-- dump date 20140619_114407 -- class Genbank::misc_feature -- table misc_feature_note -- id note 684950000001 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 684950000002 putative RNA binding site [nucleotide binding]; other site 684950000003 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 684950000004 homopentamer interface [polypeptide binding]; other site 684950000005 active site 684950000006 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 684950000007 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 684950000008 active site clefts [active] 684950000009 zinc binding site [ion binding]; other site 684950000010 dimer interface [polypeptide binding]; other site 684950000011 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 684950000012 active site 684950000013 dimer interface [polypeptide binding]; other site 684950000014 pantoate--beta-alanine ligase; Region: panC; TIGR00018 684950000015 Pantoate-beta-alanine ligase; Region: PanC; cd00560 684950000016 active site 684950000017 ATP-binding site [chemical binding]; other site 684950000018 pantoate-binding site; other site 684950000019 HXXH motif; other site 684950000020 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 684950000021 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 684950000022 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 684950000023 ring oligomerisation interface [polypeptide binding]; other site 684950000024 ATP/Mg binding site [chemical binding]; other site 684950000025 stacking interactions; other site 684950000026 hinge regions; other site 684950000027 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 684950000028 oligomerisation interface [polypeptide binding]; other site 684950000029 mobile loop; other site 684950000030 roof hairpin; other site 684950000031 DNA primase, catalytic core; Region: dnaG; TIGR01391 684950000032 CHC2 zinc finger; Region: zf-CHC2; pfam01807 684950000033 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 684950000034 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 684950000035 active site 684950000036 metal binding site [ion binding]; metal-binding site 684950000037 interdomain interaction site; other site 684950000038 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 684950000039 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 684950000040 Ligand Binding Site [chemical binding]; other site 684950000041 TrbC/VIRB2 family; Region: TrbC; cl01583 684950000042 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 684950000043 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 684950000044 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 684950000045 Walker A motif; other site 684950000046 ATP binding site [chemical binding]; other site 684950000047 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 684950000048 Walker B motif; other site 684950000049 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3014 684950000050 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 684950000051 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 684950000052 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 684950000053 active site 684950000054 phosphorylation site [posttranslational modification] 684950000055 intermolecular recognition site; other site 684950000056 dimerization interface [polypeptide binding]; other site 684950000057 carboxynorspermidine decarboxylase; Region: nspC; TIGR01047 684950000058 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Carboxynorspermidine Decarboxylase; Region: PLPDE_III_CANSDC; cd06829 684950000059 dimer interface [polypeptide binding]; other site 684950000060 active site 684950000061 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 684950000062 catalytic residues [active] 684950000063 substrate binding site [chemical binding]; other site 684950000064 lipid A 1-phosphatase; Reviewed; Region: PRK09597 684950000065 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 684950000066 active site 684950000067 lipid A phosphoethanolamine transferase; Reviewed; Region: PRK09598 684950000068 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 684950000069 Sulfatase; Region: Sulfatase; pfam00884 684950000070 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 684950000071 DNA/RNA endonuclease G, NUC1 [Nucleotide transport and metabolism]; Region: NUC1; COG1864 684950000072 DNA/RNA non-specific endonuclease; Region: Endonuclease_NS; smart00892 684950000073 prephenate dehydrogenase; Validated; Region: PRK08507 684950000074 Prephenate dehydrogenase; Region: PDH; pfam02153 684950000075 ATP-dependent protease La; Region: lon; TIGR00763 684950000076 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 684950000077 Walker A motif; other site 684950000078 ATP binding site [chemical binding]; other site 684950000079 Walker B motif; other site 684950000080 arginine finger; other site 684950000081 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 684950000082 DNA uptake lipoprotein [General function prediction only]; Region: ComL; COG4105 684950000083 flagellar assembly protein FliW; Provisional; Region: PRK13282 684950000084 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 684950000085 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 684950000086 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 684950000087 active site 684950000088 endopeptidase Clp ATP-binding regulatory subunit (clpX); Region: clpX; TIGR00382 684950000089 ClpX C4-type zinc finger; Region: zf-C4_ClpX; smart00994 684950000090 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 684950000091 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 684950000092 Walker A motif; other site 684950000093 ATP binding site [chemical binding]; other site 684950000094 Walker B motif; other site 684950000095 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 684950000096 rod shape-determining protein MreB; Provisional; Region: PRK13927 684950000097 MreB and similar proteins; Region: MreB_like; cd10225 684950000098 nucleotide binding site [chemical binding]; other site 684950000099 Mg binding site [ion binding]; other site 684950000100 putative protofilament interaction site [polypeptide binding]; other site 684950000101 RodZ interaction site [polypeptide binding]; other site 684950000102 Cell shape-determining protein [Cell envelope biogenesis, outer membrane]; Region: MreC; COG1792 684950000103 rod shape-determining protein MreC; Region: MreC; pfam04085 684950000104 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 684950000105 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 684950000106 active site 684950000107 phosphorylation site [posttranslational modification] 684950000108 intermolecular recognition site; other site 684950000109 dimerization interface [polypeptide binding]; other site 684950000110 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 684950000111 DNA binding site [nucleotide binding] 684950000112 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 684950000113 His Kinase A (phospho-acceptor) domain; Region: HisKA; pfam00512 684950000114 dimer interface [polypeptide binding]; other site 684950000115 phosphorylation site [posttranslational modification] 684950000116 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 684950000117 ATP binding site [chemical binding]; other site 684950000118 Mg2+ binding site [ion binding]; other site 684950000119 G-X-G motif; other site 684950000120 yjeF N-terminal region; Region: yjeF_nterm; TIGR00197 684950000121 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 684950000122 putative substrate binding site [chemical binding]; other site 684950000123 putative ATP binding site [chemical binding]; other site 684950000124 replicative DNA helicase; Provisional; Region: PRK08506 684950000125 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 684950000126 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 684950000127 Walker A motif; other site 684950000128 ATP binding site [chemical binding]; other site 684950000129 Walker B motif; other site 684950000130 DNA binding loops [nucleotide binding] 684950000131 Predicted membrane metal-binding protein [General function prediction only]; Region: ComEC; COG0658 684950000132 Competence protein; Region: Competence; pfam03772 684950000133 prenyltransferase; Reviewed; Region: ubiA; PRK12874 684950000134 UbiA prenyltransferase family; Region: UbiA; pfam01040 684950000135 phosphatidylserine decarboxylase; Provisional; Region: PRK03934 684950000136 Quinolinate synthetase A protein; Region: NadA; cl00420 684950000137 nicotinate-nucleotide pyrophosphorylase; Provisional; Region: PRK05848 684950000138 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 684950000139 dimerization interface [polypeptide binding]; other site 684950000140 active site 684950000141 Predicted helicase [General function prediction only]; Region: COG4889 684950000142 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 684950000143 DNA methylase; Region: N6_N4_Mtase; pfam01555 684950000144 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 684950000145 C-terminal peptidase (prc); Region: prc; TIGR00225 684950000146 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 684950000147 protein binding site [polypeptide binding]; other site 684950000148 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 684950000149 Catalytic dyad [active] 684950000150 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 684950000151 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 684950000152 putative acyl-acceptor binding pocket; other site 684950000153 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 684950000154 ligand binding site [chemical binding]; other site 684950000155 active site 684950000156 UGI interface [polypeptide binding]; other site 684950000157 catalytic site [active] 684950000158 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; pfam00044 684950000159 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 684950000160 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 684950000161 phosphoglycerate kinase; Provisional; Region: pgk; PRK00073 684950000162 Phosphoglycerate kinase; Region: PGK; pfam00162 684950000163 substrate binding site [chemical binding]; other site 684950000164 hinge regions; other site 684950000165 ADP binding site [chemical binding]; other site 684950000166 catalytic site [active] 684950000167 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 684950000168 Mg2+ transporter Helicobacter pylori CorA-like subgroup; Region: HpCorA-like; cd12836 684950000169 Cl binding site [ion binding]; other site 684950000170 oligomer interface [polypeptide binding]; other site 684950000171 Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]; Region: TerC; COG0861 684950000172 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 684950000173 DNA methylase; Region: N6_N4_Mtase; pfam01555 684950000174 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 684950000175 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 684950000176 cofactor binding site; other site 684950000177 DNA binding site [nucleotide binding] 684950000178 substrate interaction site [chemical binding]; other site 684950000179 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 684950000180 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cl00083 684950000181 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 684950000182 Na(+)/proline cotransporter PutP and related proteins; solute binding domain; Region: SLC5sbd_PutP; cd11475 684950000183 Na binding site [ion binding]; other site 684950000184 Proline dehydrogenase; Region: Pro_dh; pfam01619 684950000185 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 684950000186 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 684950000187 Glutamate binding site [chemical binding]; other site 684950000188 NAD binding site [chemical binding]; other site 684950000189 catalytic residues [active] 684950000190 SH3 domain protein; Region: SH3_and_anchor; TIGR04211 684950000191 SH3 domain protein; Region: SH3_and_anchor; TIGR04211 684950000192 Proteins of 100 residues with WXG; Region: WXG100; cl02005 684950000193 chromosome segregation protein; Provisional; Region: PRK03918 684950000194 Urease accessory protein UreH [Posttranslational modification, protein turnover, chaperones]; Region: UreH; COG0829 684950000195 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cd00882 684950000196 G1 box; other site 684950000197 GTP/Mg2+ binding site [chemical binding]; other site 684950000198 G2 box; other site 684950000199 Switch I region; other site 684950000200 G3 box; other site 684950000201 Switch II region; other site 684950000202 G4 box; other site 684950000203 G5 box; other site 684950000204 Urease accessory protein UreF [Posttranslational modification, protein turnover, chaperones]; Region: UreF; COG0830 684950000205 UreF; Region: UreF; pfam01730 684950000206 urease accessory protein UreE; Provisional; Region: ureE; PRK13261 684950000207 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 684950000208 dimer interface [polypeptide binding]; other site 684950000209 catalytic residues [active] 684950000210 AmiS/UreI family transporter; Region: AmiS_UreI; pfam02293 684950000211 urease subunit beta; Provisional; Region: ureB; PRK13985 684950000212 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 684950000213 subunit interactions [polypeptide binding]; other site 684950000214 active site 684950000215 flap region; other site 684950000216 urease subunit alpha; Provisional; Region: PRK13986 684950000217 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 684950000218 alpha-gamma subunit interface [polypeptide binding]; other site 684950000219 beta-gamma subunit interface [polypeptide binding]; other site 684950000220 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 684950000221 gamma-beta subunit interface [polypeptide binding]; other site 684950000222 alpha-beta subunit interface [polypeptide binding]; other site 684950000223 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 684950000224 phosphoglucosamine mutase; Provisional; Region: glmM; PRK14324 684950000225 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 684950000226 active site 684950000227 substrate binding site [chemical binding]; other site 684950000228 metal binding site [ion binding]; metal-binding site 684950000229 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 684950000230 peptide chain release factor 1; Validated; Region: prfA; PRK00591 684950000231 This domain is found in peptide chain release factors; Region: PCRF; smart00937 684950000232 RF-1 domain; Region: RF-1; pfam00472 684950000233 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 684950000234 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 684950000235 dimer interface [polypeptide binding]; other site 684950000236 putative CheW interface [polypeptide binding]; other site 684950000237 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 684950000238 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 684950000239 23S rRNA interface [nucleotide binding]; other site 684950000240 L3 interface [polypeptide binding]; other site 684950000241 Predicted dehydrogenase [General function prediction only]; Region: COG0579 684950000242 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl17341 684950000243 NLPC_P60 stabilising domain, N term; Region: N_NLPC_P60; pfam12912 684950000244 SH3 domain of the SH3b1 type; Region: SH3_6; pfam12913 684950000245 SH3 domain of SH3b2 type; Region: SH3_7; pfam12914 684950000246 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 684950000247 NlpC/P60 family; Region: NLPC_P60; pfam00877 684950000248 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 684950000249 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 684950000250 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 684950000251 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 684950000252 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 684950000253 DNA binding residues [nucleotide binding] 684950000254 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Region: MTA/SAH-Nsdase; TIGR01704 684950000255 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Validated; Region: PRK05584 684950000256 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 684950000257 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 684950000258 DpnII restriction endonuclease; Region: DpnII; pfam04556 684950000259 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 684950000260 Methyltransferase domain; Region: Methyltransf_26; pfam13659 684950000261 DNA methylase; Region: N6_N4_Mtase; pfam01555 684950000262 2-hydroxyacid dehydrogenase; Provisional; Region: PRK08410 684950000263 Putative D-isomer specific 2-hydroxyacid dehydrogenases; Region: 2-Hacid_dh_4; cd12162 684950000264 putative ligand binding site [chemical binding]; other site 684950000265 putative NAD binding site [chemical binding]; other site 684950000266 catalytic site [active] 684950000267 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 684950000268 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 684950000269 pyridoxal 5'-phosphate binding site [chemical binding]; other site 684950000270 catalytic residue [active] 684950000271 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 684950000272 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 684950000273 dimer interface [polypeptide binding]; other site 684950000274 putative CheW interface [polypeptide binding]; other site 684950000275 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 684950000276 Ligand Binding Site [chemical binding]; other site 684950000277 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 684950000278 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 684950000279 WfgS and WfeV are involved in O-antigen biosynthesis; Region: GT_2_WfgS_like; cd06433 684950000280 metal-binding site 684950000281 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 684950000282 HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain; Region: HAMP; smart00304 684950000283 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 684950000284 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 684950000285 dimer interface [polypeptide binding]; other site 684950000286 putative CheW interface [polypeptide binding]; other site 684950000287 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases [Nucleotide transport and metabolism]; Region: UshA; COG0737 684950000288 Escherichia coli CpdB and related proteins, N-terminal metallophosphatase domain; Region: MPP_CpdB_N; cd07410 684950000289 active site 684950000290 metal binding site [ion binding]; metal-binding site 684950000291 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 684950000292 S-Ribosylhomocysteinase (LuxS); Region: LuxS; pfam02664 684950000293 cystathionine gamma-synthase/cystathionine beta-lyase; Validated; Region: PRK06176 684950000294 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 684950000295 homodimer interface [polypeptide binding]; other site 684950000296 substrate-cofactor binding pocket; other site 684950000297 pyridoxal 5'-phosphate binding site [chemical binding]; other site 684950000298 catalytic residue [active] 684950000299 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 684950000300 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 684950000301 dimer interface [polypeptide binding]; other site 684950000302 pyridoxal 5'-phosphate binding site [chemical binding]; other site 684950000303 catalytic residue [active] 684950000304 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 684950000305 Nucleotide-binding domain of human HSPA9 and similar proteins; Region: HSPA9-Ssq1-like_NBD; cd10234 684950000306 nucleotide binding site [chemical binding]; other site 684950000307 NEF interaction site [polypeptide binding]; other site 684950000308 SBD interface [polypeptide binding]; other site 684950000309 Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: GrpE; COG0576 684950000310 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 684950000311 dimer interface [polypeptide binding]; other site 684950000312 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 684950000313 heat-inducible transcription repressor; Provisional; Region: PRK03911 684950000314 hypothetical protein; Provisional; Region: PRK05834 684950000315 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2604 684950000316 flagellin B; Provisional; Region: PRK13588 684950000317 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 684950000318 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 684950000319 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 684950000320 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 684950000321 DNA topoisomerase I; Validated; Region: PRK05582 684950000322 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 684950000323 active site 684950000324 interdomain interaction site; other site 684950000325 putative metal-binding site [ion binding]; other site 684950000326 nucleotide binding site [chemical binding]; other site 684950000327 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 684950000328 domain I; other site 684950000329 DNA binding groove [nucleotide binding] 684950000330 phosphate binding site [ion binding]; other site 684950000331 domain II; other site 684950000332 domain III; other site 684950000333 nucleotide binding site [chemical binding]; other site 684950000334 catalytic site [active] 684950000335 domain IV; other site 684950000336 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 684950000337 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 684950000338 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 684950000339 Fe-S oxidoreductases [Energy production and conversion]; Region: COG0731 684950000340 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 684950000341 FeS/SAM binding site; other site 684950000342 Helicobacter pylori protein of unknown function (DUF874); Region: DUF874; pfam05917 684950000343 phosphoenolpyruvate synthase; Validated; Region: PRK06464 684950000344 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 684950000345 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 684950000346 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 684950000347 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK12305 684950000348 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; pfam07973 684950000349 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 684950000350 active site 684950000351 dimer interface [polypeptide binding]; other site 684950000352 motif 1; other site 684950000353 motif 2; other site 684950000354 motif 3; other site 684950000355 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 684950000356 anticodon binding site; other site 684950000357 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 684950000358 translation initiation factor IF-3; Region: infC; TIGR00168 684950000359 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 684950000360 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 684950000361 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 684950000362 23S rRNA binding site [nucleotide binding]; other site 684950000363 L21 binding site [polypeptide binding]; other site 684950000364 L13 binding site [polypeptide binding]; other site 684950000365 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 684950000366 Protein of unknown function (DUF1104); Region: DUF1104; pfam06518 684950000367 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 684950000368 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 684950000369 Serine dehydratase alpha chain; Region: SDH_alpha; pfam03313 684950000370 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 684950000371 threonine/serine transporter TdcC; Provisional; Region: PRK13629; cl17672 684950000372 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase [Amino acid transport and metabolism]; Region: AroG; COG3200 684950000373 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 684950000374 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 684950000375 catalytic triad [active] 684950000376 Uncharacterized conserved protein [Function unknown]; Region: COG1556 684950000377 iron-sulfur cluster-binding protein; Region: TIGR00273 684950000378 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 684950000379 Domain of unknown function (DUF3390); Region: DUF3390; pfam11870 684950000380 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 684950000381 Cysteine-rich domain; Region: CCG; pfam02754 684950000382 Cysteine-rich domain; Region: CCG; pfam02754 684950000383 L-lactate transport; Region: lctP; TIGR00795 684950000384 L-lactate permease [Energy production and conversion]; Region: LldP; COG1620 684950000385 L-lactate permease [Energy production and conversion]; Region: LldP; COG1620 684950000386 L-lactate permease; Region: Lactate_perm; pfam02652 684950000387 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 684950000388 DNA glycosylase MutY; Provisional; Region: PRK13910 684950000389 minor groove reading motif; other site 684950000390 helix-hairpin-helix signature motif; other site 684950000391 substrate binding pocket [chemical binding]; other site 684950000392 active site 684950000393 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 684950000394 DNA binding and oxoG recognition site [nucleotide binding] 684950000395 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 684950000396 Sodium:sulfate symporter transmembrane region; Region: Na_sulph_symp; pfam00939 684950000397 transmembrane helices; other site 684950000398 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 684950000399 Low-spin heme binding site [chemical binding]; other site 684950000400 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 684950000401 D-pathway; other site 684950000402 Putative water exit pathway; other site 684950000403 Binuclear center (active site) [active] 684950000404 K-pathway; other site 684950000405 Putative proton exit pathway; other site 684950000406 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 684950000407 Cytochrome C oxidase, mono-heme subunit/FixO; Region: FixO; cl01130 684950000408 cytochrome c oxidase, cbb3-type, CcoQ subunit, epsilon-Proteobacterial; Region: cbb3_Q_epsi; TIGR02736 684950000409 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 684950000410 Cytochrome c; Region: Cytochrom_C; pfam00034 684950000411 Cytochrome c; Region: Cytochrom_C; pfam00034 684950000412 Family of unknown function (DUF4006); Region: DUF4006; pfam13179 684950000413 Predicted periplasmic solute-binding protein [General function prediction only]; Region: COG2107 684950000414 recombinase A; Provisional; Region: recA; PRK09354 684950000415 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 684950000416 hexamer interface [polypeptide binding]; other site 684950000417 Walker A motif; other site 684950000418 ATP binding site [chemical binding]; other site 684950000419 Walker B motif; other site 684950000420 enolase; Provisional; Region: eno; PRK00077 684950000421 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 684950000422 dimer interface [polypeptide binding]; other site 684950000423 metal binding site [ion binding]; metal-binding site 684950000424 substrate binding pocket [chemical binding]; other site 684950000425 AMIN domain; Region: AMIN; pfam11741 684950000426 Shikimate kinase [Amino acid transport and metabolism]; Region: AroK; COG0703 684950000427 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 684950000428 ADP binding site [chemical binding]; other site 684950000429 magnesium binding site [ion binding]; other site 684950000430 putative shikimate binding site; other site 684950000431 Cache domain; Region: Cache_1; pfam02743 684950000432 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 684950000433 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 684950000434 Ligand binding site; other site 684950000435 metal-binding site 684950000436 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 684950000437 Sel1-like repeats; Region: SEL1; smart00671 684950000438 Sel1-like repeats; Region: SEL1; smart00671 684950000439 Sel1-like repeats; Region: SEL1; smart00671 684950000440 Sel1-like repeats; Region: SEL1; smart00671 684950000441 Sel1-like repeats; Region: SEL1; smart00671 684950000442 Sel1-like repeats; Region: SEL1; smart00671 684950000443 hypothetical protein; Provisional; Region: PRK12378 684950000444 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 684950000445 dimer interface [polypeptide binding]; other site 684950000446 active site 684950000447 Schiff base residues; other site 684950000448 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 684950000449 HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain; Region: HAMP; smart00304 684950000450 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 684950000451 dimer interface [polypeptide binding]; other site 684950000452 phosphorylation site [posttranslational modification] 684950000453 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 684950000454 ATP binding site [chemical binding]; other site 684950000455 Mg2+ binding site [ion binding]; other site 684950000456 G-X-G motif; other site 684950000457 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 684950000458 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 684950000459 active site 684950000460 phosphorylation site [posttranslational modification] 684950000461 intermolecular recognition site; other site 684950000462 dimerization interface [polypeptide binding]; other site 684950000463 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 684950000464 DNA binding site [nucleotide binding] 684950000465 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 684950000466 Peptidase family U32; Region: Peptidase_U32; pfam01136 684950000467 peptide chain release factor 2; Region: prfB; TIGR00020 684950000468 This domain is found in peptide chain release factors; Region: PCRF; smart00937 684950000469 RF-1 domain; Region: RF-1; pfam00472 684950000470 Flagellar biosynthesis pathway, component FliR [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FliR; COG1684 684950000471 Etoposide-induced protein 2.4 (EI24); Region: EI24; pfam07264 684950000472 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 684950000473 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 684950000474 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 684950000475 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 684950000476 intersubunit interface [polypeptide binding]; other site 684950000477 active site 684950000478 zinc binding site [ion binding]; other site 684950000479 Na+ binding site [ion binding]; other site 684950000480 elongation factor P; Validated; Region: PRK00529 684950000481 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 684950000482 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 684950000483 RNA binding site [nucleotide binding]; other site 684950000484 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 684950000485 RNA binding site [nucleotide binding]; other site 684950000486 GTPase subunit of restriction endonuclease [Defense mechanisms]; Region: McrB; COG1401 684950000487 AAA domain (dynein-related subfamily); Region: AAA_5; pfam07728 684950000488 Walker A motif; other site 684950000489 ATP binding site [chemical binding]; other site 684950000490 Walker B motif; other site 684950000491 LlaJI restriction endonuclease; Region: RE_LlaJI; pfam09563 684950000492 pseudaminic acid synthase; Region: PseI; TIGR03586 684950000493 NeuB family; Region: NeuB; pfam03102 684950000494 C-terminal SAF domain of sialic acid synthetase; Region: SAF_NeuB_like; cd11615 684950000495 NeuB binding interface [polypeptide binding]; other site 684950000496 putative substrate binding site [chemical binding]; other site 684950000497 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 684950000498 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 684950000499 Walker A/P-loop; other site 684950000500 ATP binding site [chemical binding]; other site 684950000501 Q-loop/lid; other site 684950000502 ABC transporter signature motif; other site 684950000503 Walker B; other site 684950000504 D-loop; other site 684950000505 H-loop/switch region; other site 684950000506 apolipoprotein N-acyltransferase; Reviewed; Region: PRK12291 684950000507 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cl11424 684950000508 active site 684950000509 catalytic triad [active] 684950000510 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 684950000511 Colicin V production