ABC transporter signature motif; other site 85963003934 Walker B; other site 85963003935 D-loop; other site 85963003936 H-loop/switch region; other site 85963003937 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 85963003938 conserved hypothetical integral membrane protein; Region: TIGR00056 85963003939 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963003940 branched-chain amino acid aminotransferase; Provisional; Region: PRK13357 85963003941 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 85963003942 homodimer interface [polypeptide binding]; other site 85963003943 substrate-cofactor binding pocket; other site 85963003944 catalytic residue [active] 85963003945 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963003946 DNA polymerase I; Region: pola; TIGR00593 85963003947 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 85963003948 active site 85963003949 metal binding site 1 [ion binding]; metal-binding site 85963003950 putative 5' ssDNA interaction site; other site 85963003951 metal binding site 3; metal-binding site 85963003952 metal binding site 2 [ion binding]; metal-binding site 85963003953 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 85963003954 putative DNA binding site [nucleotide binding]; other site 85963003955 putative metal binding site [ion binding]; other site 85963003956 3'-5' exonuclease; Region: 35EXOc; smart00474 85963003957 active site 85963003958 substrate binding site [chemical binding]; other site 85963003959 catalytic site [active] 85963003960 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 85963003961 active site 85963003962 DNA binding site [nucleotide binding] 85963003963 catalytic site [active] 85963003964 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 85963003965 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 85963003966 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 85963003967 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 85963003968 thymidylate kinase; Validated; Region: tmk; PRK00698 85963003969 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 85963003970 TMP-binding site; other site 85963003971 ATP-binding site [chemical binding]; other site 85963003972 Phosphopantetheine adenylyltransferase [Coenzyme metabolism]; Region: CoaD; COG0669 85963003973 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 85963003974 active site 85963003975 (T/H)XGH motif; other site 85963003976 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Provisional; Region: PRK06029 85963003977 Flavoprotein; Region: Flavoprotein; pfam02441 85963003978 flagellar basal body P-ring biosynthesis protein FlgA; Reviewed; Region: flgA; PRK08515 85963003979 flagella basal body P-ring formation protein FlgA; Region: flgA_cterm; TIGR03170 85963003980 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 85963003981 Part of AAA domain; Region: AAA_19; pfam13245 85963003982 Family description; Region: UvrD_C_2; pfam13538 85963003983 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 85963003984 binding surface 85963003985 TPR motif; other site 85963003986 seryl-tRNA synthetase; Provisional; Region: PRK05431 85963003987 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 85963003988 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 85963003989 dimer interface [polypeptide binding]; other site 85963003990 active site 85963003991 motif 1; other site 85963003992 motif 2; other site 85963003993 motif 3; other site 85963003994 Predicted amidohydrolase [General function prediction only]; Region: COG0388 85963003995 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cd07197 85963003996 active site 85963003997 catalytic triad [active] 85963003998 dimer interface [polypeptide binding]; other site 85963003999 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK14065 85963004000 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 85963004001 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 85963004002 S-adenosylmethionine binding site [chemical binding]; other site 85963004003 Uncharacterized protein family (UPF0093); Region: UPF0093; cl00863 85963004004 uncharacterized protein, YigZ family; Region: IMPACT_YIGZ; TIGR00257 85963004005 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 85963004006 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 85963004007 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 85963004008 ABC-2 type transporter; Region: ABC2_membrane; cl17235 85963004009 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 85963004010 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 85963004011 HlyD family secretion protein; Region: HlyD_3; pfam13437 85963004012 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 85963004013 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 85963004014 Domain of unknown function DUF21; Region: DUF21; pfam01595 85963004015 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 85963004016 Transporter associated domain; Region: CorC_HlyC; smart01091 85963004017 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 85963004018 Phosphate transporter family; Region: PHO4; pfam01384 85963004019 NifU-like domain; Region: NifU; pfam01106 85963004020 UDP-N-acetylmuramyl-tripeptide synthetase; Region: murE; TIGR01085 85963004021 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 85963004022 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 85963004023 Transaldolase-like proteins from plants and bacteria; Region: Transaldolase_like; cd00955 85963004024 putative active site [active] 85963004025 transaldolase; Provisional; Region: PRK03903 85963004026 catalytic residue [active] 85963004027 ribosomal protein L25, Ctc-form; Region: ctc_TL5; TIGR00731 85963004028 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 85963004029 5S rRNA interface [nucleotide binding]; other site 85963004030 CTC domain interface [polypeptide binding]; other site 85963004031 L16 interface [polypeptide binding]; other site 85963004032 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 85963004033 putative active site [active] 85963004034 catalytic residue [active] 85963004035 Predicted permeases [General function prediction only]; Region: COG0795 85963004036 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 85963004037 Catalytic domain of type II restriction endonucleases BfiI and NgoFVII, and uncharacterized proteins with a DEAD domain; Region: PLDc_Bfil_DEXD_like; cd09117 85963004038 PLD-like domain; Region: PLDc_2; pfam13091 85963004039 homodimer interface [polypeptide binding]; other site 85963004040 putative active site [active] 85963004041 catalytic site [active] 85963004042 Uncharacterized conserved protein (DUF2161); Region: DUF2161; cl02298 85963004043 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963004044 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3399 85963004045 Putative metal-binding domain of cation transport ATPase; Region: ATPase-cat_bd; pfam12156 85963004046 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 85963004047 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 85963004048 metal-binding site [ion binding] 85963004049 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 85963004050 Soluble P-type ATPase [General function prediction only]; Region: COG4087 85963004051 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 85963004052 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 85963004053 S-adenosylmethionine binding site [chemical binding]; other site 85963004054 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 85963004055 catalytic motif [active] 85963004056 Zn binding site [ion binding]; other site 85963004057 Pyrimidine reductase, riboflavin biosynthesis [Coenzyme metabolism]; Region: RibD; COG1985 85963004058 RibD C-terminal domain; Region: RibD_C; cl17279 85963004059 sodium--glutamate symport carrier (gltS); Region: gltS; TIGR00210 85963004060 Saccharopine dehydrogenase and related proteins [Amino acid transport and metabolism]; Region: LYS9; COG1748 85963004061 NAD(P) binding domain of amino acid dehydrogenase-like proteins; Region: NAD_bind_amino_acid_DH; cl17226 85963004062 NAD(P) binding pocket [chemical binding]; other site 85963004063 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 85963004064 4Fe-4S binding domain; Region: Fer4_5; pfam12801 85963004065 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 85963004066 acyl-phosphate glycerol 3-phosphate acyltransferase; Region: TIGR00023 85963004067 Dihydroneopterin aldolase (DHNA) and 7,8-dihydroneopterin triphosphate epimerase domain (DHNTPE); these enzymes have been designated folB and folX, respectively. Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and...; Region: DHNA_DHNTPE; cd00534 85963004068 homooctamer interface [polypeptide binding]; other site 85963004069 active site 85963004070 TonB-dependent Receptor Plug Domain; Region: Plug; cl08461 85963004071 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 85963004072 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 85963004073 Selenocysteine synthase [seryl-tRNASer selenium transferase] [Amino acid transport and metabolism]; Region: SelA; COG1921 85963004074 L-seryl-tRNA selenium transferase; Region: SelA; pfam03841 85963004075 transcription elongation factor NusA; Provisional; Region: nusA; PRK12328 85963004076 NusA N-terminal domain; Region: NusA_N; pfam08529 85963004077 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 85963004078 RNA binding site [nucleotide binding]; other site 85963004079 homodimer interface [polypeptide binding]; other site 85963004080 NusA-like KH domain; Region: KH_5; pfam13184 85963004081 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 85963004082 G-X-X-G motif; other site 85963004083 Type II restriction enzyme, methylase subunits [Defense mechanisms]; Region: COG1002 85963004084 Eco57I restriction-modification methylase; Region: Eco57I; pfam07669 85963004085 TaqI-like C-terminal specificity domain; Region: TaqI_C; pfam12950 85963004086 Restriction endonuclease [Defense mechanisms]; Region: COG3587 85963004087 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 85963004088 ATP binding site [chemical binding]; other site 85963004089 putative Mg++ binding site [ion binding]; other site 85963004090 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 85963004091 DNA methylase; Region: N6_N4_Mtase; cl17433 85963004092 DNA methylase; Region: N6_N4_Mtase; pfam01555 85963004093 DNA methylase; Region: N6_N4_Mtase; cl17433 85963004094 ATP-dependent DNA helicase RecG; Region: recG; TIGR00643 85963004095 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 85963004096 ssDNA binding site; other site 85963004097 generic binding surface II; other site 85963004098 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 85963004099 ATP binding site [chemical binding]; other site 85963004100 putative Mg++ binding site [ion binding]; other site 85963004101 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 85963004102 nucleotide binding region [chemical binding]; other site 85963004103 ATP-binding site [chemical binding]; other site 85963004104 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963004105 Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Ape1-like_AP-endo; cd09087 