protein; Region: Colicin_V; pfam02674 684950000512 Apolipoprotein C-I (ApoC-1); Region: ApoC-I; pfam04691 684950000513 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 684950000514 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 684950000515 dimer interface [polypeptide binding]; other site 684950000516 putative anticodon binding site; other site 684950000517 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 684950000518 motif 1; other site 684950000519 active site 684950000520 motif 2; other site 684950000521 motif 3; other site 684950000522 serine hydroxymethyltransferase; Reviewed; Region: PRK13034 684950000523 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 684950000524 dimer interface [polypeptide binding]; other site 684950000525 active site 684950000526 glycine-pyridoxal phosphate binding site [chemical binding]; other site 684950000527 folate binding site [chemical binding]; other site 684950000528 Domain of unknown function (DUF1882); Region: DUF1882; pfam08966 684950000529 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; cl01287 684950000530 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 684950000531 Uncharacterized protein family, UPF0114; Region: UPF0114; cl01078 684950000532 Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_1; cd09111 684950000533 PLD-like domain; Region: PLDc_2; pfam13091 684950000534 putative active site [active] 684950000535 catalytic site [active] 684950000536 Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_2; cd09113 684950000537 PLD-like domain; Region: PLDc_2; pfam13091 684950000538 putative active site [active] 684950000539 catalytic site [active] 684950000540 fumarate reductase iron-sulfur subunit; Provisional; Region: frdB; PRK13552 684950000541 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 684950000542 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 684950000543 fumarate reductase flavoprotein subunit; Provisional; Region: PRK08626 684950000544 L-aspartate oxidase; Provisional; Region: PRK06175 684950000545 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 684950000546 fumarate reductase cytochrome b-556 subunit; Provisional; Region: PRK13553 684950000547 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 684950000548 Iron-sulfur protein interface; other site 684950000549 proximal heme binding site [chemical binding]; other site 684950000550 distal heme binding site [chemical binding]; other site 684950000551 dimer interface [polypeptide binding]; other site 684950000552 triosephosphate isomerase; Provisional; Region: PRK14567 684950000553 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 684950000554 substrate binding site [chemical binding]; other site 684950000555 dimer interface [polypeptide binding]; other site 684950000556 catalytic triad [active] 684950000557 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK08415 684950000558 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 684950000559 NAD binding site [chemical binding]; other site 684950000560 homotetramer interface [polypeptide binding]; other site 684950000561 homodimer interface [polypeptide binding]; other site 684950000562 substrate binding site [chemical binding]; other site 684950000563 active site 684950000564 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Region: lipid_A_lpxD; TIGR01853 684950000565 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 684950000566 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 684950000567 trimer interface [polypeptide binding]; other site 684950000568 active site 684950000569 UDP-GlcNAc binding site [chemical binding]; other site 684950000570 lipid binding site [chemical binding]; lipid-binding site 684950000571 S-adenosylmethionine synthetase; Validated; Region: PRK05250 684950000572 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 684950000573 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 684950000574 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 684950000575 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 684950000576 active site 684950000577 multimer interface [polypeptide binding]; other site 684950000578 Uncharacterized ACR, COG1399; Region: DUF177; cl00616 684950000579 Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]; Region: RpmF; COG0333 684950000580 3-oxoacyl-(acyl-carrier-protein) synthase III; Region: fabH; TIGR00747 684950000581 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 684950000582 dimer interface [polypeptide binding]; other site 684950000583 active site 684950000584 CoA binding pocket [chemical binding]; other site 684950000585 AAA domain; Region: AAA_21; pfam13304 684950000586 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cd00267 684950000587 Walker B; other site 684950000588 D-loop; other site 684950000589 H-loop/switch region; other site 684950000590 antiporter inner membrane protein; Provisional; Region: PRK11670 684950000591 Domain of unknown function DUF59; Region: DUF59; cl00941 684950000592 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 684950000593 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 684950000594 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 684950000595 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 684950000596 heat shock protein 90; Provisional; Region: PRK05218 684950000597 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 684950000598 ATP binding site [chemical binding]; other site 684950000599 Mg2+ binding site [ion binding]; other site 684950000600 G-X-G motif; other site 684950000601 TPR repeat; Region: TPR_11; pfam13414 684950000602 Sel1-like repeats; Region: SEL1; smart00671 684950000603 Sel1-like repeats; Region: SEL1; smart00671 684950000604 Sel1-like repeats; Region: SEL1; smart00671 684950000605 Sel1-like repeats; Region: SEL1; smart00671 684950000606 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 684950000607 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 684950000608 metal binding site [ion binding]; metal-binding site 684950000609 dimer interface [polypeptide binding]; other site 684950000610 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 684950000611 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 684950000612 transmembrane helices; other site 684950000613 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 684950000614 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 684950000615 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: Dxr; TIGR00243 684950000616 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 684950000617 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 684950000618 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 684950000619 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 684950000620 substrate binding site [chemical binding]; other site 684950000621 Helix-turn-helix domain; Region: HTH_28; pfam13518 684950000622 cysteine desulfurase, NifS family, epsilon proteobacteria type; Region: nifS_epsilon; TIGR03403 684950000623 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 684950000624 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 684950000625 catalytic residue [active] 684950000626 Fe-S cluster assembly protein NifU; Region: NifU_proper; TIGR02000 684950000627 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 684950000628 trimerization site [polypeptide binding]; other site 684950000629 active site 684950000630 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 684950000631 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 684950000632 DNA repair protein RadA; Region: sms; TIGR00416 684950000633 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 684950000634 Walker A motif/ATP binding site; other site 684950000635 ATP binding site [chemical binding]; other site 684950000636 Walker B motif; other site 684950000637 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 684950000638 Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: MsrA; COG0225 684950000639 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: COG0229 684950000640 SelR domain; Region: SelR; pfam01641 684950000641 Predicted permeases [General function prediction only]; Region: COG0730 684950000642 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 684950000643 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 684950000644 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 684950000645 Sulfate transporter family; Region: Sulfate_transp; pfam00916 684950000646 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 684950000647 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 684950000648 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 684950000649 Ligand binding site; other site 684950000650 oligomer interface; other site 684950000651 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 684950000652 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 684950000653 hypothetical protein; Provisional; Region: PRK04081 684950000654 Glutathionylspermidine synthase [Amino acid transport and metabolism]; Region: Gsp; COG0754 684950000655 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3295 684950000656 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 684950000657 Sel1-like repeats; Region: SEL1; smart00671 684950000658 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 684950000659 binding surface 684950000660 TPR motif; other site 684950000661 Sel1-like repeats; Region: SEL1; smart00671 684950000662 Sel1-like repeats; Region: SEL1; smart00671 684950000663 Cytochrome c; Region: Cytochrom_C; cl11414 684950000664 Porphobilinogen deaminase [Coenzyme metabolism]; Region: HemC; COG0181 684950000665 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 684950000666 domain interfaces; other site 684950000667 active site 684950000668 prolyl-tRNA synthetase, family II; Region: proS_fam_II; TIGR00409 684950000669 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 684950000670 dimer interface [polypeptide binding]; other site 684950000671 motif 1; other site 684950000672 active site 684950000673 motif 2; other site 684950000674 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 684950000675 putative deacylase active site [active] 684950000676 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 684950000677 active site 684950000678 motif 3; other site 684950000679 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 684950000680 anticodon binding site; other site 684950000681 glutamyl-tRNA reductase; Region: hemA; TIGR01035 684950000682 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 684950000683 tRNA; other site 684950000684 putative tRNA binding site [nucleotide binding]; other site 684950000685 putative NADP binding site [chemical binding]; other site 684950000686 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 684950000687 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 684950000688 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 684950000689 substrate binding pocket [chemical binding]; other site 684950000690 chain length determination region; other site 684950000691 substrate-Mg2+ binding site; other site 684950000692 catalytic residues [active] 684950000693 aspartate-rich region 1; other site 684950000694 active site lid residues [active] 684950000695 aspartate-rich region 2; other site 684950000696 Domain of unknown function (DUF2018); Region: DUF2018; pfam09442 684950000697 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 684950000698 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 684950000699 dimerization interface [polypeptide binding]; other site 684950000700 DPS ferroxidase diiron center [ion binding]; other site 684950000701 ion pore; other site 684950000702 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 684950000703 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 684950000704 dimer interface [polypeptide binding]; other site 684950000705 phosphorylation site [posttranslational modification] 684950000706 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 684950000707 ATP binding site [chemical binding]; other site 684950000708 Mg2+ binding site [ion binding]; other site 684950000709 G-X-G motif; other site 684950000710 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 684950000711 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 684950000712 Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]; Region: SrmB; COG0513 684950000713 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 684950000714 ATP binding site [chemical binding]; other site 684950000715 Mg++ binding site [ion binding]; other site 684950000716 motif III; other site 684950000717 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 684950000718 nucleotide binding region [chemical binding]; other site 684950000719 ATP-binding site [chemical binding]; other site 684950000720 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 684950000721 SPFH domain / Band 7 family; Region: Band_7; pfam01145 684950000722 Protein of unknown function (DUF2393); Region: DUF2393; pfam09624 684950000723 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 684950000724 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 684950000725 Walker A/P-loop; other site 684950000726 ATP binding site [chemical binding]; other site 684950000727 Q-loop/lid; other site 684950000728 ABC transporter signature motif; other site 684950000729 Walker B; other site 684950000730 D-loop; other site 684950000731 H-loop/switch region; other site 684950000732 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 684950000733 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 684950000734 Walker A/P-loop; other site 684950000735 ATP binding site [chemical binding]; other site 684950000736 Q-loop/lid; other site 684950000737 ABC transporter signature motif; other site 684950000738 Walker B; other site 684950000739 D-loop; other site 684950000740 H-loop/switch region; other site 684950000741 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 684950000742 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4239 684950000743 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 684950000744 dimer interface [polypeptide binding]; other site 684950000745 conserved gate region; other site 684950000746 putative PBP binding loops; other site 684950000747 ABC-ATPase subunit interface; other site 684950000748 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 684950000749 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 684950000750 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 684950000751 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 684950000752 GDP-binding site [chemical binding]; other site 684950000753 ACT binding site; other site 684950000754 IMP binding site; other site 684950000755 Flagellar FliJ protein; Region: FliJ; pfam02050 684950000756 Uncharacterized conserved protein [Function unknown]; Region: COG3334 684950000757 RIP metalloprotease RseP; Region: TIGR00054 684950000758 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 684950000759 active site 684950000760 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 684950000761 protein binding site [polypeptide binding]; other site 684950000762 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic...; Region: S2P-M50; cl10020 684950000763 putative substrate binding region [chemical binding]; other site 684950000764 exodeoxyribonuclease VII, large subunit; Region: xseA; TIGR00237 684950000765 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 684950000766 generic binding surface II; other site 684950000767 generic binding surface I; other site 684950000768 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 684950000769 DNA methylase; Region: N6_N4_Mtase; pfam01555 684950000770 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 684950000771 DNA methylase; Region: N6_N4_Mtase; pfam01555 684950000772 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 684950000773 Clp amino terminal domain; Region: Clp_N; pfam02861 684950000774 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 684950000775 Walker A motif; other site 684950000776 ATP binding site [chemical binding]; other site 684950000777 Walker B motif; other site 684950000778 arginine finger; other site 684950000779 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 684950000780 Walker A motif; other site 684950000781 ATP binding site [chemical binding]; other site 684950000782 Walker B motif; other site 684950000783 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 684950000784 Cytochrome c biogenesis protein [Posttranslational modification, protein turnover, chaperones]; Region: CcdA; COG0785 684950000785 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; pfam02683 684950000786 dihydroorotase; Provisional; Region: PRK08417 684950000787 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 684950000788 active site 684950000789 chlorohydrolase; Provisional; Region: PRK08418 684950000790 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 684950000791 active site 684950000792 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 684950000793 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14339 684950000794 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 684950000795 FeS/SAM binding site; other site 684950000796 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: DUF374; Region: LPLAT_DUF374-like; cd07983 684950000797 putative acyl-acceptor binding pocket; other site 684950000798 Predicted Fe-S-cluster oxidoreductase [General function prediction only]; Region: COG0727 684950000799 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 684950000800 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 684950000801 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 684950000802 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 684950000803 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 684950000804 putative active site [active] 684950000805 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 684950000806 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 684950000807 putative acyl-acceptor binding pocket; other site 684950000808 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 684950000809 tRNA-guanine family transglycosylase; Region: tgt_general; TIGR00449 684950000810 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3400 684950000811 TrkA-C domain; Region: TrkA_C; pfam02080 684950000812 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 684950000813 active site 684950000814 dimer interface [polypeptide binding]; other site 684950000815 metal binding site [ion binding]; metal-binding site 684950000816 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 684950000817 Mechanosensitive ion channel; Region: MS_channel; pfam00924 684950000818 radical SAM methylthiotransferase, MiaB/RimO family; Region: TIGR00089 684950000819 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 684950000820 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 684950000821 FeS/SAM binding site; other site 684950000822 ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]; Region: HflB; COG0465 684950000823 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 684950000824 Walker A motif; other site 684950000825 ATP binding site [chemical binding]; other site 684950000826 Walker B motif; other site 684950000827 arginine finger; other site 684950000828 Domain of unknown function (DUF4149); Region: DUF4149; pfam13664 684950000829 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 684950000830 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 684950000831 PPE-repeat proteins [Cell motility and secretion]; Region: COG5651 684950000832 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 684950000833 Autotransporter beta-domain; Region: Autotransporter; pfam03797 684950000834 diaminopimelate decarboxylase; Region: lysA; TIGR01048 684950000835 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 684950000836 active site 684950000837 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 684950000838 substrate binding site [chemical binding]; other site 684950000839 catalytic residues [active] 684950000840 dimer interface [polypeptide binding]; other site 684950000841 Chorismate mutase [Amino acid transport and metabolism]; Region: PheA; COG1605 684950000842 Uncharacterized conserved protein [Function unknown]; Region: COG4866 684950000843 aminodeoxychorismate synthase; Provisional; Region: PRK07508 684950000844 chorismate binding enzyme; Region: Chorismate_bind; cl10555 684950000845 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 684950000846 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 684950000847 substrate-cofactor binding pocket; other site 684950000848 pyridoxal 5'-phosphate binding site [chemical binding]; other site 684950000849 catalytic residue [active] 684950000850 acylamide amidohydrolase; Provisional; Region: amiE; PRK13286 684950000851 aliphatic amidases (class 2 nitrilases); Region: aliphatic_amidase; cd07565 684950000852 multimer interface [polypeptide binding]; other site 684950000853 active site 684950000854 catalytic triad [active] 684950000855 dimer interface [polypeptide binding]; other site 684950000856 flagellar hook-associated protein FlgL; Validated; Region: flgL; PRK08412 684950000857 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 684950000858 ribosomal protein L21; Region: L21; TIGR00061 684950000859 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 684950000860 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 684950000861 The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; Region: PBP2_DppA_like; cd08493 684950000862 peptide binding site [polypeptide binding]; other site 684950000863 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 684950000864 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 684950000865 dimer interface [polypeptide binding]; other site 684950000866 conserved gate region; other site 684950000867 putative PBP binding loops; other site 684950000868 ABC-ATPase subunit interface; other site 684950000869 dipeptide transporter; Provisional; Region: PRK10913 684950000870 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 684950000871 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 684950000872 dimer interface [polypeptide binding]; other site 684950000873 conserved gate region; other site 684950000874 putative PBP binding loops; other site 684950000875 ABC-ATPase subunit interface; other site 684950000876 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 684950000877 nickel import ATP-binding protein NikD; Region: nickel_nikD; TIGR02770 684950000878 Walker A/P-loop; other site 684950000879 ATP binding site [chemical binding]; other site 684950000880 Q-loop/lid; other site 684950000881 ABC transporter signature motif; other site 684950000882 Walker B; other site 684950000883 D-loop; other site 684950000884 H-loop/switch region; other site 684950000885 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 684950000886 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 684950000887 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 684950000888 Walker A/P-loop; other site 684950000889 ATP binding site [chemical binding]; other site 684950000890 Q-loop/lid; other site 684950000891 ABC transporter signature motif; other site 684950000892 Walker B; other site 684950000893 D-loop; other site 684950000894 H-loop/switch region; other site 684950000895 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; pfam08352 684950000896 GTPase CgtA; Reviewed; Region: obgE; PRK12299 684950000897 GTP1/OBG; Region: GTP1_OBG; pfam01018 684950000898 Obg GTPase; Region: Obg; cd01898 684950000899 G1 box; other site 684950000900 GTP/Mg2+ binding site [chemical binding]; other site 684950000901 Switch I region; other site 684950000902 G2 box; other site 684950000903 G3 box; other site 684950000904 Switch II region; other site 684950000905 G4 box; other site 684950000906 Alginate lyase; Region: Alginate_lyase; pfam05426 684950000907 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 684950000908 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 684950000909 inhibitor-cofactor binding pocket; inhibition site 684950000910 pyridoxal 5'-phosphate binding site [chemical binding]; other site 684950000911 catalytic residue [active] 684950000912 Putative F0F1-ATPase subunit (ATPase_gene1); Region: ATPase_gene1; pfam09527 684950000913 Predicted amidohydrolase [General function prediction only]; Region: COG0388 684950000914 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cd07197 684950000915 active site 684950000916 catalytic triad [active] 684950000917 dimer interface [polypeptide binding]; other site 684950000918 Catalytic domain of Helicobacter pylori peptidoglycan deacetylase (HpPgdA) and similar proteins; Region: CE4_HpPgdA_like; cd10938 684950000919 active site 684950000920 catalytic site [active] 684950000921 Zn binding site [ion binding]; other site 684950000922 tetramer interface [polypeptide binding]; other site 684950000923 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 684950000924 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 684950000925 CobW/HypB/UreG, nucleotide-binding domain; Region: cobW; pfam02492 684950000926 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; pfam07683 684950000927 Arabinose efflux permease [Carbohydrate transport and metabolism]; Region: AraJ; COG2814 684950000928 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 684950000929 putative substrate translocation pore; other site 684950000930 heme oxygenase, HugZ family; Region: heme_ox_HugZ; TIGR04109 684950000931 Protein of unknown function (DUF2470); Region: DUF2470; pfam10615 684950000932 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 684950000933 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 684950000934 arginyl-tRNA synthetase; Region: argS; TIGR00456 684950000935 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 684950000936 active site 684950000937 HIGH motif; other site 684950000938 KMSK motif region; other site 684950000939 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 684950000940 tRNA binding surface [nucleotide binding]; other site 684950000941 anticodon binding site; other site 684950000942 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 684950000943 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 684950000944 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 684950000945 catalytic site [active] 684950000946 G-X2-G-X-G-K; other site 684950000947 nuclease NucT; Provisional; Region: PRK13912 684950000948 Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6, and similar proteins; Region: PLDc_Nuc_like; cd09116 684950000949 putative active site [active] 684950000950 catalytic site [active] 684950000951 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 684950000952 Flagellar basal body L-ring protein [Cell motility and secretion]; Region: FlgH; COG2063 684950000953 flagellar basal body L-ring protein; Reviewed; Region: flgH; PRK00249 684950000954 CMP-NeuAc_Synthase activates N-acetylneuraminic acid by adding CMP moiety; Region: CMP-NeuAc_Synthase; cd02513 684950000955 ligand binding site; other site 684950000956 tetramer interface; other site 684950000957 Spore coat polysaccharide biosynthesis protein, predicted glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: spsG; COG3980 684950000958 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 684950000959 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 684950000960 NAD synthetase; Provisional; Region: PRK13980 684950000961 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 684950000962 homodimer interface [polypeptide binding]; other site 684950000963 NAD binding pocket [chemical binding]; other site 684950000964 ATP binding pocket [chemical binding]; other site 684950000965 Mg binding site [ion binding]; other site 684950000966 active-site loop [active] 684950000967 ketol-acid reductoisomerase; Provisional; Region: PRK05479 684950000968 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 684950000969 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 684950000970 Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]; Region: MinD; COG2894 684950000971 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 684950000972 Switch I; other site 684950000973 Switch II; other site 684950000974 cell division topological specificity factor MinE; Region: minE; TIGR01215 684950000975 DNA protecting protein DprA; Region: dprA; TIGR00732 684950000976 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 684950000977 Holliday junction resolvase-like protein; Reviewed; Region: PRK00109 684950000978 Tetratricopeptide repeat; Region: TPR_2; pfam07719 684950000979 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 684950000980 Sel1-like repeats; Region: SEL1; smart00671 684950000981 TRAP-type mannitol/chloroaromatic compound transport system, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT1; COG4663 684950000982 catalytic residue [active] 684950000983 Phage lysozyme; Region: Phage_lysozyme; pfam00959 684950000984 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 684950000985 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 684950000986 active site 684950000987 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 684950000988 DHH family; Region: DHH; pfam01368 684950000989 DHHA1 domain; Region: DHHA1; pfam02272 684950000990 CTP synthetase; Validated; Region: pyrG; PRK05380 684950000991 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 684950000992 Catalytic site [active] 684950000993 active site 684950000994 UTP binding site [chemical binding]; other site 684950000995 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 684950000996 active site 684950000997 putative oxyanion hole; other site 684950000998 catalytic triad [active] 684950000999 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 684950001000 active site 684950001001 flagellar basal-body M-ring protein/flagellar hook-basal body protein (fliF); Region: fliF; TIGR00206 684950001002 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; pfam01514 684950001003 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 684950001004 flagellar motor switch protein FliG; Region: fliG; TIGR00207 684950001005 FliG C-terminal domain; Region: FliG_C; pfam01706 684950001006 flagellar assembly protein H; Validated; Region: fliH; PRK06669 684950001007 Flagellar assembly protein FliH; Region: FliH; pfam02108 684950001008 1-deoxy-D-xylulose-5-phosphate synthase; Region: dxs; TIGR00204 684950001009 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 684950001010 TPP-binding site; other site 684950001011 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 684950001012 PYR/PP interface [polypeptide binding]; other site 684950001013 dimer interface [polypeptide binding]; other site 684950001014 TPP binding site [chemical binding]; other site 684950001015 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 684950001016 GTP-binding protein LepA; Provisional; Region: PRK05433 684950001017 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 684950001018 G1 box; other site 684950001019 putative GEF interaction site [polypeptide binding]; other site 684950001020 GTP/Mg2+ binding site [chemical binding]; other site 684950001021 Switch I region; other site 684950001022 G2 box; other site 684950001023 G3 box; other site 684950001024 Switch II region; other site 684950001025 G4 box; other site 684950001026 G5 box; other site 684950001027 Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to...; Region: Translation_Factor_II_like; cl02787 684950001028 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 684950001029 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 684950001030 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 684950001031 DNA-methyltransferase (dcm); Region: dcm; TIGR00675 684950001032 cofactor binding site; other site 684950001033 DNA binding site [nucleotide binding] 684950001034 substrate interaction site [chemical binding]; other site 684950001035 Flagellar basal body rod protein [Cell motility and secretion]; Region: FlgG; COG4786 684950001036 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 684950001037 alpha-ketoglutarate transporter; Provisional; Region: PRK10406 684950001038 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 684950001039 putative substrate translocation pore; other site 684950001040 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 684950001041 TspO/MBR family; Region: TspO_MBR; cl01379 684950001042 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 684950001043 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 684950001044 Inactivated superfamily I helicase [DNA replication, recombination, and repair]; Region: COG3893 684950001045 RecB family exonuclease [DNA replication, recombination, and repair]; Region: COG2887 684950001046 transketolase, bacterial and yeast; Region: tktlase_bact; TIGR00232 684950001047 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 684950001048 TPP-binding site [chemical binding]; other site 684950001049 dimer interface [polypeptide binding]; other site 684950001050 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 684950001051 PYR/PP interface [polypeptide binding]; other site 684950001052 dimer interface [polypeptide binding]; other site 684950001053 TPP binding site [chemical binding]; other site 684950001054 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 684950001055 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 684950001056 riboflavin kinase/FMN adenylyltransferase; Region: ribF; TIGR00083 684950001057 active site 684950001058 Riboflavin kinase; Region: Flavokinase; smart00904 684950001059 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 684950001060 hemolysin TlyA family protein; Region: tly; TIGR00478 684950001061 RNA binding surface [nucleotide binding]; other site 684950001062 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 684950001063 S-adenosylmethionine binding site [chemical binding]; other site 684950001064 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 684950001065 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 684950001066 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 684950001067 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 684950001068 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 684950001069 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 684950001070 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 684950001071 Walker A/P-loop; other site 684950001072 ATP binding site [chemical binding]; other site 684950001073 Q-loop/lid; other site 684950001074 ABC transporter signature motif; other site 684950001075 Walker B; other site 684950001076 D-loop; other site 684950001077 H-loop/switch region; other site 684950001078 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 684950001079 Predicted endonuclease distantly related to archaeal Holliday junction resolvase and Mrr-like restriction enzymes [Defense mechanisms]; Region: COG1787 684950001080 Restriction endonuclease; Region: Mrr_cat; pfam04471 684950001081 Predicted ATPases [General function prediction only]; Region: COG1106 684950001082 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 684950001083 Walker A/P-loop; other site 684950001084 ATP binding site [chemical binding]; other site 684950001085 High-affinity nickel permease [Inorganic ion transport and metabolism]; Region: HoxN; COG3376 684950001086 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cd00596 684950001087 active site 684950001088 Zn binding site [ion binding]; other site 684950001089 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 684950001090 metal-binding site [ion binding] 684950001091 copper-(or silver)-translocating P-type ATPase; Region: ATPase-IB1_Cu; TIGR01511 684950001092 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 684950001093 Soluble P-type ATPase [General function prediction only]; Region: COG4087 684950001094 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 684950001095 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 684950001096 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 684950001097 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 684950001098 Walker A motif; other site 684950001099 ATP binding site [chemical binding]; other site 684950001100 Walker B motif; other site 684950001101 arginine finger; other site 684950001102 Peptidase family M41; Region: Peptidase_M41; pfam01434 684950001103 ribosomal protein L11 methyltransferase; Region: prmA; TIGR00406 684950001104 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 684950001105 S-adenosylmethionine binding site [chemical binding]; other site 684950001106 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 684950001107 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 684950001108 active site 684950001109 phosphorylation site [posttranslational modification] 684950001110 intermolecular recognition site; other site 684950001111 dimerization interface [polypeptide binding]; other site 684950001112 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 684950001113 rRNA small subunit methyltransferase G; Region: GidB; pfam02527 684950001114 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 684950001115 S-adenosylmethionine binding site [chemical binding]; other site 684950001116 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 684950001117 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 684950001118 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 684950001119 sec-independent translocase; Provisional; Region: PRK04098 684950001120 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 684950001121 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 684950001122 Walker A motif; other site 684950001123 ATP binding site [chemical binding]; other site 684950001124 Walker B motif; other site 684950001125 arginine finger; other site 684950001126 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 684950001127 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 684950001128 oligomerization interface [polypeptide binding]; other site 684950001129 active site 684950001130 metal binding site [ion binding]; metal-binding site 684950001131 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 684950001132 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 684950001133 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 684950001134 septum formation inhibitor; Reviewed; Region: minC; PRK00556 684950001135 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 684950001136 UDP-3-0-acyl N-acetylglucosamine deacetylase; Region: lpxC; TIGR00325 684950001137 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 684950001138 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214 684950001139 homoserine kinase; Region: thrB; TIGR00191 684950001140 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 684950001141 Predicted nucleic-acid-binding protein implicated in transcription termination [Transcription]; Region: COG2740 684950001142 putative RNA binding cleft [nucleotide binding]; other site 684950001143 translation initiation factor IF-2; Region: IF-2; TIGR00487 684950001144 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 684950001145 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 684950001146 G1 box; other site 684950001147 putative GEF interaction site [polypeptide binding]; other site 684950001148 GTP/Mg2+ binding site [chemical binding]; other site 684950001149 Switch I region; other site 684950001150 G2 box; other site 684950001151 G3 box; other site 684950001152 Switch II region; other site 684950001153 G4 box; other site 684950001154 G5 box; other site 684950001155 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 684950001156 Translation-initiation factor 2; Region: IF-2; pfam11987 684950001157 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 684950001158 Ribosome-binding factor A; Region: RBFA; cl00542 684950001159 Uncharacterized BCR, YhbC family COG0779; Region: DUF150; pfam02576 684950001160 Sm and related proteins; Region: Sm_like; cl00259 684950001161 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 684950001162 putative oligomer interface [polypeptide binding]; other site 684950001163 putative RNA binding site [nucleotide binding]; other site 684950001164 acetyl-CoA synthetase; Provisional; Region: PRK00174 684950001165 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 684950001166 active site 684950001167 CoA binding site [chemical binding]; other site 684950001168 acyl-activating enzyme (AAE) consensus motif; other site 684950001169 AMP binding site [chemical binding]; other site 684950001170 acetate binding site [chemical binding]; other site 684950001171 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 684950001172 putative active site [active] 684950001173 putative metal binding site [ion binding]; other site 684950001174 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 684950001175 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 684950001176 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 684950001177 active site 684950001178 intermolecular recognition site; other site 684950001179 dimerization interface [polypeptide binding]; other site 684950001180 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 684950001181 DNA binding site [nucleotide binding] 684950001182 Predicted phosphohydrolase (DHH superfamily) [General function prediction only]; Region: COG2404 684950001183 DHH family; Region: DHH; pfam01368 684950001184 flagellar biosynthesis protein FlhA; Region: FlhA; TIGR01398 684950001185 FHIPEP family; Region: FHIPEP; pfam00771 684950001186 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 684950001187 16S/18S rRNA binding site [nucleotide binding]; other site 684950001188 S13e-L30e interaction site [polypeptide binding]; other site 684950001189 25S rRNA binding site [nucleotide binding]; other site 684950001190 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 684950001191 O-Antigen ligase; Region: Wzy_C; pfam04932 684950001192 Dehydroquinase class II; Region: DHquinase_II; pfam01220 684950001193 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 684950001194 trimer interface [polypeptide binding]; other site 684950001195 active site 684950001196 dimer interface [polypeptide binding]; other site 684950001197 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 684950001198 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 684950001199 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 684950001200 active site 684950001201 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 684950001202 catalytic center binding site [active] 684950001203 ATP binding site [chemical binding]; other site 684950001204 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK05703 684950001205 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 684950001206 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 684950001207 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 684950001208 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 684950001209 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 684950001210 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 684950001211 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 684950001212 DNA binding residues [nucleotide binding] 684950001213 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 684950001214 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 684950001215 flagellar motor switch protein FliY; Validated; Region: PRK08432 684950001216 flagellar motor switch protein FliN; Region: fliN; TIGR02480 684950001217 Beta-galactosidase, beta subunit [Carbohydrate transport and metabolism]; Region: EbgC; COG2731 684950001218 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4731 684950001219 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 684950001220 metal binding site 2 [ion binding]; metal-binding site 684950001221 putative DNA binding helix; other site 684950001222 metal binding site 1 [ion binding]; metal-binding site 684950001223 dimer interface [polypeptide binding]; other site 684950001224 structural Zn2+ binding site [ion binding]; other site 684950001225 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]; Region: MGS1; COG2256 684950001226 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 684950001227 Walker A motif; other site 684950001228 ATP binding site [chemical binding]; other site 684950001229 Walker B motif; other site 684950001230 arginine finger; other site 684950001231 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 684950001232 Helix-Turn-Helix DNA binding domain of the HspR transcription regulator; Region: HTH_HspR; cd04766 684950001233 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 684950001234 DNA binding residues [nucleotide binding] 684950001235 putative dimer interface [polypeptide binding]; other site 684950001236 chaperone protein DnaJ; Provisional; Region: PRK14299 684950001237 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 684950001238 HSP70 interaction site [polypeptide binding]; other site 684950001239 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 684950001240 substrate binding site [polypeptide binding]; other site 684950001241 dimer interface [polypeptide binding]; other site 684950001242 5'-3' exonuclease; Provisional; Region: PRK14976 684950001243 PIN (PilT N terminus) domain: Superfamily; Region: PIN_SF; cl14812 684950001244 putative active site [active] 684950001245 Helix-hairpin-helix class 2 (Pol1 family) motifs; Region: HhH2; smart00279 684950001246 DNA binding site [nucleotide binding] 684950001247 metal binding site [ion binding]; metal-binding site 684950001248 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 684950001249 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 684950001250 active site 684950001251 dimerization interface [polypeptide binding]; other site 684950001252 bifunctional 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase/2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase protein; Provisional; Region: ispDF; PRK09382 684950001253 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 684950001254 substrate binding site; other site 684950001255 dimer interface; other site 684950001256 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 684950001257 homotrimer interaction site [polypeptide binding]; other site 684950001258 zinc binding site [ion binding]; other site 684950001259 CDP-binding sites; other site 684950001260 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 684950001261 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 684950001262 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 684950001263 protein binding site [polypeptide binding]; other site 684950001264 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 684950001265 protein binding site [polypeptide binding]; other site 684950001266 S-methylmethionine transporter; Provisional; Region: PRK11387 684950001267 CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase; Region: pgsA; TIGR00560 684950001268 7-alpha-hydroxysteroid dehydrogenase; Provisional; Region: PRK08416 684950001269 1-cyclohexenylcarbonyl_coenzyme A_reductase (ChcA)_like, classical (c) SDRs; Region: ChcA_like_SDR_c; cd05359 684950001270 putative NAD(P) binding site [chemical binding]; other site 684950001271 active site 684950001272 dihydrodipicolinate synthase; Region: dapA; TIGR00674 684950001273 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 684950001274 dimer interface [polypeptide binding]; other site 684950001275 active site 684950001276 catalytic residue [active] 684950001277 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 684950001278 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 684950001279 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 684950001280 dihydroorotate dehydrogenase, subfamily 2; Region: pyrD_sub2; TIGR01036 684950001281 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 684950001282 quinone interaction residues [chemical binding]; other site 684950001283 active site 684950001284 catalytic residues [active] 684950001285 FMN binding site [chemical binding]; other site 684950001286 substrate binding site [chemical binding]; other site 684950001287 Polyphosphate kinase [Inorganic ion transport and metabolism]; Region: Ppk; COG0855 684950001288 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 684950001289 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 684950001290 Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C1_like; cd09165 684950001291 putative domain interface [polypeptide binding]; other site 684950001292 putative active site [active] 684950001293 catalytic site [active] 684950001294 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 684950001295 putative active site [active] 684950001296 putative domain interface [polypeptide binding]; other site 684950001297 catalytic site [active] 684950001298 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 684950001299 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 684950001300 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 684950001301 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 684950001302 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 684950001303 ATP binding site [chemical binding]; other site 684950001304 putative Mg++ binding site [ion binding]; other site 684950001305 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2604 684950001306 N-terminal tellurium resistance protein terB-like domain of heat shock DnaJ-like proteins; Region: terB_like_DjlA; cd07316 684950001307 putative metal binding site [ion binding]; other site 684950001308 CoB--CoM heterodisulfide reductase, subunit B; Region: CoB_CoM_SS_B; TIGR03288 684950001309 oligoendopeptidase, pepF/M3 family; Region: M3_fam_3; TIGR02290 684950001310 Peptidase family M3B Oligopeptidase F (PepF); Region: M3B_PepF_5; cd09610 684950001311 active site 684950001312 Zn binding site [ion binding]; other site 684950001313 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 684950001314 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 684950001315 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 684950001316 ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: ModA; COG0725 684950001317 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 684950001318 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 684950001319 putative bacteriocin export ABC transporter, lactococcin 972 group; Region: L_ocin_972_ABC; TIGR03608 684950001320 Walker A/P-loop; other site 684950001321 ATP binding site [chemical binding]; other site 684950001322 Q-loop/lid; other site 684950001323 ABC transporter signature motif; other site 684950001324 Walker B; other site 684950001325 D-loop; other site 684950001326 H-loop/switch region; other site 684950001327 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 684950001328 glutamyl-Q tRNA(Asp) synthetase; Reviewed; Region: PRK05710 684950001329 active site 684950001330 HIGH motif; other site 684950001331 nucleotide binding site [chemical binding]; other site 684950001332 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 684950001333 active site 684950001334 KMSKS motif; other site 684950001335 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 684950001336 Helix-turn-helix domain; Region: HTH_17; pfam12728 684950001337 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0827 684950001338 Methyltransferase domain; Region: Methyltransf_26; pfam13659 684950001339 TaqI-like C-terminal specificity domain; Region: TaqI_C; pfam12950 684950001340 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 684950001341 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 684950001342 ADP-heptose:LPS heptosyl transferase I; Provisional; Region: PRK10964; cl15782 684950001343 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 684950001344 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 684950001345 G1 box; other site 684950001346 putative GEF interaction site [polypeptide binding]; other site 684950001347 GTP/Mg2+ binding site [chemical binding]; other site 684950001348 Switch I region; other site 684950001349 G2 box; other site 684950001350 G3 box; other site 684950001351 Switch II region; other site 684950001352 G4 box; other site 684950001353 G5 box; other site 684950001354 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 684950001355 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 684950001356 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 684950001357 GIY-YIG motif/motif A; other site 684950001358 DNA binding site [nucleotide binding] 684950001359 active site 684950001360 catalytic site [active] 684950001361 metal binding site [ion binding]; metal-binding site 684950001362 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 684950001363 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 684950001364 cofactor binding site; other site 684950001365 DNA binding site [nucleotide binding] 684950001366 substrate interaction site [chemical binding]; other site 684950001367 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 684950001368 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 684950001369 Catalase-like heme-binding proteins similar to the uncharacterized srpA; Region: srpA_like; cd08153 684950001370 putative heme binding pocket [chemical binding]; other site 684950001371 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 684950001372 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 684950001373 Protein of unknown function (DUF3519); Region: DUF3519; pfam12033 684950001374 Uncharacterized conserved protein [Function unknown]; Region: COG1432 684950001375 LabA_like proteins; Region: LabA_like; cd06167 684950001376 putative metal binding site [ion binding]; other site 684950001377 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 684950001378 active site 684950001379 putative DNA-binding cleft [nucleotide binding]; other site 684950001380 dimer interface [polypeptide binding]; other site 684950001381 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 684950001382 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 684950001383 TonB dependent receptor; Region: TonB_dep_Rec; pfam00593 684950001384 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 684950001385 Clade 3 of the heme-binding enzyme catalase; Region: catalase_clade_3; cd08156 684950001386 tetramer interface [polypeptide binding]; other site 684950001387 heme binding pocket [chemical binding]; other site 684950001388 NADPH binding site [chemical binding]; other site 684950001389 alkylphosphonate utilization operon protein PhnA; Region: phnA; TIGR00686 684950001390 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; pfam08274 684950001391 PhnA protein; Region: PhnA; pfam03831 684950001392 CDP-diacylglycerol pyrophosphatase, bacterial type; Region: cdh; TIGR00672 684950001393 flagellar hook protein FlgE; Validated; Region: flgE; PRK08425 684950001394 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 684950001395 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 684950001396 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 684950001397 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 684950001398 hydrogenase nickel incorporation protein; Provisional; Region: hypA; PRK00564 684950001399 Hydrogenase expression/synthesis hypA family; Region: HypA; pfam01155 684950001400 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 684950001401 lipid-A-disaccharide synthase; Region: lpxB; TIGR00215 684950001402 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 684950001403 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 684950001404 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 684950001405 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 684950001406 trimer interface [polypeptide binding]; other site 684950001407 active site 684950001408 PQQ-like domain; Region: PQQ_2; pfam13360 684950001409 pantothenate kinase; Reviewed; Region: PRK13333 684950001410 Uncharacterized conserved protein [Function unknown]; Region: COG2836 684950001411 D,D-heptose 1,7-bisphosphate phosphatase; Region: GmhB_yaeD; TIGR00213 684950001412 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 684950001413 active site 684950001414 motif I; other site 684950001415 motif II; other site 684950001416 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 684950001417 ADP-L-glycero-D-manno-heptose-6-epimerase; Region: heptose_epim; TIGR02197 684950001418 NAD(P) binding site [chemical binding]; other site 684950001419 active site 684950001420 ADP-heptose synthase, bifunctional sugar kinase/adenylyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaE; COG2870 684950001421 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 684950001422 putative ribose interaction site [chemical binding]; other site 684950001423 putative ADP binding site [chemical binding]; other site 684950001424 rfaE bifunctional protein, domain II; Region: rfaE_dom_II; TIGR02199 684950001425 active site 684950001426 nucleotide binding site [chemical binding]; other site 684950001427 HIGH motif; other site 684950001428 KMSKS motif; other site 684950001429 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 684950001430 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 684950001431 dimer interface [polypeptide binding]; other site 684950001432 active site 684950001433 guanosine 5'-monophosphate oxidoreductase; Provisional; Region: PRK05458 684950001434 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 684950001435 active site 684950001436 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 684950001437 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 684950001438 Walker A/P-loop; other site 684950001439 ATP binding site [chemical binding]; other site 684950001440 Q-loop/lid; other site 684950001441 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 684950001442 ABC transporter; Region: ABC_tran_2; pfam12848 684950001443 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 684950001444 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2958 684950001445 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 684950001446 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 684950001447 active site 684950001448 type I restriction system adenine methylase (hsdM); Region: hsdM; TIGR00497 684950001449 HsdM N-terminal domain; Region: HsdM_N; pfam12161 684950001450 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 684950001451 S-adenosylmethionine binding site [chemical binding]; other site 684950001452 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 684950001453 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 684950001454 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 684950001455 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 684950001456 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 684950001457 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 684950001458 ATP binding site [chemical binding]; other site 684950001459 putative Mg++ binding site [ion binding]; other site 684950001460 Prolyl 4-Hydroxylase alpha-subunit, N-terminal region; Region: P4Ha_N; pfam08336 684950001461 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 684950001462 substrate binding site [chemical binding]; other site 684950001463 multimerization interface [polypeptide binding]; other site 684950001464 ATP binding site [chemical binding]; other site 684950001465 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 684950001466 dimer interface [polypeptide binding]; other site 684950001467 substrate binding site [chemical binding]; other site 684950001468 ATP binding site [chemical binding]; other site 684950001469 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 684950001470 active site 684950001471 thiamine phosphate binding site [chemical binding]; other site 684950001472 pyrophosphate binding site [ion binding]; other site 684950001473 phosphopantothenoylcysteine decarboxylase / phosphopantothenate--cysteine ligase; Region: coaBC_dfp; TIGR00521 684950001474 Flavoprotein; Region: Flavoprotein; pfam02441 684950001475 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 684950001476 UDP-N-acetylglucosamine 4,6-dehydratase; Region: PseB; TIGR03589 684950001477 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 684950001478 NAD(P) binding site [chemical binding]; other site 684950001479 homodimer interface [polypeptide binding]; other site 684950001480 substrate binding site [chemical binding]; other site 684950001481 active site 684950001482 Long-chain fatty acid transport protein [Lipid metabolism]; Region: FadL; COG2067 684950001483 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3018 684950001484 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3018 684950001485 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 684950001486 IHF dimer interface [polypeptide binding]; other site 684950001487 IHF - DNA interface [nucleotide binding]; other site 684950001488 spermidine synthase; Provisional; Region: speE; PRK00536 684950001489 spermidine synthase; Provisional; Region: PRK00811 684950001490 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 684950001491 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 684950001492 CoA-binding site [chemical binding]; other site 684950001493 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit; Region: gatA; TIGR00132 684950001494 indole acetimide hydrolase; Validated; Region: PRK07488 684950001495 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 684950001496 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 684950001497 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 684950001498 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 684950001499 active site 684950001500 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 684950001501 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 684950001502 RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins; Region: RRM_HP0827_like; cd12399 684950001503 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 684950001504 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 684950001505 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 684950001506 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 684950001507 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 684950001508 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 684950001509 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 684950001510 catalytic residues [active] 684950001511 Predicted endonuclease distantly related to archaeal Holliday junction resolvase [DNA replication, recombination, and repair]; Region: COG0792 684950001512 homoserine dehydrogenase; Provisional; Region: PRK06349 684950001513 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 684950001514 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 684950001515 excinuclease ABC, C subunit; Region: uvrC; TIGR00194 684950001516 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 684950001517 GIY-YIG motif/motif A; other site 684950001518 active site 684950001519 catalytic site [active] 684950001520 putative DNA binding site [nucleotide binding]; other site 684950001521 metal binding site [ion binding]; metal-binding site 684950001522 UvrB/uvrC motif; Region: UVR; pfam02151 684950001523 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 684950001524 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 684950001525 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 684950001526 Walker A/P-loop; other site 684950001527 ATP binding site [chemical binding]; other site 684950001528 Q-loop/lid; other site 684950001529 ABC transporter signature motif; other site 684950001530 Walker B; other site 684950001531 D-loop; other site 684950001532 H-loop/switch region; other site 684950001533 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 684950001534 dimer interface [polypeptide binding]; other site 684950001535 conserved gate region; other site 684950001536 ABC-ATPase subunit interface; other site 684950001537 Periplasmic glycine betaine/choline-binding (lipo)protein of an ABC-type transport system (osmoprotectant binding protein) [Cell envelope biogenesis, outer membrane]; Region: OpuBC; COG1732 684950001538 ABC-type proline/glycine betaine transport systems, periplasmic components [Amino acid transport and metabolism]; Region: ProX; cl17891 684950001539 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 684950001540 DNA methylase; Region: N6_N4_Mtase; pfam01555 684950001541 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 684950001542 DNA methylase; Region: N6_N4_Mtase; pfam01555 684950001543 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 684950001544 DEAD-like helicases superfamily; Region: DEXDc; smart00487 684950001545 ATP binding site [chemical binding]; other site 684950001546 putative Mg++ binding site [ion binding]; other site 684950001547 flagellar motor protein MotB; Reviewed; Region: motB; PRK08457 684950001548 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 684950001549 ligand binding site [chemical binding]; other site 684950001550 flagellar motor protein