85963004106 active site 85963004107 putative catalytic site [active] 85963004108 DNA binding site [nucleotide binding] 85963004109 putative phosphate binding site [ion binding]; other site 85963004110 metal binding site A [ion binding]; metal-binding site 85963004111 AP binding site [nucleotide binding]; other site 85963004112 metal binding site B [ion binding]; metal-binding site 85963004113 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 85963004114 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 85963004115 Walker A motif; other site 85963004116 ATP binding site [chemical binding]; other site 85963004117 Walker B motif; other site 85963004118 arginine finger; other site 85963004119 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 85963004120 DnaA box-binding interface [nucleotide binding]; other site 85963004121 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 85963004122 Protein of unknown function (DUF2443); Region: DUF2443; pfam10398 85963004123 glucosamine--fructose-6-phosphate aminotransferase (isomerizing); Region: glmS; TIGR01135 85963004124 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 85963004125 glutaminase active site [active] 85963004126 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 85963004127 dimer interface [polypeptide binding]; other site 85963004128 active site 85963004129 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 85963004130 dimer interface [polypeptide binding]; other site 85963004131 active site 85963004132 Predicted alternative thymidylate synthase [Nucleotide transport and metabolism]; Region: THY1; COG1351 85963004133 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 85963004134 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 85963004135 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 85963004136 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 85963004137 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 85963004138 HsdM N-terminal domain; Region: HsdM_N; pfam12161 85963004139 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 85963004140 type I site-specific deoxyribonuclease, HsdR family; Region: hsdR; TIGR00348 85963004141 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 85963004142 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 85963004143 ATP binding site [chemical binding]; other site 85963004144 putative Mg++ binding site [ion binding]; other site 85963004145 Protein of unknown function DUF45; Region: DUF45; pfam01863 85963004146 Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]; Region: FecA; COG4772 85963004147 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 85963004148 N-terminal plug; other site 85963004149 ligand-binding site [chemical binding]; other site 85963004150 Arginase family; Region: Arginase; cd09989 85963004151 active site 85963004152 Mn binding site [ion binding]; other site 85963004153 oligomer interface [polypeptide binding]; other site 85963004154 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 85963004155 Alanine dehydrogenase NAD-binding and catalytic domains; Region: L-AlaDH; cd05305 85963004156 hexamer interface [polypeptide binding]; other site 85963004157 ligand binding site [chemical binding]; other site 85963004158 putative active site [active] 85963004159 NAD(P) binding site [chemical binding]; other site 85963004160 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 85963004161 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD1; cd05283 85963004162 putative NAD(P) binding site [chemical binding]; other site 85963004163 putative substrate binding site [chemical binding]; other site 85963004164 catalytic Zn binding site [ion binding]; other site 85963004165 structural Zn binding site [ion binding]; other site 85963004166 dimer interface [polypeptide binding]; other site 85963004167 Uncharacterized conserved protein [Function unknown]; Region: COG1479 85963004168 Protein of unknown function DUF262; Region: DUF262; pfam03235 85963004169 Uncharacterized conserved protein [Function unknown]; Region: COG1479 85963004170 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 85963004171 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 85963004172 NAD kinase [Coenzyme metabolism]; Region: nadF; COG0061 85963004173 ATP-NAD kinase; Region: NAD_kinase; pfam01513 85963004174 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 85963004175 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 85963004176 Walker A/P-loop; other site 85963004177 ATP binding site [chemical binding]; other site 85963004178 Q-loop/lid; other site 85963004179 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 85963004180 ABC transporter signature motif; other site 85963004181 Walker B; other site 85963004182 D-loop; other site 85963004183 H-loop/switch region; other site 85963004184 Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]; Region: COG1293 85963004185 Domain of unknown function (DUF814); Region: DUF814; pfam05670 85963004186 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 85963004187 Sel1-like repeats; Region: SEL1; smart00671 85963004188 Sel1-like repeats; Region: SEL1; smart00671 85963004189 DNA polymerase III subunit epsilon; Provisional; Region: PRK08517 85963004190 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 85963004191 active site 85963004192 catalytic site [active] 85963004193 substrate binding site [chemical binding]; other site 85963004194 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 85963004195 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 85963004196 substrate binding site [chemical binding]; other