MotA; Validated; Region: PRK08456 684950001551 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 684950001552 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 2 [Coenzyme metabolism]; Region: ThiF; COG0476 684950001553 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 684950001554 ATP binding site [chemical binding]; other site 684950001555 substrate interface [chemical binding]; other site 684950001556 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 684950001557 Uncharacterized conserved protein [Function unknown]; Region: COG1565 684950001558 RNA methyltransferase, RsmD family; Region: TIGR00095 684950001559 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 684950001560 flagellar basal body-associated protein FliL; Reviewed; Region: fliL; PRK08455 684950001561 holo-[acyl-carrier-protein] synthase; Region: acpS; TIGR00516 684950001562 Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]; Region: FecA; COG4772 684950001563 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 684950001564 N-terminal plug; other site 684950001565 ligand-binding site [chemical binding]; other site 684950001566 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG1451 684950001567 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 684950001568 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional; Region: PRK09314 684950001569 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: ribB; TIGR00506 684950001570 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; cl00522 684950001571 Domain of unknown function (DUF3943); Region: DUF3943; pfam13084 684950001572 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 684950001573 dimerization interface [polypeptide binding]; other site 684950001574 active site 684950001575 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 684950001576 MoaE interaction surface [polypeptide binding]; other site 684950001577 MoeB interaction surface [polypeptide binding]; other site 684950001578 thiocarboxylated glycine; other site 684950001579 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 684950001580 MoaE homodimer interface [polypeptide binding]; other site 684950001581 MoaD interaction [polypeptide binding]; other site 684950001582 active site residues [active] 684950001583 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 684950001584 MPT binding site; other site 684950001585 trimer interface [polypeptide binding]; other site 684950001586 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 684950001587 trimer interface [polypeptide binding]; other site 684950001588 dimer interface [polypeptide binding]; other site 684950001589 putative active site [active] 684950001590 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 684950001591 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 684950001592 trigger factor; Provisional; Region: tig; PRK01490 684950001593 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 684950001594 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 684950001595 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 684950001596 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 684950001597 oligomer interface [polypeptide binding]; other site 684950001598 active site residues [active] 684950001599 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 684950001600 active site 684950001601 catalytic residues [active] 684950001602 metal binding site [ion binding]; metal-binding site 684950001603 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 684950001604 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 684950001605 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 684950001606 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 684950001607 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 684950001608 metal-binding site [ion binding] 684950001609 heavy metal-(Cd/Co/Hg/Pb/Zn)-translocating P-type ATPase; Region: ATPase-IB2_Cd; TIGR01512 684950001610 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 684950001611 Soluble P-type ATPase [General function prediction only]; Region: COG4087 684950001612 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 684950001613 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 684950001614 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 684950001615 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 684950001616 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 684950001617 FtsX-like permease family; Region: FtsX; pfam02687 684950001618 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 684950001619 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 684950001620 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 684950001621 nucleotide binding region [chemical binding]; other site 684950001622 ATP-binding site [chemical binding]; other site 684950001623 SEC-C motif; Region: SEC-C; pfam02810 684950001624 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 684950001625 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 684950001626 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 684950001627 FOG: Transposase [DNA replication, recombination, and repair]; Region: COG5659 684950001628 Predicted periplasmic solute-binding protein [General function prediction only]; Region: COG1427 684950001629 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 684950001630 putative nucleotide binding site [chemical binding]; other site 684950001631 uridine monophosphate binding site [chemical binding]; other site 684950001632 homohexameric interface [polypeptide binding]; other site 684950001633 DNA-directed RNA polymerase, subunit K/omega [Transcription]; Region: RpoZ; COG1758 684950001634 (p)ppGpp synthetase, RelA/SpoT family; Region: spoT_relA; TIGR00691 684950001635 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 684950001636 Zn2+ binding site [ion binding]; other site 684950001637 Mg2+ binding site [ion binding]; other site 684950001638 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 684950001639 synthetase active site [active] 684950001640 NTP binding site [chemical binding]; other site 684950001641 metal binding site [ion binding]; metal-binding site 684950001642 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 684950001643 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 684950001644 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 684950001645 active site 684950001646 HIGH motif; other site 684950001647 dimer interface [polypeptide binding]; other site 684950001648 KMSKS motif; other site 684950001649 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 684950001650 RNA binding surface [nucleotide binding]; other site 684950001651 Nitronate monooxygenase; Region: NMO; pfam03060 684950001652 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 684950001653 FMN binding site [chemical binding]; other site 684950001654 substrate binding site [chemical binding]; other site 684950001655 putative catalytic residue [active] 684950001656 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 684950001657 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 684950001658 active site 684950001659 metal binding site [ion binding]; metal-binding site 684950001660 flagellar biosynthetic protein FlhB; Region: flhB; TIGR00328 684950001661 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 684950001662 Mu-like prophage protein [General function prediction only]; Region: COG3941 684950001663 Predicted Fe-S-cluster oxidoreductase [General function prediction only]; Region: COG0727 684950001664 signal recognition particle-docking protein FtsY; Region: ftsY; TIGR00064 684950001665 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 684950001666 phosphodiesterase; Provisional; Region: PRK12704 684950001667 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 684950001668 nucleic acid binding region [nucleotide binding]; other site 684950001669 G-X-X-G motif; other site 684950001670 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 684950001671 Zn2+ binding site [ion binding]; other site 684950001672 Mg2+ binding site [ion binding]; other site 684950001673 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Thermotoga marina NorM; Region: MATE_NorM_like; cd13137 684950001674 putative efflux protein, MATE family; Region: matE; TIGR00797 684950001675 Predicted permease [General function prediction only]; Region: COG2056 684950001676 Na+-H+ antiporter family; Region: Na_H_antiport_2; pfam13726 684950001677 Predicted membrane protein [Function unknown]; Region: COG1288; cl17886 684950001678 N-carbamoylputrescine amidohydrolase (CPA) (class 11 nitrilases); Region: CPA; cd07573 684950001679 N-carbamoylputrescine amidase; Region: agmatine_aguB; TIGR03381 684950001680 putative active site; other site 684950001681 catalytic triad [active] 684950001682 putative dimer interface [polypeptide binding]; other site 684950001683 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 684950001684 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 684950001685 putative ATP binding site [chemical binding]; other site 684950001686 putative substrate interface [chemical binding]; other site 684950001687 flagellar biosynthetic protein FliS; Region: fliS; TIGR00208 684950001688 flagellar capping protein; Validated; Region: fliD; PRK08453 684950001689 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 684950001690 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 684950001691 flagellar protein FlaG; Provisional; Region: PRK08452 684950001692 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 684950001693 Peptidase family M23; Region: Peptidase_M23; pfam01551 684950001694 putative protein insertion permease FtsX; Region: ftsX; TIGR00439 684950001695 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 684950001696 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 684950001697 Walker A/P-loop; other site 684950001698 ATP binding site [chemical binding]; other site 684950001699 Q-loop/lid; other site 684950001700 ABC transporter signature motif; other site 684950001701 Walker B; other site 684950001702 D-loop; other site 684950001703 H-loop/switch region; other site 684950001704 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 684950001705 S-adenosylmethionine binding site [chemical binding]; other site 684950001706 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 684950001707 Interdomain contacts; other site 684950001708 Fibronectin type 3 domain-containing protein [General function prediction only]; Region: COG3401 684950001709 Cytokine receptor motif; other site 684950001710 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 684950001711 Interdomain contacts; other site 684950001712 Cytokine receptor motif; other site 684950001713 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 684950001714 Interdomain contacts; other site 684950001715 Cytokine receptor motif; other site 684950001716 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 684950001717 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 684950001718 active site 684950001719 Predicted GTPase [General function prediction only]; Region: COG3596 684950001720 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 684950001721 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cd00882 684950001722 G1 box; other site 684950001723 G1 box; other site 684950001724 GTP/Mg2+ binding site [chemical binding]; other site 684950001725 GTP/Mg2+ binding site [chemical binding]; other site 684950001726 G2 box; other site 684950001727 Switch I region; other site 684950001728 G3 box; other site 684950001729 Switch II region; other site 684950001730 Uncharacterized protein/domain associated with GTPases [Function unknown]; Region: COG3597 684950001731 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 684950001732 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 684950001733 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 684950001734 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 684950001735 active site 684950001736 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 684950001737 nucleotide binding site/active site [active] 684950001738 HIT family signature motif; other site 684950001739 catalytic residue [active] 684950001740 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 684950001741 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 684950001742 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 684950001743 D-alanyl-alanine synthetase A; Reviewed; Region: ddl; PRK01966 684950001744 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 684950001745 ATP-grasp domain; Region: ATP-grasp_4; cl17255 684950001746 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 684950001747 tetramer interfaces [polypeptide binding]; other site 684950001748 binuclear metal-binding site [ion binding]; other site 684950001749 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]; Region: COG0075 684950001750 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 684950001751 catalytic residue [active] 684950001752 Predicted phosphoribosyltransferases [General function prediction only]; Region: COG2236 684950001753 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 684950001754 active site 684950001755 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 684950001756 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 684950001757 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 684950001758 FeS/SAM binding site; other site 684950001759 Dynamin family; Region: Dynamin_N; pfam00350 684950001760 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 684950001761 G1 box; other site 684950001762 GTP/Mg2+ binding site [chemical binding]; other site 684950001763 G2 box; other site 684950001764 Switch I region; other site 684950001765 G3 box; other site 684950001766 Switch II region; other site 684950001767 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14337 684950001768 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 684950001769 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 684950001770 Ligand Binding Site [chemical binding]; other site 684950001771 tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; Region: COG0042 684950001772 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 684950001773 FMN binding site [chemical binding]; other site 684950001774 active site 684950001775 catalytic residues [active] 684950001776 substrate binding site [chemical binding]; other site 684950001777 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 684950001778 Type II (periplasmic) bacterial L-asparaginase; Region: L-asparaginase_II; cd08964 684950001779 active site 684950001780 homotetramer interface [polypeptide binding]; other site 684950001781 homodimer interface [polypeptide binding]; other site 684950001782 anaerobic c4-dicarboxylate membrane transporter family protein; Region: Dcu; TIGR00770 684950001783 Anaerobic C4-dicarboxylate transporter [General function prediction only]; Region: DcuB; COG2704 684950001784 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 684950001785 Protein of unknown function (DUF1104); Region: DUF1104; pfam06518 684950001786 Protein of unknown function (DUF1104); Region: DUF1104; pfam06518 684950001787 Lysine efflux permease [General function prediction only]; Region: COG1279 684950001788 DNA polymerase III subunits gamma and tau; Validated; Region: PRK08451 684950001789 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 684950001790 Walker A motif; other site 684950001791 ATP binding site [chemical binding]; other site 684950001792 Walker B motif; other site 684950001793 arginine finger; other site 684950001794 Uncharacterized P-loop hydrolase UPF0079; Region: UPF0079; cl00520 684950001795 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 684950001796 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 684950001797 Walker A/P-loop; other site 684950001798 ATP binding site [chemical binding]; other site 684950001799 Q-loop/lid; other site 684950001800 ABC transporter signature motif; other site 684950001801 Walker B; other site 684950001802 D-loop; other site 684950001803 H-loop/switch region; other site 684950001804 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 684950001805 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 684950001806 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 684950001807 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 684950001808 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 684950001809 Competence protein ComGF [Intracellular trafficking and secretion]; Region: ComGF; COG4940 684950001810 Predicted hydrolases of HD superfamily [General function prediction only]; Region: COG1896 684950001811 Uncharacterized conserved protein [Function unknown]; Region: COG1912 684950001812 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG0275 684950001813 MraW methylase family; Region: Methyltransf_5; cl17771 684950001814 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 684950001815 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 684950001816 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 684950001817 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 684950001818 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 684950001819 Response regulator receiver domain; Region: Response_reg; pfam00072 684950001820 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 684950001821 active site 684950001822 phosphorylation site [posttranslational modification] 684950001823 intermolecular recognition site; other site 684950001824 dimerization interface [polypeptide binding]; other site 684950001825 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 684950001826 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 684950001827 Walker A motif; other site 684950001828 ATP binding site [chemical binding]; other site 684950001829 Walker B motif; other site 684950001830 arginine finger; other site 684950001831 DNA gyrase subunit A; Validated; Region: PRK05560 684950001832 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 684950001833 CAP-like domain; other site 684950001834 active site 684950001835 primary dimer interface [polypeptide binding]; other site 684950001836 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 684950001837 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 684950001838 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 684950001839 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 684950001840 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 684950001841 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 684950001842 Diacylglycerol kinase [Cell envelope biogenesis, outer membrane]; Region: DgkA; COG0818 684950001843 Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcxC; COG4647 684950001844 Acetone carboxylase gamma subunit; Region: Acetone_carb_G; pfam08882 684950001845 N-methylhydantoinase B/acetone carboxylase, alpha subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuB; COG0146 684950001846 Hydantoinase B/oxoprolinase; Region: Hydantoinase_B; pfam02538 684950001847 N-methylhydantoinase A/acetone carboxylase, beta subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuA; COG0145 684950001848 Hydantoinase/oxoprolinase N-terminal region; Region: Hydant_A_N; pfam05378 684950001849 Hydantoinase/oxoprolinase; Region: Hydantoinase_A; pfam01968 684950001850 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3528 684950001851 Short chain fatty acid transporter; Region: SCFA_trans; pfam02667 684950001852 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 684950001853 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 684950001854 putative acyltransferase; Provisional; Region: PRK05790 684950001855 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 684950001856 dimer interface [polypeptide binding]; other site 684950001857 active site 684950001858 Predicted 3'-5' exonuclease related to the exonuclease domain of PolB [DNA replication, recombination, and repair]; Region: COG3298 684950001859 CfrBI restriction endonuclease; Region: RE_CfrBI; pfam09516 684950001860 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 684950001861 DNA methylase; Region: N6_N4_Mtase; pfam01555 684950001862 Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; Region: DNA_polB_like1_exo; cd05782 684950001863 active site 684950001864 catalytic site [active] 684950001865 substrate binding site [chemical binding]; other site 684950001866 Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; Region: DNA_pol_B_exo2; pfam10108 684950001867 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 684950001868 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 684950001869 G1 box; other site 684950001870 GTP/Mg2+ binding site [chemical binding]; other site 684950001871 Switch I region; other site 684950001872 G2 box; other site 684950001873 G3 box; other site 684950001874 Switch II region; other site 684950001875 G4 box; other site 684950001876 G5 box; other site 684950001877 Nucleoside recognition; Region: Gate; pfam07670 684950001878 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 684950001879 Nucleoside recognition; Region: Gate; pfam07670 684950001880 Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]; Region: FecA; COG4772 684950001881 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 684950001882 N-terminal plug; other site 684950001883 ligand-binding site [chemical binding]; other site 684950001884 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK05699 684950001885 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK14359 684950001886 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 684950001887 Substrate binding site; other site 684950001888 Mg++ binding site; other site 684950001889 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 684950001890 active site 684950001891 substrate binding site [chemical binding]; other site 684950001892 CoA binding site [chemical binding]; other site 684950001893 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK08447 684950001894 ATP cone domain; Region: ATP-cone; pfam03477 684950001895 Class I ribonucleotide reductase; Region: RNR_I; cd01679 684950001896 active site 684950001897 dimer interface [polypeptide binding]; other site 684950001898 catalytic residues [active] 684950001899 effector binding site; other site 684950001900 R2 peptide binding site; other site 684950001901 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 684950001902 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 684950001903 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 684950001904 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 684950001905 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 684950001906 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 684950001907 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 684950001908 DNA binding site [nucleotide binding] 684950001909 active site 684950001910 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 684950001911 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 684950001912 active site 684950001913 DNA binding site [nucleotide binding] 684950001914 Int/Topo IB signature motif; other site 684950001915 aspartate aminotransferase; Provisional; Region: PRK05764 684950001916 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 684950001917 pyridoxal 5'-phosphate binding site [chemical binding]; other site 684950001918 homodimer interface [polypeptide binding]; other site 684950001919 catalytic residue [active] 684950001920 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 684950001921 SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+; Region: SIR2; cl00195 684950001922 Restriction endonuclease; Region: Mrr_cat_2; pfam13156 684950001923 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 684950001924 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 684950001925 Cysteine-rich domain; Region: CCG; pfam02754 684950001926 Cysteine-rich domain; Region: CCG; pfam02754 684950001927 oxygen-independent coproporphyrinogen III oxidase; Region: hemN; TIGR00538 684950001928 HemN C-terminal domain; Region: HemN_C; pfam06969 684950001929 Protein of unknown function (DUF2603); Region: DUF2603; pfam10788 684950001930 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 684950001931 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 684950001932 Tetramer interface [polypeptide binding]; other site 684950001933 active site 684950001934 FMN-binding site [chemical binding]; other site 684950001935 ribonuclease III; Reviewed; Region: rnc; PRK00102 684950001936 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 684950001937 dimerization interface [polypeptide binding]; other site 684950001938 active site 684950001939 metal binding site [ion binding]; metal-binding site 684950001940 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 684950001941 dsRNA binding site [nucleotide binding]; other site 684950001942 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 684950001943 RNA/DNA hybrid binding site [nucleotide binding]; other site 684950001944 active site 684950001945 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]; Region: COG2956 684950001946 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]; Region: COG1439 684950001947 SurA N-terminal domain; Region: SurA_N; pfam09312 684950001948 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 684950001949 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 684950001950 GatB domain; Region: GatB_Yqey; smart00845 684950001951 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 684950001952 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 684950001953 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 684950001954 hypothetical protein; Provisional; Region: PRK08445 684950001955 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 684950001956 FeS/SAM binding site; other site 684950001957 Outer membrane protein/protective antigen OMA87 [Cell envelope biogenesis, outer membrane]; Region: COG4775 684950001958 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 684950001959 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 684950001960 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 684950001961 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 684950001962 Surface antigen; Region: Bac_surface_Ag; pfam01103 684950001963 hypothetical protein; Provisional; Region: PRK08444 684950001964 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 684950001965 FeS/SAM binding site; other site 684950001966 nonheme-containing ferritins; Region: Nonheme_Ferritin; cd01055 684950001967 Ferritin-like domain; Region: Ferritin; pfam00210 684950001968 ferroxidase diiron center [ion binding]; other site 684950001969 phosphoserine phosphatase SerB; Region: serB; TIGR00338 684950001970 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 684950001971 motif II; other site 684950001972 Glycosyltransferase family 10 (fucosyltransferase); Region: Glyco_transf_10; pfam00852 684950001973 Uracil-DNA glycosylases (UDG) and related enzymes; Region: UDG_like; cl00483 684950001974 ligand binding site [chemical binding]; other site 684950001975 active site 684950001976 aspartate ammonia-lyase; Provisional; Region: aspA; PRK12273 684950001977 Aspartase; Region: Aspartase; cd01357 684950001978 active sites [active] 684950001979 tetramer interface [polypeptide binding]; other site 684950001980 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 684950001981 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 684950001982 hinge; other site 684950001983 active site 684950001984 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 684950001985 dTDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]; Region: RfbA; COG1209 684950001986 active site 684950001987 tetramer interface; other site 684950001988 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 684950001989 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 684950001990 N-acetyl-D-glucosamine binding site [chemical binding]; other site 684950001991 catalytic residue [active] 684950001992 YGGT family; Region: YGGT; pfam02325 684950001993 glutamylglutaminyl-tRNA synthetase; Provisional; Region: PRK12410 684950001994 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 684950001995 active site 684950001996 HIGH motif; other site 684950001997 nucleotide binding site [chemical binding]; other site 684950001998 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 684950001999 active site 684950002000 KMSKS motif; other site 684950002001 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 684950002002 dimer interface [polypeptide binding]; other site 684950002003 FMN binding site [chemical binding]; other site 684950002004 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 684950002005 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 684950002006 active site 684950002007 NTP binding site [chemical binding]; other site 684950002008 metal binding triad [ion binding]; metal-binding site 684950002009 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 684950002010 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 684950002011 Ligand Binding Site [chemical binding]; other site 684950002012 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 684950002013 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 684950002014 nickel binding site [ion binding]; other site 684950002015 putative substrate-binding site; other site 684950002016 Ni,Fe-hydrogenase I cytochrome b subunit [Energy production and conversion]; Region: HyaC; COG1969 684950002017 Ni,Fe-hydrogenase I large subunit [Energy production and conversion]; Region: HyaB; COG0374 684950002018 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; pfam00374 684950002019 hydrogenase (NiFe) small subunit (hydA); Region: hydA; TIGR00391 684950002020 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 684950002021 Putative NADPH-quinone reductase (modulator of drug activity B) [General function prediction only]; Region: MdaB; COG2249 684950002022 Uncharacterized conserved protein [Function unknown]; Region: COG1479 684950002023 Protein of unknown function DUF262; Region: DUF262; pfam03235 684950002024 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 684950002025 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 684950002026 Sel1-like repeats; Region: SEL1; smart00671 684950002027 Sel1-like repeats; Region: SEL1; smart00671 684950002028 Sel1 repeat; Region: Sel1; cl02723 684950002029 Sel1-like repeats; Region: SEL1; smart00671 684950002030 Tetrahydrodipicolinate N-succinyltransferase [Amino acid transport and metabolism]; Region: DapD; COG2171 684950002031 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 684950002032 putative trimer interface [polypeptide binding]; other site 684950002033 putative CoA binding site [chemical binding]; other site 684950002034 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 684950002035 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 684950002036 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 684950002037 hypothetical protein; Provisional; Region: PRK05839 684950002038 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 684950002039 pyridoxal 5'-phosphate binding site [chemical binding]; other site 684950002040 homodimer interface [polypeptide binding]; other site 684950002041 catalytic residue [active] 684950002042 UDP-N-acetylmuramate--alanine ligase; Region: murC; TIGR01082 684950002043 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 684950002044 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 684950002045 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 684950002046 MutS2 family protein; Region: mutS2; TIGR01069 684950002047 ATPase domain of DNA mismatch repair MUTS family; Region: MUTSac; smart00534 684950002048 Walker A/P-loop; other site 684950002049 ATP binding site [chemical binding]; other site 684950002050 Q-loop/lid; other site 684950002051 ABC transporter signature motif; other site 684950002052 Walker B; other site 684950002053 D-loop; other site 684950002054 H-loop/switch region; other site 684950002055 Smr domain; Region: Smr; pfam01713 684950002056 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 684950002057 dimer interface [polypeptide binding]; other site 684950002058 substrate binding site [chemical binding]; other site 684950002059 metal binding sites [ion binding]; metal-binding site 684950002060 Glycosyltransferase involved in LPS biosynthesis [Cell envelope biogenesis, outer membrane]; Region: COG3306 684950002061 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 684950002062 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 684950002063 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 684950002064 adenylate kinase; Reviewed; Region: adk; PRK00279 684950002065 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 684950002066 AMP-binding site [chemical binding]; other site 684950002067 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 684950002068 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 684950002069 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 684950002070 dimer interface [polypeptide binding]; other site 684950002071 anticodon binding site; other site 684950002072 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 684950002073 homodimer interface [polypeptide binding]; other site 684950002074 motif 1; other site 684950002075 active site 684950002076 motif 2; other site 684950002077 GAD domain; Region: GAD; pfam02938 684950002078 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 684950002079 active site 684950002080 motif 3; other site 684950002081 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 684950002082 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 684950002083 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 684950002084 active site 684950002085 phosphorylation site [posttranslational modification] 684950002086 intermolecular recognition site; other site 684950002087 dimerization interface [polypeptide binding]; other site 684950002088 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 684950002089 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 684950002090 nucleotide binding pocket [chemical binding]; other site 684950002091 K-X-D-G motif; other site 684950002092 catalytic site [active] 684950002093 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 684950002094 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 684950002095 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 684950002096 Dimer interface [polypeptide binding]; other site 684950002097 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 684950002098 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 684950002099 Walker A/P-loop; other site 684950002100 ATP binding site [chemical binding]; other site 684950002101 Q-loop/lid; other site 684950002102 ABC transporter signature motif; other site 684950002103 Walker B; other site 684950002104 D-loop; other site 684950002105 H-loop/switch region; other site 684950002106 PPE-repeat proteins [Cell motility and secretion]; Region: COG5651 684950002107 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 684950002108 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 684950002109 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 684950002110 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 684950002111 PPE-repeat proteins [Cell motility and secretion]; Region: COG5651 684950002112 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 684950002113 Autotransporter beta-domain; Region: Autotransporter; pfam03797 684950002114 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 684950002115 AcrB/AcrD/AcrF family; Region: ACR_tran; pfam00873 684950002116 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 684950002117 HlyD family secretion protein; Region: HlyD_3; pfam13437 684950002118 Outer membrane efflux protein; Region: OEP; pfam02321 684950002119 Outer membrane efflux protein; Region: OEP; pfam02321 684950002120 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 684950002121 substrate binding site [chemical binding]; other site 684950002122 active site 684950002123 3-methyladenine DNA glycosylase; Provisional; Region: PRK13913 684950002124 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 684950002125 minor groove reading motif; other site 684950002126 helix-hairpin-helix signature motif; other site 684950002127 active site 684950002128 flagellin A; Reviewed; Region: PRK12584 684950002129 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 684950002130 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 684950002131 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 684950002132 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 684950002133 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 684950002134 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 684950002135 ATP-binding cassette domain of multidrug resistance protein-like transporters; Region: ABCC_MRP_Like; cd03228 684950002136 Walker A/P-loop; other site 684950002137 ATP binding site [chemical binding]; other site 684950002138 Q-loop/lid; other site 684950002139 ABC transporter signature motif; other site 684950002140 Walker B; other site 684950002141 D-loop; other site 684950002142 H-loop/switch region; other site 684950002143 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 684950002144 dimer interface [polypeptide binding]; other site 684950002145 putative CheW interface [polypeptide binding]; other site 684950002146 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 684950002147 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 684950002148 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 684950002149 catalytic residue [active] 684950002150 Transglycosylase; Region: Transgly; pfam00912 684950002151 penicillin-binding protein, 1A family; Region: PBP_1a_fam; TIGR02074 684950002152 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 684950002153 tumor necrosis factor alpha-inducing protein; Reviewed; Region: PRK12303 684950002154 Disulfide bond formation protein DsbB [Posttranslational modification, protein turnover, chaperones]; Region: DsbB; COG1495 684950002155 2-oxoglutarate-acceptor oxidoreductase subunit OorC; Reviewed; Region: oorC; PRK08441 684950002156 2-oxoglutarate ferredoxin oxidoreductase subunit gamma; Validated; Region: PRK08537 684950002157 2-oxoglutarate-acceptor oxidoreductase subunit OorB; Reviewed; Region: oorB; PRK09628 684950002158 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 684950002159 TPP-binding site [chemical binding]; other site 684950002160 2-oxoglutarate-acceptor oxidoreductase subunit OorA; Reviewed; Region: oorA; PRK09627 684950002161 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 684950002162 dimer interface [polypeptide binding]; other site 684950002163 PYR/PP interface [polypeptide binding]; other site 684950002164 TPP binding site [chemical binding]; other site 684950002165 substrate binding site [chemical binding]; other site 684950002166 2-oxoglutarate-acceptor oxidoreductase subunit OorD; Reviewed; Region: oorD; PRK09626 684950002167 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 684950002168 YceG-like family; Region: YceG; pfam02618 684950002169 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 684950002170 dimerization interface [polypeptide binding]; other site 684950002171 Protein of unknown function; Region: DUF3971; pfam13116 684950002172 AsmA-like C-terminal region; Region: AsmA_1; pfam13109 684950002173 Fe2+ transport system protein A [Inorganic ion transport and metabolism]; Region: FeoA; COG1918 684950002174 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 684950002175 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 684950002176 minor groove reading motif; other site 684950002177 helix-hairpin-helix signature motif; other site 684950002178 substrate binding pocket [chemical binding]; other site 684950002179 active site 684950002180 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 684950002181 flagellar motor switch protein; Validated; Region: PRK08433 684950002182 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 684950002183 TonB family C-terminal domain; Region: tonB_Cterm; TIGR01352 684950002184 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 684950002185 active site 684950002186 substrate binding pocket [chemical binding]; other site 684950002187 dimer interface [polypeptide binding]; other site 684950002188 Predicted neuraminidase (sialidase) [Carbohydrate transport and metabolism]; Region: COG4692 684950002189 BNR repeat-like domain; Region: BNR_2; pfam13088 684950002190 Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]; Region: MdoB; COG1368 684950002191 Sulfatase; Region: Sulfatase; pfam00884 684950002192 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14191 684950002193 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 684950002194 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 684950002195 homodimer interface [polypeptide binding]; other site 684950002196 NADP binding site [chemical binding]; other site 684950002197 substrate binding site [chemical binding]; other site 684950002198 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 684950002199 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 684950002200 Catalytic site [active] 684950002201 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 684950002202 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 684950002203 Peptidase family M50; Region: Peptidase_M50; pfam02163 684950002204 active site 684950002205 putative substrate binding region [chemical binding]; other site 684950002206 Ribose/Galactose Isomerase; Region: LacAB_rpiB; cl00485 684950002207 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 684950002208 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 684950002209 active site 684950002210 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 684950002211 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 684950002212 multifunctional aminopeptidase A; Provisional; Region: PRK00913 684950002213 interface (dimer of trimers) [polypeptide binding]; other site 684950002214 Substrate-binding/catalytic site; other site 684950002215 Zn-binding sites [ion binding]; other site 684950002216 GTP-binding protein YchF; Reviewed; Region: PRK09601 684950002217 YchF GTPase; Region: YchF; cd01900 684950002218 G1 box; other site 684950002219 GTP/Mg2+ binding site [chemical binding]; other site 684950002220 Switch I region; other site 684950002221 G2 box; other site 684950002222 Switch II region; other site 684950002223 G3 box; other site 684950002224 G4 box; other site 684950002225 G5 box; other site 684950002226 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 684950002227 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 684950002228 FeS/SAM binding site; other site 684950002229 Domain of unknown function (DUF4008); Region: DUF4008; pfam13186 684950002230 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 684950002231 Domain of unknown function DUF20; Region: UPF0118; pfam01594 684950002232 diaminopimelate epimerase; Region: DapF; TIGR00652 684950002233 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 684950002234 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 684950002235 Predicted membrane protein [Function unknown]; Region: COG3059 684950002236 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 684950002237 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 684950002238 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 684950002239 NAD(P) binding site [chemical binding]; other site 684950002240 active site 684950002241 acyl carrier protein; Provisional; Region: acpP; PRK00982 684950002242 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK08439 684950002243 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 684950002244 dimer interface [polypeptide binding]; other site 684950002245 active site 684950002246 acetyl-CoA carboxylase, carboxyl transferase, alpha subunit; Region: accA; TIGR00513 684950002247 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 684950002248 rRNA methylase, putative, group 3; Region: rRNA_methyl_3; TIGR00186 684950002249 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 684950002250 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 684950002251 Predicted methyltransferases [General function prediction only]; Region: COG0313 684950002252 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 684950002253 putative SAM binding site [chemical binding]; other site 684950002254 putative homodimer interface [polypeptide binding]; other site 684950002255 Ribosomal protein L31; Region: Ribosomal_L31; pfam01197 684950002256 transcription termination factor Rho; Provisional; Region: rho; PRK09376 684950002257 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 684950002258 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 684950002259 RNA binding site [nucleotide binding]; other site 684950002260 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 684950002261 multimer interface [polypeptide binding]; other site 684950002262 Walker A motif; other site 684950002263 ATP binding site [chemical binding]; other site 684950002264 Walker B motif; other site 684950002265 Asp/Glu/Hydantoin racemase; Region: Asp_Glu_race; cl00518 684950002266 CagA exotoxin; Region: CagA; pfam03507 684950002267 CagA exotoxin; Region: CagA; pfam03507 684950002268 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 684950002269 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 684950002270 prolyl-tRNA synthetase; Provisional; Region: PRK08661 684950002271 Cag pathogenicity island protein Cag12; Region: Cag12; pfam13117 684950002272 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 684950002273 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cl11423 684950002274 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cl11423 684950002275 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 684950002276 VirB7 interaction site; other site 684950002277 DC-EC Repeat; Region: CagY_M; pfam07337 684950002278 DC-EC Repeat; Region: CagY_M; pfam07337 684950002279 DC-EC Repeat; Region: CagY_M; pfam07337 684950002280 DC-EC Repeat; Region: CagY_M; pfam07337 684950002281 DC-EC Repeat; Region: CagY_M; pfam07337 684950002282 DC-EC Repeat; Region: CagY_M; pfam07337 684950002283 DC-EC Repeat; Region: CagY_M; pfam07337 684950002284 DC-EC Repeat; Region: CagY_M; pfam07337 684950002285 DC-EC Repeat; Region: CagY_M; pfam07337 684950002286 DC-EC Repeat; Region: CagY_M; pfam07337 684950002287 DC-EC Repeat; Region: CagY_M; pfam07337 684950002288 Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion]; Region: VirB10; COG2948 684950002289 CagZ; Region: CagZ; pfam09053 684950002290 P-type DNA transfer ATPase VirB11; Region: VirB11; TIGR02788 684950002291 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 684950002292 ATP binding site [chemical binding]; other site 684950002293 Walker A motif; other site 684950002294 hexamer interface [polypeptide binding]; other site 684950002295 Walker B motif; other site 684950002296 Type IV secretory pathway, VirD4 components [Intracellular trafficking and secretion]; Region: VirD4; COG3505 684950002297 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 684950002298 Walker A motif; other site 684950002299 ATP binding site [chemical binding]; other site 684950002300 Walker B motif; other site 684950002301 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 684950002302 Sel1-like repeats; Region: SEL1; smart00671 684950002303 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3034 684950002304 GTPase [General function prediction only]; Region: Era; COG1159 684950002305 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 684950002306 G1 box; other site 684950002307 GTP/Mg2+ binding site [chemical binding]; other site 684950002308 Switch I region; other site 684950002309 G2 box; other site 684950002310 Switch II region; other site 684950002311 G3 box; other site 684950002312 G4 box; other site 684950002313 G5 box; other site 684950002314 KH domain; Region: KH_2; pfam07650 684950002315 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 684950002316 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 684950002317 Walker A motif; other site 684950002318 ATP binding site [chemical binding]; other site 684950002319 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 684950002320 Walker B motif; other site 684950002321 arginine finger; other site 684950002322 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 684950002323 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 684950002324 active site 684950002325 HslU subunit interaction site [polypeptide binding]; other site 684950002326 ribosomal protein L9; Region: L9; TIGR00158 684950002327 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 684950002328 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 684950002329 Uncharacterized conserved protein [Function unknown]; Region: COG1479 684950002330 Protein of unknown function DUF262; Region: DUF262; pfam03235 684950002331 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 684950002332 Uncharacterized conserved protein [Function unknown]; Region: COG3586 684950002333 glutamine synthetase, type I; Region: GlnA; TIGR00653 684950002334 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 684950002335 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 684950002336 dihydrodipicolinate reductase; Region: dapB; TIGR00036 684950002337 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 684950002338 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 684950002339 FAD binding domain; Region: FAD_binding_4; pfam01565 684950002340 glycolate oxidase, subunit GlcD; Region: glcD; TIGR00387 684950002341 Protein-interacting Bro1-like domain of mammalian Alix and related domains; Region: BRO1_Alix_like; cl14649 684950002342 nudix-type nucleoside diphosphatase, YffH/AdpP family; Region: TIGR00052 684950002343 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 684950002344 dimer interface [polypeptide binding]; other site 684950002345 ADP-ribose binding site [chemical binding]; other site 684950002346 active site 684950002347 nudix motif; other site 684950002348 metal binding site [ion binding]; metal-binding site 684950002349 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 684950002350 Peptidase family M23; Region: Peptidase_M23; pfam01551 684950002351 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 684950002352 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 684950002353 Mg2+ binding site [ion binding]; other site 684950002354 G-X-G motif; other site 684950002355 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 684950002356 anchoring element; other site 684950002357 dimer interface [polypeptide binding]; other site 684950002358 ATP binding site [chemical binding]; other site 684950002359 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 684950002360 active site 684950002361 putative metal-binding site [ion binding]; other site 684950002362 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 684950002363 DNA polymerase III, beta subunit; Region: dnan; TIGR00663 684950002364 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 684950002365 putative DNA binding surface [nucleotide binding]; other site 684950002366 dimer interface [polypeptide binding]; other site 684950002367 beta-clamp/translesion DNA polymerase binding surface; other site 684950002368 beta-clamp/clamp loader binding surface; other site 684950002369 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 684950002370 dimerization interface [polypeptide binding]; other site 684950002371 substrate binding site [chemical binding]; other site 684950002372 active site 684950002373 calcium binding site [ion binding]; other site 684950002374 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 684950002375 Na2 binding site [ion binding]; other site 684950002376 putative substrate binding site 1 [chemical binding]; other site 684950002377 Na binding site 1 [ion binding]; other site 684950002378 putative substrate binding site 2 [chemical binding]; other site 684950002379 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 684950002380 Na2 binding site [ion binding]; other site 684950002381 putative substrate binding site 1 [chemical binding]; other site 684950002382 Na binding site 1 [ion binding]; other site 684950002383 putative substrate binding site 2 [chemical binding]; other site 684950002384 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 684950002385 active site 684950002386 Protein of unknown function (DUF493); Region: DUF493; pfam04359 684950002387 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK03815 684950002388 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 684950002389 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 684950002390 phospho-N-acetylmuramoyl-pentapeptide-transferase; Region: mraY; TIGR00445 684950002391 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 684950002392 Mg++ binding site [ion binding]; other site 684950002393 putative catalytic motif [active] 684950002394 putative substrate binding site [chemical binding]; other site 684950002395 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 684950002396 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 684950002397 Cation transport protein; Region: TrkH; cl17365 684950002398 Kef-type K+ transport systems, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: Kch; COG1226 684950002399 TrkA-N domain; Region: TrkA_N; pfam02254 684950002400 TrkA-C domain; Region: TrkA_C; pfam02080 684950002401 Protein of unknown function (DUF3519); Region: DUF3519; pfam12033 684950002402 Protein of unknown function (DUF3519); Region: DUF3519; pfam12033 684950002403 Protein of unknown function (DUF3519); Region: DUF3519; pfam12033 684950002404 Holliday junction DNA helicase, RuvA subunit; Region: ruvA; TIGR00084 684950002405 RuvA N terminal domain; Region: RuvA_N; pfam01330 684950002406 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 684950002407 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 684950002408 MviN-like protein; Region: MVIN; pfam03023 684950002409 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 684950002410 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 684950002411 active site 684950002412 HIGH motif; other site 684950002413 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 684950002414 KMSKS motif; other site 684950002415 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 684950002416 tRNA binding surface [nucleotide binding]; other site 684950002417 anticodon binding site; other site 684950002418 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 684950002419 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 684950002420 Walker A/P-loop; other site 684950002421 ATP binding site [chemical binding]; other site 684950002422 Q-loop/lid; other site 684950002423 ABC transporter signature motif; other site 684950002424 Walker B; other site 684950002425 D-loop; other site 684950002426 H-loop/switch region; other site 684950002427 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 684950002428 ABC-ATPase subunit interface; other site 684950002429 dimer interface [polypeptide binding]; other site 684950002430 putative PBP binding regions; other site 684950002431 short chain dehydrogenase; Validated; Region: PRK06182 684950002432 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 684950002433 NADP binding site [chemical binding]; other site 684950002434 active site 684950002435 steroid binding site; other site 684950002436 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 684950002437 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3041 684950002438 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 684950002439 hydrogenase expression/formation protein HypD; Region: hypD; TIGR00075 684950002440 hydrogenase isoenzymes formation protein HypD; Provisional; Region: PRK15062 684950002441 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypC; COG0298 684950002442 hydrogenase accessory protein HypB; Region: hypB; TIGR00073 684950002443 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 684950002444 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 684950002445 BioD-like N-terminal domain of phosphotransacetylase [General function prediction only]; Region: Pta; COG0857 684950002446 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl17212 684950002447 Acetokinase family; Region: Acetate_kinase; cl17229 684950002448 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 684950002449 flagellar basal body rod modification protein; Reviewed; Region: flgD; PRK05842 684950002450 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 684950002451 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 684950002452 TolA protein; Region: tolA_full; TIGR02794 684950002453 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0827 684950002454 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 684950002455 S-adenosylmethionine binding site [chemical binding]; other site 684950002456 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 684950002457 Part of AAA domain; Region: AAA_19; pfam13245 684950002458 Family description; Region: UvrD_C_2; pfam13538 684950002459 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 684950002460 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 684950002461 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 684950002462 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 684950002463 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 684950002464 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 684950002465 ATP-grasp domain; Region: ATP-grasp_4; cl17255 684950002466 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 684950002467 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 684950002468 ATP-grasp domain; Region: ATP-grasp_4; cl17255 684950002469 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 684950002470 IMP binding site; other site 684950002471 dimer interface [polypeptide binding]; other site 684950002472 interdomain contacts; other site 684950002473 partial ornithine binding site; other site 684950002474 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 684950002475 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 684950002476 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; pfam00044 684950002477 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 684950002478 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 684950002479 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 684950002480 Mechanosensitive ion channel porin domain; Region: MscS_porin; pfam12795 684950002481 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 684950002482 PPE-repeat proteins [Cell motility and secretion]; Region: COG5651 684950002483 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 684950002484 Autotransporter beta-domain; Region: Autotransporter; pfam03797 684950002485 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 684950002486 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 684950002487 active site 1 [active] 684950002488 dimer interface [polypeptide binding]; other site 684950002489 hexamer interface [polypeptide binding]; other site 684950002490 active site 2 [active] 684950002491 recombination protein RecR; Region: recR; TIGR00615 684950002492 RecR protein; Region: RecR; pfam02132 684950002493 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 684950002494 putative active site [active] 684950002495 putative metal-binding site [ion binding]; other site 684950002496 tetramer interface [polypeptide binding]; other site 684950002497 tRNA pseudouridine synthase, TruD family; Region: tRNA_TruD_broad; TIGR00094 684950002498 Pseudouridine synthase, similar to Escherichia coli TruD; Region: PseudoU_synth_EcTruD; cd02575 684950002499 Permutation of conserved domain; other site 684950002500 active site 684950002501 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 684950002502 heat shock protein HtpX; Provisional; Region: PRK02870 684950002503 GTP cyclohydrolase I; Region: folE; TIGR00063 684950002504 GTP cyclohydrolase I; Provisional; Region: PLN03044 684950002505 active site 684950002506 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 684950002507 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 684950002508 substrate binding pocket [chemical binding]; other site 684950002509 chain length determination region; other site 684950002510 substrate-Mg2+ binding site; other site 684950002511 catalytic residues [active] 684950002512 aspartate-rich region 1; other site 684950002513 active site lid residues [active] 684950002514 aspartate-rich region 2; other site 684950002515 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 684950002516 6-pyruvoyl-tetrahydropterin synthase [Coenzyme metabolism]; Region: COG0720 684950002517 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 684950002518 putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE; Region: rSAM_QueE_Ecoli; TIGR04322 684950002519 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 684950002520 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 684950002521 Coenzyme A binding pocket [chemical binding]; other site 684950002522 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 684950002523 metabolite-proton symporter; Region: 2A0106; TIGR00883 684950002524 Protein of unknown function DUF262; Region: DUF262; pfam03235 684950002525 Uncharacterized conserved protein [Function unknown]; Region: COG1479 684950002526 Protein of unknown function DUF262; Region: DUF262; pfam03235 684950002527 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 684950002528 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 684950002529 dimer interface [polypeptide binding]; other site 684950002530 conserved gate region; other site 684950002531 putative PBP binding loops; other site 684950002532 ABC-ATPase subunit interface; other site 684950002533 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 684950002534 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 684950002535 substrate binding pocket [chemical binding]; other site 684950002536 membrane-bound complex binding site; other site 684950002537 hinge residues; other site 684950002538 alanine racemase; Region: alr; TIGR00492 684950002539 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 684950002540 active site 684950002541 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 684950002542 dimer interface [polypeptide binding]; other site 684950002543 substrate binding site [chemical binding]; other site 684950002544 catalytic residues [active] 684950002545 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 684950002546 amino acid carrier protein; Region: agcS; TIGR00835 684950002547 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 684950002548 Streptococcal 67 kDa myosin-cross-reactive antigen like family; Region: Strep_67kDa_ant; cl17487 684950002549 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 684950002550 homotrimer interaction site [polypeptide binding]; other site 684950002551 TRL-like protein family; Region: TRL; pfam13146 684950002552 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 684950002553 Uncharacterized conserved protein [Function unknown]; Region: COG1576 684950002554 acetyl-CoA carboxylase, carboxyl transferase, beta subunit; Region: accD; TIGR00515 684950002555 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 684950002556 putative recombination protein RecO; Provisional; Region: PRK13908 684950002557 competence/damage-inducible protein CinA C-terminal domain; Region: cinA_cterm; TIGR00199 684950002558 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 684950002559 dimer interface [polypeptide binding]; other site 684950002560 FMN binding site [chemical binding]; other site 684950002561 prolipoprotein diacylglyceryl transferase; Region: lgt; TIGR00544 684950002562 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 684950002563 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 684950002564 active site 684950002565 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 684950002566 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 684950002567 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]; Region: COG1579 684950002568 Putative zinc ribbon domain; Region: DUF164; pfam02591 684950002569 dinuclear metal center protein, YbgI/SA1388 family; Region: YbgI_SA1388; TIGR00486 684950002570 Uncharacterized conserved protein [Function unknown]; Region: COG0327 684950002571 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 684950002572 dimer interface [polypeptide binding]; other site 684950002573 motif 1; other site 684950002574 active site 684950002575 motif 2; other site 684950002576 motif 3; other site 684950002577 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 684950002578 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 684950002579 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 684950002580 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 684950002581 Dynamin family; Region: Dynamin_N; pfam00350 