site 85963004197 hexamer interface [polypeptide binding]; other site 85963004198 metal binding site [ion binding]; metal-binding site 85963004199 Fructose-1,6-bisphosphatase, an enzyme that catalyzes the hydrolysis of fructose-1,6-biphosphate into fructose-6-phosphate and is critical in gluconeogenesis pathway. The alignment model also includes chloroplastic FBPases and sedoheptulose-1; Region: FBPase; cd00354 85963004200 AMP binding site [chemical binding]; other site 85963004201 metal binding site [ion binding]; metal-binding site 85963004202 active site 85963004203 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 85963004204 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 85963004205 active site 85963004206 phosphorylation site [posttranslational modification] 85963004207 intermolecular recognition site; other site 85963004208 dimerization interface [polypeptide binding]; other site 85963004209 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 85963004210 DNA binding site [nucleotide binding] 85963004211 elongation factor Ts; Provisional; Region: tsf; PRK09377 85963004212 UBA/TS-N domain; Region: UBA; pfam00627 85963004213 Elongation factor TS; Region: EF_TS; pfam00889 85963004214 Elongation factor TS; Region: EF_TS; pfam00889 85963004215 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 85963004216 rRNA interaction site [nucleotide binding]; other site 85963004217 S8 interaction site; other site 85963004218 putative laminin-1 binding site; other site 85963004219 putative recombination protein RecB; Provisional; Region: PRK13909 85963004220 Family description; Region: UvrD_C_2; pfam13538 85963004221 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 85963004222 pH-dependent sodium/proton antiporter; Provisional; Region: nhaA; PRK14856 85963004223 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 85963004224 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 85963004225 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 85963004226 protein-export membrane protein SecF; Region: 3a0501s07; TIGR00966 85963004227 Protein export membrane protein; Region: SecD_SecF; pfam02355 85963004228 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 85963004229 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 85963004230 HIGH motif; other site 85963004231 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 85963004232 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 85963004233 active site 85963004234 KMSKS motif; other site 85963004235 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 85963004236 tRNA binding surface [nucleotide binding]; other site 85963004237 anticodon binding site; other site 85963004238 Lipopolysaccharide-assembly; Region: LptE; pfam04390 85963004239 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 85963004240 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 85963004241 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 85963004242 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 85963004243 Peptidase family M23; Region: Peptidase_M23; pfam01551 85963004244 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 85963004245 Peptidase family M23; Region: Peptidase_M23; pfam01551 85963004246 Integral membrane protein CcmA involved in cell shape determination [Cell envelope biogenesis, outer membrane]; Region: CcmA; COG1664 85963004247 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 85963004248 transcription-repair coupling factor (mfd); Region: mfd; TIGR00580 85963004249 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 85963004250 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 85963004251 ATP binding site [chemical binding]; other site 85963004252 putative Mg++ binding site [ion binding]; other site 85963004253 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 85963004254 nucleotide binding region [chemical binding]; other site 85963004255 ATP-binding site [chemical binding]; other site 85963004256 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 85963004257 Rieske Fe-S protein [Energy production and conversion]; Region: QcrA; COG0723 85963004258 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 85963004259 [2Fe-2S] cluster binding site [ion binding]; other site 85963004260 Cytochrome b subunit of the bc complex [Energy production and conversion]; Region: QcrB; COG1290 85963004261 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 85963004262 intrachain domain interface; other site 85963004263 interchain domain interface [polypeptide binding]; other site 85963004264 heme bH binding site [chemical binding]; other site 85963004265 Qi binding site; other site 85963004266 heme bL binding site [chemical binding]; other site 85963004267 Qo binding site; other site 85963004268 interchain domain interface [polypeptide binding]; other site 85963004269 intrachain domain interface; other site 85963004270 Qi binding site; other site 85963004271 Cytochrome b(C-terminal)/b6/petD; Region: Cytochrom_B_C; pfam00032 85963004272 Qo binding site; other site 85963004273 Cytochrome c1 [Energy production and conversion]; Region: CYT1; COG2857 85963004274 Cytochrome c; Region: Cytochrom_C; pfam00034 85963004275 Cytochrome c; Region: Cytochrom_C; cl11414 85963004276 Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from...; Region: TOPRIM; cl00718 85963004277 active site 85963004278 metal binding site [ion binding]; metal-binding site 85963004279 Predicted ATPases [General function prediction only]; Region: COG1106 85963004280 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 85963004281 Walker A/P-loop; other site 85963004282 ATP binding site [chemical binding]; other site 85963004283 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 85963004284 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 85963004285 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 85963004286 flagellar hook-basal body protein FliE; Reviewed; Region: fliE; PRK03907 85963004287 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 85963004288 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 85963004289 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK05680 85963004290 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK07182 85963004291 Cell cycle protein; Region: FTSW_RODA_SPOVE; pfam01098 85963004292 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 85963004293 Periplasmic binding protein TroA_d. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a...; Region: TroA_d; cd01141 85963004294 putative ligand binding site [chemical binding]; other site 85963004295 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 85963004296 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 85963004297 Periplasmic binding protein TroA_d. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a...; Region: TroA_d; cd01141 85963004298 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 85963004299 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 85963004300 dimer interface [polypeptide binding]; other site 85963004301 decamer (pentamer of dimers) interface [polypeptide binding]; other site 85963004302 catalytic triad [active] 85963004303 peroxidatic and resolving cysteines [active] 85963004304 ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]; Region: NlpA; COG1464 85963004305 NLPA lipoprotein; Region: Lipoprotein_9; pfam03180 85963004306 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 85963004307 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 85963004308 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 85963004309 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 85963004310 G1 box; other site 85963004311 GTP/Mg2+ binding site [chemical binding]; other site 85963004312 Switch I region; other site 85963004313 G2 box; other site 85963004314 G3 box; other site 85963004315 Switch II region; other site 85963004316 G4 box; other site 85963004317 G5 box; other site 85963004318 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1934 85963004319 OstA-like protein; Region: OstA; pfam03968 85963004320 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 85963004321 motif II; other site 85963004322 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 85963004323 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 85963004324 Sporulation related domain; Region: SPOR; pfam05036 85963004325 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 85963004326 N-acetyl-D-glucosamine binding site [chemical binding]; other site 85963004327 catalytic residue [active] 85963004328 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 85963004329 Predicted metal-dependent hydrolases with the TIM-barrel fold [General function prediction only]; Region: COG1099 85963004330 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 85963004331 active site 85963004332 riboflavin synthase, alpha subunit; Region: ribE; TIGR00187 85963004333 Lumazine binding domain; Region: Lum_binding; pfam00677 85963004334 Lumazine binding domain; Region: Lum_binding; pfam00677 85963004335 flhB C-terminus-related protein; Region: flhB_rel; TIGR00789 85963004336 DL-methionine transporter ATP-binding subunit; Provisional; Region: metN; PRK11153 85963004337 ATP-binding cassette domain of methionine transporter; Region: ABC_MetN_methionine_transporter; cd03258 85963004338 Walker A/P-loop; other site 85963004339 ATP binding site [chemical binding]; other site 85963004340 Q-loop/lid; other site 85963004341 ABC transporter signature motif; other site 85963004342 Walker B; other site 85963004343 D-loop; other site 85963004344 H-loop/switch region; other site 85963004345 NIL domain; Region: NIL; pfam09383 85963004346 ABC-type metal ion transport system, permease component [Inorganic ion transport and metabolism]; Region: AbcD; COG2011 85963004347 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 85963004348 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 85963004349 active site 85963004350 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 85963004351 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 85963004352 Mg++ binding site [ion binding]; other site 85963004353 putative catalytic motif [active] 85963004354 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 85963004355 active site 85963004356 hydrophilic channel; other site 85963004357 dimerization interface [polypeptide binding]; other site 85963004358 catalytic residues [active] 85963004359 active site lid [active] 85963004360 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 85963004361 4-hydroxythreonine-4-phosphate dehydrogenase; Provisional; Region: pdxA; PRK03946 85963004362 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 85963004363 metallohydrolase, glycoprotease/Kae1 family; Region: gcp_kae1; TIGR00329 85963004364 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 85963004365 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 85963004366 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 85963004367 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4735 85963004368 hypothetical protein; Provisional; Region: PRK10236 85963004369 Domain of unknown function (DUF3944); Region: DUF3944; pfam13099 85963004370 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4735