684950002582 G1 box; other site 684950002583 GTP/Mg2+ binding site [chemical binding]; other site 684950002584 G2 box; other site 684950002585 Switch I region; other site 684950002586 G3 box; other site 684950002587 Switch II region; other site 684950002588 G4 box; other site 684950002589 G5 box; other site 684950002590 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 684950002591 G1 box; other site 684950002592 GTP/Mg2+ binding site [chemical binding]; other site 684950002593 G2 box; other site 684950002594 Switch I region; other site 684950002595 G3 box; other site 684950002596 Switch II region; other site 684950002597 G4 box; other site 684950002598 Uncharacterized virulence-associated protein D [Function unknown]; Region: VapD; COG3309 684950002599 Protein of unknown function (DUF3240); Region: DUF3240; pfam11582 684950002600 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 684950002601 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 684950002602 HlyD family secretion protein; Region: HlyD_3; pfam13437 684950002603 Outer membrane efflux protein; Region: OEP; pfam02321 684950002604 Outer membrane efflux protein; Region: OEP; pfam02321 684950002605 glycyl-tRNA synthetase, tetrameric type, beta subunit; Region: glyS; TIGR00211 684950002606 phosphoglyceromutase; Provisional; Region: PRK05434 684950002607 2,3-bisphosphoglycerate-independent phosphoglycerate mutase; Region: pgm_bpd_ind; TIGR01307 684950002608 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C subunit; Region: gatC; TIGR00135 684950002609 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK05964 684950002610 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 684950002611 inhibitor-cofactor binding pocket; inhibition site 684950002612 pyridoxal 5'-phosphate binding site [chemical binding]; other site 684950002613 catalytic residue [active] 684950002614 SurA N-terminal domain; Region: SurA_N_3; cl07813 684950002615 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 684950002616 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 684950002617 cell division protein FtsA; Region: ftsA; TIGR01174 684950002618 Cell division protein FtsA; Region: FtsA; smart00842 684950002619 Cell division protein FtsA; Region: FtsA; pfam14450 684950002620 cell division protein FtsZ; Validated; Region: PRK09330 684950002621 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 684950002622 nucleotide binding site [chemical binding]; other site 684950002623 SulA interaction site; other site 684950002624 Mechanosensitive ion channel; Region: MS_channel; pfam00924 684950002625 Uncharacterized conserved protein [Function unknown]; Region: COG1479 684950002626 Protein of unknown function DUF262; Region: DUF262; pfam03235 684950002627 Protein of unknown function DUF262; Region: DUF262; pfam03235 684950002628 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 684950002629 Arginine decarboxylase (spermidine biosynthesis) [Amino acid transport and metabolism]; Region: SpeA; COG1166 684950002630 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase; Region: PLPDE_III_ADC; cd06830 684950002631 active site 684950002632 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 684950002633 catalytic residues [active] 684950002634 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 684950002635 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 684950002636 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 684950002637 putative ADP-binding pocket [chemical binding]; other site 684950002638 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cd03440 684950002639 active site 2 [active] 684950002640 active site 1 [active] 684950002641 Methyltransferase domain; Region: Methyltransf_23; pfam13489 684950002642 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 684950002643 S-adenosylmethionine binding site [chemical binding]; other site 684950002644 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 684950002645 methionyl-tRNA synthetase; Reviewed; Region: PRK12267 684950002646 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 684950002647 active site 684950002648 HIGH motif; other site 684950002649 KMSKS motif; other site 684950002650 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 684950002651 anticodon binding site; other site 684950002652 tRNA binding surface [nucleotide binding]; other site 684950002653 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 684950002654 dimer interface [polypeptide binding]; other site 684950002655 putative tRNA-binding site [nucleotide binding]; other site 684950002656 Mycolic acid cyclopropane synthetase; Region: CMAS; pfam02353 684950002657 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 684950002658 S-adenosylmethionine binding site [chemical binding]; other site 684950002659 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 684950002660 Mechanosensitive ion channel; Region: MS_channel; pfam00924 684950002661 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 684950002662 GMP synthase; Reviewed; Region: guaA; PRK00074 684950002663 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 684950002664 AMP/PPi binding site [chemical binding]; other site 684950002665 candidate oxyanion hole; other site 684950002666 catalytic triad [active] 684950002667 potential glutamine specificity residues [chemical binding]; other site 684950002668 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 684950002669 ATP Binding subdomain [chemical binding]; other site 684950002670 Ligand Binding sites [chemical binding]; other site 684950002671 Dimerization subdomain; other site 684950002672 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 684950002673 molybdopterin cofactor binding site; other site 684950002674 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 684950002675 molybdopterin cofactor binding site; other site 684950002676 Protein of unknown function (DUF3972); Region: DUF3972; pfam13118 684950002677 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 684950002678 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 684950002679 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 684950002680 catalytic residue [active] 684950002681 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 684950002682 nucleotide binding site/active site [active] 684950002683 HIT family signature motif; other site 684950002684 catalytic residue [active] 684950002685 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 684950002686 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 684950002687 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 684950002688 dimer interface [polypeptide binding]; other site 684950002689 motif 1; other site 684950002690 active site 684950002691 motif 2; other site 684950002692 motif 3; other site 684950002693 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 684950002694 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 684950002695 putative tRNA-binding site [nucleotide binding]; other site 684950002696 tRNA synthetase B5 domain; Region: B5; pfam03484 684950002697 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 684950002698 dimer interface [polypeptide binding]; other site 684950002699 motif 1; other site 684950002700 motif 3; other site 684950002701 motif 2; other site 684950002702 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 684950002703 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 684950002704 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 684950002705 hinge; other site 684950002706 active site 684950002707 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 684950002708 LytB protein; Region: LYTB; pfam02401 684950002709 ribosomal protein S1; Region: rpsA; TIGR00717 684950002710 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 684950002711 RNA binding site [nucleotide binding]; other site 684950002712 Ribosomal protein S1-like RNA-binding domain; Region: S1; smart00316 684950002713 RNA binding site [nucleotide binding]; other site 684950002714 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 684950002715 RNA binding site [nucleotide binding]; other site 684950002716 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 684950002717 RNA binding site [nucleotide binding]; other site 684950002718 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 684950002719 RNA binding site [nucleotide binding]; other site 684950002720 D-3-phosphoglycerate dehydrogenase; Region: PGDH; TIGR01327 684950002721 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_4; cd12173 684950002722 ligand binding site [chemical binding]; other site 684950002723 NAD binding site [chemical binding]; other site 684950002724 dimerization interface [polypeptide binding]; other site 684950002725 catalytic site [active] 684950002726 C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH); Region: ACT_3PGDH-xct; cd04902 684950002727 putative L-serine binding site [chemical binding]; other site 684950002728 menaquinone biosynthesis decarboxylase, SCO4490 family; Region: mena_SCO4490; TIGR03701 684950002729 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 684950002730 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 684950002731 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 684950002732 catalytic residue [active] 684950002733 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 684950002734 putative active site [active] 684950002735 putative metal binding site [ion binding]; other site 684950002736 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 684950002737 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 684950002738 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 684950002739 active site 684950002740 phosphorylation site [posttranslational modification] 684950002741 intermolecular recognition site; other site 684950002742 dimerization interface [polypeptide binding]; other site 684950002743 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 684950002744 putative binding surface; other site 684950002745 active site 684950002746 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 684950002747 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 684950002748 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 684950002749 ATP binding site [chemical binding]; other site 684950002750 Mg2+ binding site [ion binding]; other site 684950002751 G-X-G motif; other site 684950002752 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 684950002753 Response regulator receiver domain; Region: Response_reg; pfam00072 684950002754 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 684950002755 active site 684950002756 phosphorylation site [posttranslational modification] 684950002757 intermolecular recognition site; other site 684950002758 dimerization interface [polypeptide binding]; other site 684950002759 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 684950002760 putative CheA interaction surface; other site 684950002761 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 684950002762 dimer interface [polypeptide binding]; other site 684950002763 catalytic triad [active] 684950002764 peroxidatic and resolving cysteines [active] 684950002765 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 684950002766 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 684950002767 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 684950002768 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 684950002769 S-adenosylmethionine binding site [chemical binding]; other site 684950002770 primosome assembly protein PriA; Validated; Region: PRK05580 684950002771 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 684950002772 ATP binding site [chemical binding]; other site 684950002773 putative Mg++ binding site [ion binding]; other site 684950002774 helicase superfamily c-terminal domain; Region: HELICc; smart00490 684950002775 Sporulation related domain; Region: SPOR; pfam05036 684950002776 Peptidase family M48; Region: Peptidase_M48; pfam01435 684950002777 HemK family putative methylases; Region: hemK_fam; TIGR00536 684950002778 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 684950002779 glutamate dehydrogenase; Provisional; Region: PRK09414 684950002780 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 684950002781 NAD(P) binding domain of glutamate dehydrogenase, subgroup 2; Region: NAD_bind_2_Glu_DH; cd05313 684950002782 NAD(P) binding site [chemical binding]; other site 684950002783 Glycosyltransferase family 10 (fucosyltransferase); Region: Glyco_transf_10; pfam00852 684950002784 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 684950002785 cytochrome c-type biogenesis protein CcsB; Region: cytochr_II_ccsB; TIGR03144 684950002786 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 684950002787 catalytic residues [active] 684950002788 ferrochelatase; Region: hemH; TIGR00109 684950002789 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 684950002790 C-terminal domain interface [polypeptide binding]; other site 684950002791 active site 684950002792 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 684950002793 active site 684950002794 N-terminal domain interface [polypeptide binding]; other site 684950002795 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385 684950002796 RNA methyltransferase, RsmE family; Region: TIGR00046 684950002797 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 684950002798 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 684950002799 trimer interface [polypeptide binding]; other site 684950002800 active site 684950002801 acetyl-CoA carboxylase, biotin carboxyl carrier protein; Region: BCCP; TIGR00531 684950002802 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 684950002803 carboxyltransferase (CT) interaction site; other site 684950002804 biotinylation site [posttranslational modification]; other site 684950002805 biotin carboxylase; Validated; Region: PRK08462 684950002806 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 684950002807 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 684950002808 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 684950002809 Methyltransferase domain; Region: Methyltransf_26; pfam13659 684950002810 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 684950002811 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 684950002812 inhibitor-cofactor binding pocket; inhibition site 684950002813 pyridoxal 5'-phosphate binding site [chemical binding]; other site 684950002814 catalytic residue [active] 684950002815 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 684950002816 dimer interface [polypeptide binding]; other site 684950002817 putative radical transfer pathway; other site 684950002818 diiron center [ion binding]; other site 684950002819 tyrosyl radical; other site 684950002820 protein-L-isoaspartate(D-aspartate) O-methyltransferase; Region: pimt; TIGR00080 684950002821 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 684950002822 S-adenosylmethionine binding site [chemical binding]; other site 684950002823 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 684950002824 Predicted permeases [General function prediction only]; Region: COG0795 684950002825 tRNA pseudouridine(38-40) synthase; Region: hisT_truA; TIGR00071 684950002826 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 684950002827 dimerization interface 3.5A [polypeptide binding]; other site 684950002828 active site 684950002829 UDP-glucose-4-epimerase GalE; Region: galE; TIGR01179 684950002830 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 684950002831 NAD binding site [chemical binding]; other site 684950002832 homodimer interface [polypeptide binding]; other site 684950002833 active site 684950002834 substrate binding site [chemical binding]; other site 684950002835 classical (c) SDR, subgroup 5; Region: SDR_c5; cd05346 684950002836 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 684950002837 putative NAD(P) binding site [chemical binding]; other site 684950002838 homodimer interface [polypeptide binding]; other site 684950002839 homotetramer interface [polypeptide binding]; other site 684950002840 active site 684950002841 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 684950002842 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 684950002843 binding surface 684950002844 TPR motif; other site 684950002845 Sel1-like repeats; Region: SEL1; smart00671 684950002846 Sel1-like repeats; Region: SEL1; smart00671 684950002847 Sel1-like repeats; Region: SEL1; smart00671 684950002848 Entner-Doudoroff aldolase; Region: eda; TIGR01182 684950002849 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 684950002850 active site 684950002851 intersubunit interface [polypeptide binding]; other site 684950002852 catalytic residue [active] 684950002853 phosphogluconate dehydratase; Validated; Region: PRK09054 684950002854 6-phosphogluconate dehydratase; Region: edd; TIGR01196 684950002855 Glucose-6-phosphate 1-dehydrogenase [Carbohydrate transport and metabolism]; Region: Zwf; COG0364 684950002856 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 684950002857 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 684950002858 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 684950002859 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 684950002860 putative active site [active] 684950002861 glucokinase, proteobacterial type; Region: glk; TIGR00749 684950002862 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 684950002863 nucleotide binding site [chemical binding]; other site 684950002864 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 684950002865 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD1; cd05283 684950002866 putative NAD(P) binding site [chemical binding]; other site 684950002867 putative substrate binding site [chemical binding]; other site 684950002868 catalytic Zn binding site [ion binding]; other site 684950002869 structural Zn binding site [ion binding]; other site 684950002870 dimer interface [polypeptide binding]; other site 684950002871 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 684950002872 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 684950002873 active site 684950002874 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 684950002875 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 684950002876 active site 684950002877 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 684950002878 pyruvate flavodoxin oxidoreductase subunit gamma; Validated; Region: PRK05844 684950002879 pyruvate/ketoisovalerate ferredoxin oxidoreductase subunit gamma; Provisional; Region: PRK14029 684950002880 pyruvate flavodoxin oxidoreductase subunit delta; Reviewed; Region: porD; PRK09625 684950002881 4Fe-4S binding domain; Region: Fer4; pfam00037 684950002882 pyruvate flavodoxin oxidoreductase subunit alpha; Reviewed; Region: porA; PRK09622 684950002883 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 684950002884 dimer interface [polypeptide binding]; other site 684950002885 PYR/PP interface [polypeptide binding]; other site 684950002886 TPP binding site [chemical binding]; other site 684950002887 substrate binding site [chemical binding]; other site 684950002888 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 684950002889 pyruvate ferredoxin oxidoreductase subunit beta; Provisional; Region: PRK11865 684950002890 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 684950002891 TPP-binding site [chemical binding]; other site 684950002892 putative dimer interface [polypeptide binding]; other site 684950002893 adenylosuccinate lyase; Provisional; Region: PRK08470 684950002894 Adenylsuccinate lyase (ASL)_subgroup 1; Region: Adenylsuccinate_lyase_1; cd01360 684950002895 tetramer interface [polypeptide binding]; other site 684950002896 active site 684950002897 Adenylosuccinate lyase C-terminus; Region: ADSL_C; smart00998 684950002898 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 684950002899 excinuclease ABC subunit B; Provisional; Region: PRK05298 684950002900 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 684950002901 ATP binding site [chemical binding]; other site 684950002902 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 684950002903 putative Mg++ binding site [ion binding]; other site 684950002904 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 684950002905 nucleotide binding region [chemical binding]; other site 684950002906 ATP-binding site [chemical binding]; other site 684950002907 Ultra-violet resistance protein B; Region: UvrB; pfam12344 684950002908 UvrB/uvrC motif; Region: UVR; pfam02151 684950002909 Protein of unknown function (DUF3519); Region: DUF3519; pfam12033 684950002910 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 684950002911 binding surface 684950002912 TPR motif; other site 684950002913 TPR repeat; Region: TPR_11; pfam13414 684950002914 Sel1-like repeats; Region: SEL1; smart00671 684950002915 Sel1-like repeats; Region: SEL1; smart00671 684950002916 Sel1-like repeats; Region: SEL1; smart00671 684950002917 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 684950002918 gamma-glutamyltranspeptidase; Region: g_glut_trans; TIGR00066 684950002919 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK08471 684950002920 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 684950002921 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 684950002922 DNA-methyltransferase (dcm); Region: dcm; TIGR00675 684950002923 cofactor binding site; other site 684950002924 DNA binding site [nucleotide binding] 684950002925 substrate interaction site [chemical binding]; other site 684950002926 Anti-sigma-28 factor, FlgM; Region: FlgM; cl01052 684950002927 FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]; Region: SlpA; COG1047 684950002928 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 684950002929 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 684950002930 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 684950002931 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 684950002932 ligand binding site [chemical binding]; other site 684950002933 translocation protein TolB; Provisional; Region: tolB; PRK04043 684950002934 TolB amino-terminal domain; Region: TolB_N; pfam04052 684950002935 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 684950002936 TonB C terminal; Region: TonB_2; pfam13103 684950002937 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 684950002938 TolR protein; Region: tolR; TIGR02801 684950002939 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; pfam01618 684950002940 ATP synthase, F1 epsilon subunit (delta in mitochondria); Region: ATP_synt_epsi; TIGR01216 684950002941 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 684950002942 gamma subunit interface [polypeptide binding]; other site 684950002943 epsilon subunit interface [polypeptide binding]; other site 684950002944 LBP interface [polypeptide binding]; other site 684950002945 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 684950002946 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 684950002947 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 684950002948 alpha subunit interaction interface [polypeptide binding]; other site 684950002949 Walker A motif; other site 684950002950 ATP binding site [chemical binding]; other site 684950002951 Walker B motif; other site 684950002952 inhibitor binding site; inhibition site 684950002953 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 684950002954 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 684950002955 core domain interface [polypeptide binding]; other site 684950002956 delta subunit interface [polypeptide binding]; other site 684950002957 epsilon subunit interface [polypeptide binding]; other site 684950002958 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 684950002959 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 684950002960 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 684950002961 beta subunit interaction interface [polypeptide binding]; other site 684950002962 Walker A motif; other site 684950002963 ATP binding site [chemical binding]; other site 684950002964 Walker B motif; other site 684950002965 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 684950002966 F0F1 ATP synthase subunit delta; Provisional; Region: PRK13431 684950002967 F0F1 ATP synthase subunit B; Validated; Region: PRK08475 684950002968 F0F1 ATP synthase subunit B'; Validated; Region: PRK08476 684950002969 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 684950002970 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 684950002971 ParB-like nuclease domain; Region: ParB; smart00470 684950002972 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 684950002973 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 684950002974 P-loop; other site 684950002975 Magnesium ion binding site [ion binding]; other site 684950002976 biotin--protein ligase; Provisional; Region: PRK08477 684950002977 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 684950002978 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 684950002979 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 684950002980 putative active site [active] 684950002981 substrate binding site [chemical binding]; other site 684950002982 putative cosubstrate binding site; other site 684950002983 catalytic site [active] 684950002984 Formyl transferase, C-terminal domain; Region: Formyl_trans_C; pfam02911 684950002985 AAA domain; Region: AAA_13; pfam13166 684950002986 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4487 684950002987 Uncharacterized protein conserved in bacteria (DUF2130); Region: DUF2130; pfam09903 684950002988 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 684950002989 tRNA (guanine-N1)-methyltransferase; Region: trmD; TIGR00088 684950002990 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK14593 684950002991 RimM N-terminal domain; Region: RimM; pfam01782 684950002992 PRC-barrel domain; Region: PRC; pfam05239 684950002993 Predicted RNA-binding protein (contains KH domain) [General function prediction only]; Region: COG1837 684950002994 KH domain; Region: KH_4; pfam13083 684950002995 G-X-X-G motif; other site 684950002996 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 684950002997 signal recognition particle protein; Provisional; Region: PRK10867 684950002998 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 684950002999 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 684950003000 P loop; other site 684950003001 GTP binding site [chemical binding]; other site 684950003002 Signal peptide binding domain; Region: SRP_SPB; pfam02978 684950003003 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 684950003004 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 684950003005 active site 684950003006 HIGH motif; other site 684950003007 nucleotide binding site [chemical binding]; other site 684950003008 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 684950003009 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 684950003010 active site 684950003011 KMSKS motif; other site 684950003012 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 684950003013 anticodon binding site; other site 684950003014 flagellar assembly protein FliW; Provisional; Region: PRK13283 684950003015 undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase; Region: murG; TIGR01133 684950003016 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 684950003017 active site 684950003018 homodimer interface [polypeptide binding]; other site 684950003019 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 684950003020 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 684950003021 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 684950003022 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 684950003023 Protein involved in cell division [Cell division and chromosome partitioning]; Region: Fic; COG2184 684950003024 Fic/DOC family; Region: Fic; cl00960 684950003025 metal-binding heat shock protein; Provisional; Region: PRK00016 684950003026 flavodoxin FldA; Validated; Region: PRK09267 684950003027 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 684950003028 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 684950003029 Uncharacterized protein, possibly involved in nitrogen fixation [Inorganic ion transport and metabolism]; Region: FixS; COG3197 684950003030 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 684950003031 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 684950003032 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 684950003033 Major Facilitator Superfamily; Region: MFS_1; pfam07690 684950003034 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 684950003035 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 684950003036 active site 684950003037 dimer interface [polypeptide binding]; other site 684950003038 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 684950003039 dimer interface [polypeptide binding]; other site 684950003040 active site 684950003041 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 684950003042 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 684950003043 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 684950003044 dimer interface [polypeptide binding]; other site 684950003045 conserved gate region; other site 684950003046 putative PBP binding loops; other site 684950003047 ABC-ATPase subunit interface; other site 684950003048 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 684950003049 dimer interface [polypeptide binding]; other site 684950003050 conserved gate region; other site 684950003051 putative PBP binding loops; other site 684950003052 ABC-ATPase subunit interface; other site 684950003053 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 684950003054 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 684950003055 Walker A/P-loop; other site 684950003056 ATP binding site [chemical binding]; other site 684950003057 Q-loop/lid; other site 684950003058 ABC transporter signature motif; other site 684950003059 Walker B; other site 684950003060 D-loop; other site 684950003061 H-loop/switch region; other site 684950003062 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 684950003063 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 684950003064 substrate binding pocket [chemical binding]; other site 684950003065 membrane-bound complex binding site; other site 684950003066 hinge residues; other site 684950003067 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 684950003068 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 684950003069 putative substrate translocation pore; other site 684950003070 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 684950003071 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 684950003072 purine-nucleoside phosphorylase, family 1 (deoD); Region: deoD; TIGR00107 684950003073 Nucleoside permease [Nucleotide transport and metabolism]; Region: NupC; COG1972 684950003074 Na+ dependent nucleoside transporter N-terminus; Region: Nucleos_tra2_N; pfam01773 684950003075 Nucleoside recognition; Region: Gate; pfam07670 684950003076 Na+ dependent nucleoside transporter C-terminus; Region: Nucleos_tra2_C; pfam07662 684950003077 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 684950003078 Major Facilitator Superfamily; Region: MFS_1; pfam07690 684950003079 putative substrate translocation pore; other site 684950003080 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 684950003081 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 684950003082 Ligand Binding Site [chemical binding]; other site 684950003083 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 684950003084 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 684950003085 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 684950003086 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA; Region: MATE_MepA_like; cd13143 684950003087 putative arabinose transporter; Provisional; Region: PRK03545 684950003088 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 684950003089 putative substrate translocation pore; other site 684950003090 Carbonic anhydrase [Inorganic ion transport and metabolism]; Region: Cah; COG3338 684950003091 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 684950003092 active site 684950003093 zinc binding site [ion binding]; other site 684950003094 Helicobacter pylori protein of unknown function (DUF874); Region: DUF874; pfam05917 684950003095 aspartate-semialdehyde dehydrogenase (peptidoglycan organisms); Region: asd_B; TIGR01296 684950003096 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 684950003097 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 684950003098 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 684950003099 putative active site [active] 684950003100 elongation factor G; Reviewed; Region: PRK00007 684950003101 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 684950003102 G1 box; other site 684950003103 putative GEF interaction site [polypeptide binding]; other site 684950003104 GTP/Mg2+ binding site [chemical binding]; other site 684950003105 Switch I region; other site 684950003106 G2 box; other site 684950003107 G3 box; other site 684950003108 Switch II region; other site 684950003109 G4 box; other site 684950003110 G5 box; other site 684950003111 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 684950003112 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 684950003113 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 684950003114 30S ribosomal protein S7; Validated; Region: PRK05302 684950003115 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 684950003116 S17 interaction site [polypeptide binding]; other site 684950003117 S8 interaction site; other site 684950003118 16S rRNA interaction site [nucleotide binding]; other site 684950003119 streptomycin interaction site [chemical binding]; other site 684950003120 23S rRNA interaction site [nucleotide binding]; other site 684950003121 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 684950003122 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed; Region: PRK09603 684950003123 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 684950003124 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 684950003125 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 684950003126 RPB11 interaction site [polypeptide binding]; other site 684950003127 RPB12 interaction site [polypeptide binding]; other site 684950003128 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 684950003129 RPB3 interaction site [polypeptide binding]; other site 684950003130 RPB1 interaction site [polypeptide binding]; other site 684950003131 RPB11 interaction site [polypeptide binding]; other site 684950003132 RPB10 interaction site [polypeptide binding]; other site 684950003133 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 684950003134 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 684950003135 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 684950003136 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 684950003137 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 684950003138 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 684950003139 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 684950003140 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 684950003141 DNA binding site [nucleotide binding] 684950003142 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 684950003143 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 684950003144 core dimer interface [polypeptide binding]; other site 684950003145 peripheral dimer interface [polypeptide binding]; other site 684950003146 L10 interface [polypeptide binding]; other site 684950003147 L11 interface [polypeptide binding]; other site 684950003148 putative EF-Tu interaction site [polypeptide binding]; other site 684950003149 putative EF-G interaction site [polypeptide binding]; other site 684950003150 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 684950003151 23S rRNA interface [nucleotide binding]; other site 684950003152 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 684950003153 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 684950003154 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 684950003155 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 684950003156 23S rRNA interface [nucleotide binding]; other site 684950003157 L7/L12 interface [polypeptide binding]; other site 684950003158 putative thiostrepton binding site; other site 684950003159 L25 interface [polypeptide binding]; other site 684950003160 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 684950003161 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 684950003162 putative homodimer interface [polypeptide binding]; other site 684950003163 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 684950003164 heterodimer interface [polypeptide binding]; other site 684950003165 homodimer interface [polypeptide binding]; other site 684950003166 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 684950003167 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 684950003168 elongation factor Tu; Reviewed; Region: PRK00049 684950003169 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 684950003170 G1 box; other site 684950003171 GEF interaction site [polypeptide binding]; other site 684950003172 GTP/Mg2+ binding site [chemical binding]; other site 684950003173 Switch I region; other site 684950003174 G2 box; other site 684950003175 G3 box; other site 684950003176 Switch II region; other site 684950003177 G4 box; other site 684950003178 G5 box; other site 684950003179 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 684950003180 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 684950003181 Antibiotic Binding Site [chemical binding]; other site 684950003182 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 684950003183 ATP-binding cassette domain of multidrug resistance protein-like transporters; Region: ABCC_MRP_Like; cd03228 684950003184 Walker A/P-loop; other site 684950003185 ATP binding site [chemical binding]; other site 684950003186 Q-loop/lid; other site 684950003187 ABC transporter signature motif; other site 684950003188 Walker B; other site 684950003189 D-loop; other site 684950003190 H-loop/switch region; other site 684950003191 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 684950003192 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; cl17915 684950003193 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG3392 684950003194 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; pfam02086 684950003195 ICEA Protein; Region: ICEA; pfam05315 684950003196 serine O-acetyltransferase; Region: cysE; TIGR01172 684950003197 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 684950003198 trimer interface [polypeptide binding]; other site 684950003199 active site 684950003200 substrate binding site [chemical binding]; other site 684950003201 CoA binding site [chemical binding]; other site 684950003202 F0F1 ATP synthase subunit C; Validated; Region: PRK08482 684950003203 RNase PH-like 3'-5' exoribonucleases; Region: RNase_PH; cl03114 684950003204 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 684950003205 oligomer interface [polypeptide binding]; other site 684950003206 RNA binding site [nucleotide binding]; other site 684950003207 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 684950003208 RNase PH-like 3'-5' exoribonucleases; Region: RNase_PH; cl03114 684950003209 oligomer interface [polypeptide binding]; other site 684950003210 RNA binding site [nucleotide binding]; other site 684950003211 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 684950003212 putative nucleic acid binding region [nucleotide binding]; other site 684950003213 G-X-X-G motif; other site 684950003214 Ribosomal protein S1-like RNA-binding domain; Region: S1; smart00316 684950003215 RNA binding site [nucleotide binding]; other site 684950003216 Predicted phosphoribosyltransferases [General function prediction only]; Region: COG1926 684950003217 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 684950003218 Organic solvent tolerance protein; Region: OstA_C; pfam04453 684950003219 Predicted membrane protein/domain [Function unknown]; Region: COG1714 684950003220 phosphoribosylamine--glycine ligase; Region: purD; TIGR00877 684950003221 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 684950003222 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 684950003223 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 684950003224 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 684950003225 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 684950003226 Walker A/P-loop; other site 684950003227 ATP binding site [chemical binding]; other site 684950003228 Q-loop/lid; other site 684950003229 ABC transporter signature motif; other site 684950003230 Walker B; other site 684950003231 D-loop; other site 684950003232 H-loop/switch region; other site 684950003233 Undecaprenyl pyrophosphate synthase [Lipid metabolism]; Region: UppS; COG0020 684950003234 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 684950003235 catalytic residue [active] 684950003236 putative FPP diphosphate binding site; other site 684950003237 putative FPP binding hydrophobic cleft; other site 684950003238 dimer interface [polypeptide binding]; other site 684950003239 putative IPP diphosphate binding site; other site 684950003240 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 684950003241 FAD binding domain; Region: FAD_binding_4; pfam01565 684950003242 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 684950003243 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 684950003244 active site residue [active] 684950003245 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 684950003246 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 684950003247 active site 684950003248 camphor resistance protein CrcB; Provisional; Region: PRK14204 684950003249 coproporphyrinogen III oxidase; Provisional; Region: PRK08446 684950003250 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 684950003251 FeS/SAM binding site; other site 684950003252 HemN C-terminal domain; Region: HemN_C; pfam06969 684950003253 Cytochrome c553 [Energy production and conversion]; Region: COG2863 684950003254 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 684950003255 putative active site [active] 684950003256 Ap4A binding site [chemical binding]; other site 684950003257 nudix motif; other site 684950003258 putative metal binding site [ion binding]; other site 684950003259 aspartate kinase; Reviewed; Region: PRK06635 684950003260 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 684950003261 putative nucleotide binding site [chemical binding]; other site 684950003262 putative catalytic residues [active] 684950003263 putative Mg ion binding site [ion binding]; other site 684950003264 putative aspartate binding site [chemical binding]; other site 684950003265 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 684950003266 putative allosteric regulatory site; other site 684950003267 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 684950003268 putative allosteric regulatory residue; other site 684950003269 DNA replication regulator; Region: HobA; pfam12163 684950003270 DNA polymerase III subunit delta'; Validated; Region: PRK08485 684950003271 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 684950003272 dihydropteroate synthase; Region: DHPS; TIGR01496 684950003273 substrate binding pocket [chemical binding]; other site 684950003274 dimer interface [polypeptide binding]; other site 684950003275 inhibitor binding site; inhibition site 684950003276 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 684950003277 EamA-like transporter family; Region: EamA; pfam00892 684950003278 EamA-like transporter family; Region: EamA; cl17759 684950003279 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl17364 684950003280 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2952 684950003281 Carbamoylphosphate synthase small subunit [Amino acid transport and metabolism / Nucleotide transport and metabolism]; Region: CarA; COG0505 684950003282 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; pfam00988 684950003283 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 684950003284 catalytic site [active] 684950003285 subunit interface [polypeptide binding]; other site 684950003286 formamidase; Provisional; Region: amiF; PRK13287 684950003287 aliphatic amidases (class 2 nitrilases); Region: aliphatic_amidase; cd07565 684950003288 multimer interface [polypeptide binding]; other site 684950003289 active site 684950003290 catalytic triad [active] 684950003291 dimer interface [polypeptide binding]; other site 684950003292 Maf-like protein; Reviewed; Region: PRK04056 684950003293 putative active site [active] 684950003294 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 684950003295 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 684950003296 motif 1; other site 684950003297 active site 684950003298 motif 2; other site 684950003299 motif 3; other site 684950003300 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 684950003301 DHHA1 domain; Region: DHHA1; pfam02272 684950003302 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2841 684950003303 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 684950003304 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 684950003305 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 684950003306 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 684950003307 dimer interface [polypeptide binding]; other site 684950003308 ssDNA binding site [nucleotide binding]; other site 684950003309 tetramer (dimer of dimers) interface [polypeptide binding]; other site 684950003310 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 684950003311 DNA polymerase III subunit delta; Validated; Region: PRK08487 684950003312 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 684950003313 Exoribonuclease R [Transcription]; Region: VacB; COG0557 684950003314 RNB domain; Region: RNB; pfam00773 684950003315 shikimate 5-dehydrogenase; Region: aroE; TIGR00507 684950003316 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 684950003317 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 684950003318 shikimate binding site; other site 684950003319 NAD(P) binding site [chemical binding]; other site 684950003320 Bacterial SH3 domain; Region: SH3_3; pfam08239 684950003321 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4174 684950003322 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 684950003323 dimer interface [polypeptide binding]; other site 684950003324 conserved gate region; other site 684950003325 putative PBP binding loops; other site 684950003326 ABC-ATPase subunit interface; other site 684950003327 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 684950003328 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 684950003329 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 684950003330 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 684950003331 active site 684950003332 HIGH motif; other site 684950003333 dimer interface [polypeptide binding]; other site 684950003334 KMSKS motif; other site 684950003335 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 684950003336 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 684950003337 S-adenosylmethionine binding site [chemical binding]; other site 684950003338 Preprotein translocase subunit SecG [Intracellular trafficking and secretion]; Region: SecG; COG1314 684950003339 ribosome recycling factor; Reviewed; Region: frr; PRK00083 684950003340 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 684950003341 hinge region; other site 684950003342 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 684950003343 active site 684950003344 RDD family; Region: RDD; pfam06271 684950003345 NADH dehydrogenase subunit A; Validated; Region: PRK08489 684950003346 NADH dehydrogenase subunit B; Validated; Region: PRK06411 684950003347 NADH dehydrogenase subunit C; Provisional; Region: PRK08491 684950003348 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 684950003349 NADH dehydrogenase subunit D; Validated; Region: PRK06075 684950003350 NADH dehydrogenase I, D subunit; Region: NuoD; TIGR01962 684950003351 NADH dehydrogenase subunit G; Validated; Region: PRK08493 684950003352 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 684950003353 catalytic loop [active] 684950003354 iron binding site [ion binding]; other site 684950003355 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 684950003356 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 684950003357 molybdopterin cofactor binding site; other site 684950003358 Domain of unknown function (DUF4350); Region: DUF4350; pfam14258 684950003359 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 684950003360 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 684950003361 NADH-quinone oxidoreductase, chain I; Region: NuoI; TIGR01971 684950003362 4Fe-4S binding domain; Region: Fer4; cl02805 684950003363 4Fe-4S binding domain; Region: Fer4; pfam00037 684950003364 NADH:ubiquinone oxidoreductase subunit 6 (chain J) [Energy production and conversion]; Region: NuoJ; COG0839 684950003365 NADH dehydrogenase subunit J; Provisional; Region: PRK06433 684950003366 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 684950003367 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 684950003368 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 684950003369 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 684950003370 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 684950003371 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 684950003372 proton-translocating NADH-quinone oxidoreductase, chain N; Region: NDH_I_N; TIGR01770 684950003373 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 684950003374 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 684950003375 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 684950003376 active site 684950003377 substrate binding site [chemical binding]; other site 684950003378 metal binding site [ion binding]; metal-binding site 684950003379 tryptophan synthase alpha subunit; Provisional; Region: trpA; CHL00200 684950003380 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 684950003381 substrate binding site [chemical binding]; other site 684950003382 active site 684950003383 catalytic residues [active] 684950003384 heterodimer interface [polypeptide binding]; other site 684950003385 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 684950003386 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 684950003387 pyridoxal 5'-phosphate binding site [chemical binding]; other site 684950003388 catalytic residue [active] 684950003389 bifunctional indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase; Provisional; Region: PRK09427 684950003390 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 684950003391 active site 684950003392 ribulose/triose binding site [chemical binding]; other site 684950003393 phosphate binding site [ion binding]; other site 684950003394 substrate (anthranilate) binding pocket [chemical binding]; other site 684950003395 product (indole) binding pocket [chemical binding]; other site 684950003396 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 684950003397 active site 684950003398 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 684950003399 anthranilate phosphoribosyltransferase; Region: trpD; TIGR01245 684950003400 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 684950003401 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 684950003402 Glutamine amidotransferase class-I; Region: GATase; pfam00117 684950003403 glutamine binding [chemical binding]; other site 684950003404 catalytic triad [active] 684950003405 anthranilate synthase component I, proteobacterial subset; Region: trpE_proteo; TIGR00565 684950003406 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 684950003407 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 684950003408 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 684950003409 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 684950003410 putative active site [active] 684950003411 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 684950003412 active site 684950003413 motif I; other site 684950003414 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 684950003415 motif II; other site 684950003416 Uncharacterized conserved protein [Function unknown]; Region: COG2353 684950003417 TENA/THI-4/PQQC family; Region: TENA_THI-4; cl15243 684950003418 Nicotinamide mononucleotide transporter [Coenzyme metabolism]; Region: PnuC; COG3201 684950003419 Thiamine pyrophosphokinase [Coenzyme metabolism]; Region: THI80; COG1564 684950003420 Thiamine pyrophosphokinase; Region: TPK; cd07995 684950003421 active site 684950003422 dimerization interface [polypeptide binding]; other site 684950003423 thiamine binding site [chemical binding]; other site 684950003424 Ribosomal protein L17 [Translation, ribosomal structure and biogenesis]; Region: RplQ; COG0203 684950003425 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 684950003426 alphaNTD homodimer interface [polypeptide binding]; other site 684950003427 DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type; Region: rpoA; TIGR02027 684950003428 alphaNTD - beta interaction site [polypeptide binding]; other site 684950003429 alphaNTD - beta' interaction site [polypeptide binding]; other site 684950003430 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 684950003431 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 684950003432 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 684950003433 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 684950003434 RNA binding surface [nucleotide binding]; other site 684950003435 30S ribosomal protein S11; Validated; Region: PRK05309 684950003436 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 684950003437 30S ribosomal protein S13; Region: bact_S13; TIGR03631 684950003438 Ribosomal protein L36; Region: Ribosomal_L36; cl00380 684950003439 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 684950003440 rRNA binding site [nucleotide binding]; other site 684950003441 predicted 30S ribosome binding site; other site 684950003442 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 684950003443 active site 684950003444 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 684950003445 SecY translocase; Region: SecY; pfam00344 684950003446 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 684950003447 ribosomal protein S5, bacterial/organelle type; Region: rpsE_bact; TIGR01021 684950003448 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 684950003449 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 684950003450 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 684950003451 23S rRNA interface [nucleotide binding]; other site 684950003452 5S rRNA interface [nucleotide binding]; other site 684950003453 L27 interface [polypeptide binding]; other site 684950003454 L5 interface [polypeptide binding]; other site 684950003455 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 684950003456 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 684950003457 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 684950003458 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08061 684950003459 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 684950003460 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 684950003461 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 684950003462 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 684950003463 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 684950003464 RNA binding site [nucleotide binding]; other site 684950003465 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 684950003466 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 684950003467 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 684950003468 putative translocon interaction site; other site 684950003469 23S rRNA interface [nucleotide binding]; other site 684950003470 signal recognition particle (SRP54) interaction site; other site 684950003471 L23 interface [polypeptide binding]; other site 684950003472 trigger factor interaction site; other site 684950003473 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 684950003474 23S rRNA interface [nucleotide binding]; other site 684950003475 5S rRNA interface [nucleotide binding]; other site 684950003476 putative antibiotic binding site [chemical binding]; other site 684950003477 L25 interface [polypeptide binding]; other site 684950003478 L27 interface [polypeptide binding]; other site 684950003479 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 684950003480 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 684950003481 G-X-X-G motif; other site 684950003482 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 684950003483 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 684950003484 putative translocon binding site; other site 684950003485 protein-rRNA interface [nucleotide binding]; other site 684950003486 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 684950003487 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 684950003488 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 684950003489 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 684950003490 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 684950003491 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 684950003492 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 684950003493 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 684950003494 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 684950003495 AAA domain; Region: AAA_14; pfam13173 684950003496 Helix-turn-helix domain; Region: HTH_36; pfam13730 684950003497 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 684950003498 RNA/DNA hybrid binding site [nucleotide binding]; other site 684950003499 active site 684950003500 fumarate hydratase; Reviewed; Region: fumC; PRK00485 684950003501 Class II fumarases; Region: Fumarase_classII; cd01362 684950003502 active site 684950003503 tetramer interface [polypeptide binding]; other site 684950003504 YtkA-like; Region: YtkA; pfam13115 684950003505 Outer membrane efflux protein; Region: OEP; pfam02321 684950003506 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 684950003507 HlyD family secretion protein; Region: HlyD_3; pfam13437 684950003508 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 684950003509 Predicted branched-chain amino acid permeases (azaleucine resistance) [Amino acid transport and metabolism]; Region: AzlD; COG1687 684950003510 AzlC protein; Region: AzlC; cl00570 684950003511 chaperone protein DnaJ; Provisional; Region: PRK14288 684950003512 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 684950003513 HSP70 interaction site [polypeptide binding]; other site 684950003514 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 684950003515 substrate binding site [polypeptide binding]; other site 684950003516 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 684950003517 Zn binding sites [ion binding]; other site 684950003518 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 684950003519 substrate binding site [polypeptide binding]; other site 684950003520 dimer interface [polypeptide binding]; other site 684950003521 tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase; Region: trmU; TIGR00420 684950003522 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 684950003523 Ligand Binding Site [chemical binding]; other site 684950003524 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 684950003525 HSP70 interaction site [polypeptide binding]; other site 684950003526 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 684950003527 Cytidylyltransferase; Region: CTP_transf_2; pfam01467 684950003528 active site 684950003529 (T/H)XGH motif; other site 684950003530 nickel responsive regulator; Provisional; Region: PRK00630 684950003531 Ribbon-helix-helix protein, copG family; Region: RHH_1; pfam01402 684950003532 NikR C terminal nickel binding domain; Region: NikR_C; pfam08753 684950003533 tonB-system energizer ExbB, group 2; Region: exbB2; TIGR02805 684950003534 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 684950003535 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 684950003536 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 684950003537 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 684950003538 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 684950003539 DNA methylase; Region: N6_N4_Mtase; pfam01555 684950003540 Peptidylarginine deiminase and related enzymes [Amino acid transport and metabolism]; Region: COG2957 684950003541 Porphyromonas-type peptidyl-arginine deiminase; Region: PAD_porph; pfam04371 684950003542 Acylphosphatase; Region: Acylphosphatase; pfam00708 684950003543 [NiFe] hydrogenase maturation protein HypF; Region: hypF; TIGR00143 684950003544 HypF finger; Region: zf-HYPF; pfam07503 684950003545 HypF finger; Region: zf-HYPF; pfam07503 684950003546 Telomere recombination; Region: Sua5_yciO_yrdC; pfam01300 684950003547 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 684950003548 dimerization interface [polypeptide binding]; other site 684950003549 hydrogenase expression/formation protein HypE; Region: hypE; TIGR02124 684950003550 ATP binding site [chemical binding]; other site 684950003551 GDP-fucose synthetase, extended (e) SDRs; Region: GDP_FS_SDR_e; cd05239 684950003552 GDP-4-keto-6-deoxymannose-3, 5-epimerase-4-reductase; Region: PLN02725 684950003553 NADP binding site [chemical binding]; other site 684950003554 active site 684950003555 putative substrate binding site [chemical binding]; other site 684950003556 GDP-mannose 4,6-dehydratase; Region: gmd; TIGR01472 684950003557 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 684950003558 NADP-binding site; other site 684950003559 homotetramer interface [polypeptide binding]; other site 684950003560 substrate binding site [chemical binding]; other site 684950003561 homodimer interface [polypeptide binding]; other site 684950003562 active site 684950003563 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 684950003564 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 684950003565 Substrate binding site; other site 684950003566 Mannose-6-phosphate isomerase; Region: MannoseP_isomer; pfam01050 684950003567 Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion]; Region: VirB10; COG2948 684950003568 Type IV secretory pathway, VirB9 components [Intracellular trafficking and secretion]; Region: VirB9; COG3504 684950003569 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 684950003570 VirB7 interaction site; other site 684950003571 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 684950003572 Type IV secretory pathway, TrbL components [Intracellular trafficking and secretion]; Region: TrbL; COG3846 684950003573 PDZ domain; Region: PDZ_2; pfam13180 684950003574 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 684950003575 hypothetical protein; Provisional; Region: PRK03762 684950003576 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 684950003577 tetramerization interface [polypeptide binding]; other site 684950003578 active site 684950003579 ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]; Region: clpA; COG0542 684950003580 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 684950003581 Walker A motif; other site 684950003582 ATP binding site [chemical binding]; other site 684950003583 Walker B motif; other site 684950003584 arginine finger; other site 684950003585 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 684950003586 Walker A motif; other site 684950003587 ATP binding site [chemical binding]; other site 684950003588 Walker B motif; other site 684950003589 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 684950003590 Uncharacterized conserved protein [Function unknown]; Region: COG2127 684950003591 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 684950003592 Ligand Binding Site [chemical binding]; other site 684950003593 Dethiobiotin synthetase [Coenzyme metabolism]; Region: BioD; COG0132 684950003594 AAA domain; Region: AAA_26; pfam13500 684950003595 Protein of unknown function (DUF1523); Region: DUF1523; pfam07509 684950003596 isocitrate dehydrogenase; Validated; Region: PRK07362 684950003597 isocitrate dehydrogenase; Reviewed; Region: PRK07006 684950003598 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 684950003599 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 684950003600 dimer interface [polypeptide binding]; other site 684950003601 active site 684950003602 citrylCoA binding site [chemical binding]; other site 684950003603 NADH binding [chemical binding]; other site 684950003604 cationic pore residues; other site 684950003605 oxalacetate/citrate binding site [chemical binding]; other site 684950003606 coenzyme A binding site [chemical binding]; other site 684950003607 catalytic triad [active] 684950003608 DNA/RNA non-specific endonuclease; prokaryotic and eukaryotic double- and single-stranded DNA and RNA endonucleases also present in phosphodiesterases. They exists as monomers and homodimers; Region: NUC; cl00089 684950003609 potential frameshift: common BLAST hit: gi|210135567|ref|YP_002302006.1| type III R-M system methyltransferase 684950003610 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 684950003611 DNA methylase; Region: N6_N4_Mtase; cl17433 684950003612 DNA methylase; Region: N6_N4_Mtase; pfam01555 684950003613 Type III restriction/modification enzyme methylation subunit; Region: TypeIII_RM_meth; pfam12564 684950003614 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 684950003615 DNA methylase; Region: N6_N4_Mtase; cl17433 684950003616 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3421 684950003617 biotin synthase; Provisional; Region: PRK08508 684950003618 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 684950003619 FeS/SAM binding site; other site 684950003620 Biotin and Thiamin Synthesis associated domain; Region: BATS; pfam06968 684950003621 YihY family inner membrane protein; Region: yihY_not_rbn; TIGR00765 684950003622 Uncharacterized conserved protein [Function unknown]; Region: COG1479 684950003623 Protein of unknown function DUF262; Region: DUF262; pfam03235 684950003624 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 684950003625 7-cyano-7-deazaguanine reductase; Region: QueF-II; TIGR03139 684950003626 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 684950003627 tRNA dimethylallyltransferase; Region: miaA; TIGR00174 684950003628 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 684950003629 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 684950003630 Ligand binding site; other site 684950003631 metal-binding site 684950003632 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13904 684950003633 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 684950003634 flagellar biosynthesis protein FliQ; Validated; Region: fliQ; PRK05700 684950003635 flagellum-specific ATP synthase; Validated; Region: fliI; PRK08472 684950003636 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 684950003637 Walker A motif/ATP binding site; other site 684950003638 Walker B motif; other site 684950003639 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 684950003640 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 684950003641 ATP binding site [chemical binding]; other site 684950003642 Walker A motif; other site 684950003643 hexamer interface [polypeptide binding]; other site 684950003644 Walker B motif; other site 684950003645 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 684950003646 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 684950003647 active site 684950003648 HIGH motif; other site 684950003649 nucleotide binding site [chemical binding]; other site 684950003650 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 684950003651 active site 684950003652 KMSKS motif; other site 684950003653 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 684950003654 tRNA binding surface [nucleotide binding]; other site 684950003655 anticodon binding site; other site 684950003656 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 684950003657 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 684950003658 RNA binding surface [nucleotide binding]; other site 684950003659 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK14462 684950003660 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 684950003661 FeS/SAM binding site; other site 684950003662 KpsF/GutQ family protein; Region: kpsF; TIGR00393 684950003663 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 684950003664 putative active site [active] 684950003665 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 684950003666 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 684950003667 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 684950003668 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 684950003669 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 684950003670 dimethyladenosine transferase; Region: ksgA; TIGR00755 684950003671 S-adenosylmethionine binding site [chemical binding]; other site 684950003672 formyltetrahydrofolate deformylase; Region: PurU; TIGR00655 684950003673 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 684950003674 Formyltransferase, catalytic core domain; Region: FMT_core; cl00395 684950003675 active site 684950003676 substrate binding site [chemical binding]; other site 684950003677 cosubstrate binding site; other site 684950003678 catalytic site [active] 684950003679 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 684950003680 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 684950003681 tandem repeat interface [polypeptide binding]; other site 684950003682 oligomer interface [polypeptide binding]; other site 684950003683 active site residues [active] 684950003684 TIR domain; Region: TIR_2; pfam13676 684950003685 rod shape-determining protein MreC; Provisional; Region: PRK13922 684950003686 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 684950003687 active site 684950003688 carbon storage regulator; Provisional; Region: PRK00568 684950003689 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: PRK04181 684950003690 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 684950003691 SmpB-tmRNA interface; other site 684950003692 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; pfam01618 684950003693 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 684950003694 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 684950003695 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 684950003696 ribonuclease P protein component, eubacterial; Region: rnpA; TIGR00188 684950003697 hypothetical protein; Provisional; Region: PRK14374 684950003698 membrane protein insertase; Provisional; Region: PRK01318 684950003699 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 684950003700 Predicted RNA-binding protein [General function prediction only]; Region: Jag; COG1847 684950003701 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 684950003702 tRNA modification GTPase TrmE; Region: mnmE_trmE_thdF; TIGR00450 684950003703 Circularly permuted YlqF-related GTPases; Region: YlqF_related_GTPase; cl17249 684950003704 GTP/Mg2+ binding site [chemical binding]; other site 684950003705 G4 box; other site 684950003706 G5 box; other site 684950003707 trmE is a tRNA modification GTPase; Region: trmE; cd04164 684950003708 G1 box; other site 684950003709 G1 box; other site 684950003710 GTP/Mg2+ binding site [chemical binding]; other site 684950003711 Switch I region; other site 684950003712 Switch I region; other site 684950003713 G2 box; other site 684950003714 G2 box; other site 684950003715 Switch II region; other site 684950003716 G3 box; other site 684950003717 G3 box; other site 684950003718 Switch II region; other site 684950003719 G4 box; other site 684950003720 G5 box; other site 684950003721 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 684950003722 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 684950003723 LPP20 lipoprotein; Region: LPP20; pfam02169 684950003724 Collagen-binding surface adhesin SpaP (antigen I/II family) [General function prediction only]; Region: FlgN; COG3417 684950003725 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 684950003726 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 684950003727 catalytic residues [active] 684950003728 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 684950003729 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 684950003730 RNA binding surface [nucleotide binding]; other site 684950003731 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 684950003732 active site 684950003733 Cytochrome c peroxidase [Inorganic ion transport and metabolism]; Region: MauG; COG1858 684950003734 Heat shock protein [Posttranslational modification, protein turnover, chaperones]; Region: HslJ; COG3187 684950003735 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 684950003736 mce related protein; Region: MCE; pfam02470 684950003737 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 684950003738 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 684950003739 Walker A/P-loop; other site 684950003740 ATP binding site [chemical binding]; other site 684950003741 Q-loop/lid; other site 684950003742 ABC transporter signature motif; other site 684950003743 Walker B; other site 684950003744 D-loop; other site 684950003745 H-loop/switch region; other site 684950003746 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 684950003747 conserved hypothetical integral membrane protein; Region: TIGR00056 684950003748 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 684950003749 branched-chain amino acid aminotransferase; Provisional; Region: PRK13357 684950003750 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 684950003751 homodimer interface [polypeptide binding]; other site 684950003752 substrate-cofactor binding pocket; other site 684950003753 catalytic residue [active] 684950003754 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 684950003755 DNA polymerase I; Region: pola; TIGR00593 684950003756 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 684950003757 active site 684950003758 metal binding site 1 [ion binding]; metal-binding site 684950003759 putative 5' ssDNA interaction site; other site 684950003760 metal binding site 3; metal-binding site 684950003761 metal binding site 2 [ion binding]; metal-binding site 684950003762 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 684950003763 putative DNA binding site [nucleotide binding]; other site 684950003764 putative metal binding site [ion binding]; other site 684950003765 3'-5' exonuclease; Region: 35EXOc; smart00474 684950003766 active site 684950003767 substrate binding site [chemical binding]; other site 684950003768 catalytic site [active] 684950003769 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 684950003770 active site 684950003771 DNA binding site [nucleotide binding] 684950003772 catalytic site [active] 684950003773 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 684950003774 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 684950003775 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 684950003776 DNA-methyltransferase (dcm); Region: dcm; TIGR00675 684950003777 cofactor binding site; other site 684950003778 DNA binding site [nucleotide binding] 684950003779 substrate interaction site [chemical binding]; other site 684950003780 Eco47II restriction endonuclease; Region: RE_Eco47II; pfam09553 684950003781 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 684950003782 thymidylate kinase; Validated; Region: tmk; PRK00698 684950003783 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 684950003784 TMP-binding site; other site 684950003785 ATP-binding site [chemical binding]; other site 684950003786 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 684950003787 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 684950003788 active site 684950003789 (T/H)XGH motif; other site 684950003790 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Provisional; Region: PRK06029 684950003791 Flavoprotein; Region: Flavoprotein; pfam02441 684950003792 flagellar basal body P-ring biosynthesis protein FlgA; Reviewed; Region: flgA; PRK08515 684950003793 flagella basal body P-ring formation protein FlgA; Region: flgA_cterm; TIGR03170 684950003794 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 684950003795 Part of AAA domain; Region: AAA_19; pfam13245 684950003796 Family description; Region: UvrD_C_2; pfam13538 684950003797 TPR repeat; Region: TPR_11; pfam13414 684950003798 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 684950003799 TPR motif; other site 684950003800 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 684950003801 binding surface 684950003802 TPR motif; other site 684950003803 seryl-tRNA synthetase; Provisional; Region: PRK05431 684950003804 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 684950003805 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 684950003806 dimer interface [polypeptide binding]; other site 684950003807 active site 684950003808 motif 1; other site 684950003809 motif 2; other site 684950003810 motif 3; other site 684950003811 Predicted amidohydrolase [General function prediction only]; Region: COG0388 684950003812 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cd07197 684950003813 active site 684950003814 catalytic triad [active] 684950003815 dimer interface [polypeptide binding]; other site 684950003816 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK14065 684950003817 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 684950003818 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 684950003819 S-adenosylmethionine binding site [chemical binding]; other site 684950003820 Uncharacterized protein family (UPF0093); Region: UPF0093; cl00863 684950003821 uncharacterized protein, YigZ family; Region: IMPACT_YIGZ; TIGR00257 684950003822 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 684950003823 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 684950003824 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 684950003825 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 684950003826 ABC-2 type transporter; Region: ABC2_membrane; cl17235 684950003827 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 684950003828 HlyD family secretion protein; Region: HlyD_3; pfam13437 684950003829 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 684950003830 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 684950003831 Domain of unknown function DUF21; Region: DUF21; pfam01595 684950003832 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 684950003833 Transporter associated domain; Region: CorC_HlyC; smart01091 684950003834 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 684950003835 Phosphate transporter family; Region: PHO4; pfam01384 684950003836 NifU-like domain; Region: NifU; pfam01106 684950003837 UDP-N-acetylmuramyl-tripeptide synthetase; Region: murE; TIGR01085 684950003838 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 684950003839 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 684950003840 Transaldolase-like proteins from plants and bacteria; Region: Transaldolase_like; cd00955 684950003841 putative active site [active] 684950003842 transaldolase; Provisional; Region: PRK03903 684950003843 catalytic residue [active] 684950003844 ribosomal protein L25, Ctc-form; Region: ctc_TL5; TIGR00731 684950003845 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 684950003846 5S rRNA interface [nucleotide binding]; other site 684950003847 CTC domain interface [polypeptide binding]; other site 684950003848 L16 interface [polypeptide binding]; other site 684950003849 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 684950003850 putative active site [active] 684950003851 catalytic residue [active] 684950003852 Predicted permeases [General function prediction only]; Region: COG0795 684950003853 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 684950003854 Catalytic domain of type II restriction endonucleases BfiI and NgoFVII, and uncharacterized proteins with a DEAD domain; Region: PLDc_Bfil_DEXD_like; cd09117 684950003855 PLD-like domain; Region: PLDc_2; pfam13091 684950003856 homodimer interface [polypeptide binding]; other site 684950003857 putative active site [active] 684950003858 catalytic site [active] 684950003859 Uncharacterized conserved protein (DUF2161); Region: DUF2161; cl02298 684950003860 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 684950003861 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3399 684950003862 Putative metal-binding domain of cation transport ATPase; Region: ATPase-cat_bd; pfam12156 684950003863 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 684950003864 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 684950003865 metal-binding site [ion binding] 684950003866 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 684950003867 Soluble P-type ATPase [General function prediction only]; Region: COG4087 684950003868 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 684950003869 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 684950003870 S-adenosylmethionine binding site [chemical binding]; other site 684950003871 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 684950003872 catalytic motif [active] 684950003873 Zn binding site [ion binding]; other site 684950003874 Pyrimidine reductase, riboflavin biosynthesis [Coenzyme metabolism]; Region: RibD; COG1985 684950003875 RibD C-terminal domain; Region: RibD_C; cl17279 684950003876 sodium--glutamate symport carrier (gltS); Region: gltS; TIGR00210 684950003877 Saccharopine dehydrogenase and related proteins [Amino acid transport and metabolism]; Region: LYS9; COG1748 684950003878 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 684950003879 4Fe-4S binding domain; Region: Fer4_5; pfam12801 684950003880 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 684950003881 acyl-phosphate glycerol 3-phosphate acyltransferase; Region: TIGR00023 684950003882 FolB domain; Region: folB_dom; TIGR00526 684950003883 active site 684950003884 TonB-dependent Receptor Plug Domain; Region: Plug; cl08461 684950003885 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 684950003886 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 684950003887 Selenocysteine synthase [seryl-tRNASer selenium transferase] [Amino acid transport and metabolism]; Region: SelA; COG1921 684950003888 L-seryl-tRNA selenium transferase; Region: SelA; pfam03841 684950003889 transcription elongation factor NusA; Provisional; Region: nusA; PRK12328 684950003890 NusA N-terminal domain; Region: NusA_N; pfam08529 684950003891 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 684950003892 RNA binding site [nucleotide binding]; other site 684950003893 homodimer interface [polypeptide binding]; other site 684950003894 NusA-like KH domain; Region: KH_5; pfam13184 684950003895 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 684950003896 G-X-X-G motif; other site 684950003897 Type II restriction enzyme, methylase subunits [Defense mechanisms]; Region: COG1002 684950003898 Eco57I restriction-modification methylase; Region: Eco57I; pfam07669 684950003899 TaqI-like C-terminal specificity domain; Region: TaqI_C; pfam12950 684950003900 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cd00267 684950003901 ABC transporter signature motif; other site 684950003902 Walker B; other site 684950003903 D-loop; other site 684950003904 H-loop/switch region; other site 684950003905 Restriction endonuclease [Defense mechanisms]; Region: COG3587 684950003906 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 684950003907 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 684950003908 DNA methylase; Region: N6_N4_Mtase; pfam01555 684950003909 DNA methylase; Region: N6_N4_Mtase; pfam01555 684950003910 ATP-dependent DNA helicase RecG; Region: recG; TIGR00643 684950003911 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 684950003912 ssDNA binding site; other site 684950003913 generic binding surface II; other site 684950003914 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 684950003915 ATP binding site [chemical binding]; other site 684950003916 putative Mg++ binding site [ion binding]; other site 684950003917 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 684950003918 nucleotide binding region [chemical binding]; other site 684950003919 ATP-binding site [chemical binding]; other site 684950003920 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 684950003921 Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Ape1-like_AP-endo; cd09087 684950003922 active site 684950003923 putative catalytic site [active] 684950003924 DNA binding site [nucleotide binding] 684950003925 putative phosphate binding site [ion binding]; other site 684950003926 metal binding site A [ion binding]; metal-binding site 684950003927 AP binding site [nucleotide binding]; other site 684950003928 metal binding site B [ion binding]; metal-binding site 684950003929 chromosomal replication initiator protein DnaA; Region: DnaA; TIGR00362 684950003930 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 684950003931 Walker A motif; other site 684950003932 ATP binding site [chemical binding]; other site 684950003933 Walker B motif; other site 684950003934 arginine finger; other site 684950003935 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 684950003936 DnaA box-binding interface [nucleotide binding]; other site 684950003937 Nucleoside phosphorylase [Nucleotide transport and metabolism]; Region: Pfs; COG0775 684950003938 Protein of unknown function (DUF2443); Region: DUF2443; pfam10398 684950003939 glucosamine--fructose-6-phosphate aminotransferase (isomerizing); Region: glmS; TIGR01135 684950003940 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 684950003941 glutaminase active site [active] 684950003942 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 684950003943 dimer interface [polypeptide binding]; other site 684950003944 active site 684950003945 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 684950003946 dimer interface [polypeptide binding]; other site 684950003947 active site 684950003948 Predicted alternative thymidylate synthase [Nucleotide transport and metabolism]; Region: THY1; COG1351 684950003949 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 684950003950 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 684950003951 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 684950003952 HsdM N-terminal domain; Region: HsdM_N; pfam12161 684950003953 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 684950003954 type I site-specific deoxyribonuclease, HsdR family; Region: hsdR; TIGR00348 684950003955 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 684950003956 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 684950003957 ATP binding site [chemical binding]; other site 684950003958 putative Mg++ binding site [ion binding]; other site 684950003959 Protein of unknown function DUF45; Region: DUF45; pfam01863 684950003960 Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]; Region: FecA; COG4772 684950003961 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 684950003962 N-terminal plug; other site 684950003963 ligand-binding site [chemical binding]; other site 684950003964 Arginase family; Region: Arginase; cd09989 684950003965 active site 684950003966 Mn binding site [ion binding]; other site 684950003967 oligomer interface [polypeptide binding]; other site 684950003968 S-methylmethionine transporter; Provisional; Region: PRK11387 684950003969 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 684950003970 Alanine dehydrogenase NAD-binding and catalytic domains; Region: L-AlaDH; cd05305 684950003971 hexamer interface [polypeptide binding]; other site 684950003972 ligand binding site [chemical binding]; other site 684950003973 putative active site [active] 684950003974 NAD(P) binding site [chemical binding]; other site 684950003975 Protein of unknown function DUF262; Region: DUF262; pfam03235 684950003976 Uncharacterized conserved protein [Function unknown]; Region: COG1479 684950003977 Protein of unknown function DUF262; Region: DUF262; pfam03235 684950003978 Uncharacterized conserved protein [Function unknown]; Region: COG1479 684950003979 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 684950003980 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 684950003981 NAD kinase [Coenzyme metabolism]; Region: nadF; COG0061 684950003982 ATP-NAD kinase; Region: NAD_kinase; pfam01513 684950003983 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 684950003984 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 684950003985 Walker A/P-loop; other site 684950003986 ATP binding site [chemical binding]; other site 684950003987 Q-loop/lid; other site 684950003988 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 684950003989 ABC transporter signature motif; other site 684950003990 Walker B; other site 684950003991 D-loop; other site 684950003992 H-loop/switch region; other site 684950003993 Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]; Region: COG1293 684950003994 Domain of unknown function (DUF814); Region: DUF814; pfam05670 684950003995 DNA polymerase III subunit epsilon; Provisional; Region: PRK08517 684950003996 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 684950003997 active site 684950003998 catalytic site [active] 684950003999 substrate binding site [chemical binding]; other site 684950004000 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 684950004001 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 684950004002 substrate binding site [chemical binding]; other site 684950004003 hexamer interface [polypeptide binding]; other site 684950004004 metal binding site [ion binding]; metal-binding site 684950004005 Fructose-1,6-bisphosphatase [Carbohydrate transport and metabolism]; Region: Fbp; COG0158 684950004006 active site 684950004007 Methyltransferase domain; Region: Methyltransf_26; pfam13659 684950004008 elongation factor Ts; Provisional; Region: tsf; PRK09377 684950004009 UBA/TS-N domain; Region: UBA; pfam00627 684950004010 Elongation factor TS; Region: EF_TS; pfam00889 684950004011 Elongation factor TS; Region: EF_TS; pfam00889 684950004012 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 684950004013 rRNA interaction site [nucleotide binding]; other site 684950004014 S8 interaction site; other site 684950004015 putative laminin-1 binding site; other site 684950004016 putative recombination protein RecB; Provisional; Region: PRK13909 684950004017 Family description; Region: UvrD_C_2; pfam13538 684950004018 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 684950004019 pH-dependent sodium/proton antiporter; Provisional; Region: nhaA; PRK14856 684950004020 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 684950004021 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 684950004022 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 684950004023 protein-export membrane protein SecF; Region: 3a0501s07; TIGR00966 684950004024 Protein export membrane protein; Region: SecD_SecF; pfam02355 684950004025 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 684950004026 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 684950004027 HIGH motif; other site 684950004028 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 684950004029 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 684950004030 active site 684950004031 KMSKS motif; other site 684950004032 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 684950004033 tRNA binding surface [nucleotide binding]; other site 684950004034 Lipopolysaccharide-assembly; Region: LptE; pfam04390 684950004035 folylpolyglutamate synthase/dihydrofolate synthase; Region: folC; TIGR01499 684950004036 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 684950004037 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 684950004038 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 684950004039 Peptidase family M23; Region: Peptidase_M23; pfam01551 684950004040 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 684950004041 Peptidase family M23; Region: Peptidase_M23; pfam01551 684950004042 Integral membrane protein CcmA involved in cell shape determination [Cell envelope biogenesis, outer membrane]; Region: CcmA; COG1664 684950004043 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 684950004044 transcription-repair coupling factor (mfd); Region: mfd; TIGR00580 684950004045 CarD-like/TRCF domain; Region: CarD_CdnL_TRCF; pfam02559 684950004046 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 684950004047 ATP binding site [chemical binding]; other site 684950004048 putative Mg++ binding site [ion binding]; other site 684950004049 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 684950004050 nucleotide binding region [chemical binding]; other site 684950004051 ATP-binding site [chemical binding]; other site 684950004052 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 684950004053 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 684950004054 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes; Region: Rieske; cl00938 684950004055 iron-sulfur cluster [ion binding]; other site 684950004056 [2Fe-2S] cluster binding site [ion binding]; other site 684950004057 Cytochrome b subunit of the bc complex [Energy production and conversion]; Region: QcrB; COG1290 684950004058 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 684950004059 intrachain domain interface; other site 684950004060 interchain domain interface [polypeptide binding]; other site 684950004061 heme bH binding site [chemical binding]; other site 684950004062 Qi binding site; other site 684950004063 heme bL binding site [chemical binding]; other site 684950004064 Qo binding site; other site 684950004065 interchain domain interface [polypeptide binding]; other site 684950004066 intrachain domain interface; other site 684950004067 Qi binding site; other site 684950004068 Cytochrome b(C-terminal)/b6/petD; Region: Cytochrom_B_C; pfam00032 684950004069 Qo binding site; other site 684950004070 Cytochrome c1 [Energy production and conversion]; Region: CYT1; COG2857 684950004071 Cytochrome c; Region: Cytochrom_C; pfam00034 684950004072 Cytochrome c; Region: Cytochrom_C; cl11414 684950004073 potential frameshift: common BLAST hit: gi|315454048|ref|YP_004074318.1| sulfatase 684950004074 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 684950004075 Sulfatase; Region: Sulfatase; cl17466 684950004076 Sulfatase; Region: Sulfatase; cl17466 684950004077 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 684950004078 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 684950004079 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 684950004080 flagellar hook-basal body protein FliE; Reviewed; Region: fliE; PRK03907 684950004081 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 684950004082 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 684950004083 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK05680 684950004084 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK07182 684950004085 Cell cycle protein; Region: FTSW_RODA_SPOVE; pfam01098 684950004086 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 684950004087 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 684950004088 putative ligand binding site [chemical binding]; other site 684950004089 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 684950004090 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 684950004091 intersubunit interface [polypeptide binding]; other site 684950004092 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 684950004093 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 684950004094 dimer interface [polypeptide binding]; other site 684950004095 decamer (pentamer of dimers) interface [polypeptide binding]; other site 684950004096 catalytic triad [active] 684950004097 peroxidatic and resolving cysteines [active] 684950004098 ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]; Region: NlpA; COG1464 684950004099 NLPA lipoprotein; Region: Lipoprotein_9; pfam03180 684950004100 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 684950004101 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 684950004102 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 684950004103 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 684950004104 G1 box; other site 684950004105 GTP/Mg2+ binding site [chemical binding]; other site 684950004106 Switch I region; other site 684950004107 G2 box; other site 684950004108 G3 box; other site 684950004109 Switch II region; other site 684950004110 G4 box; other site 684950004111 G5 box; other site 684950004112 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1934 684950004113 OstA-like protein; Region: OstA; pfam03968 684950004114 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 684950004115 motif II; other site 684950004116 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 684950004117 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 684950004118 Sporulation related domain; Region: SPOR; pfam05036 684950004119 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 684950004120 N-acetyl-D-glucosamine binding site [chemical binding]; other site 684950004121 catalytic residue [active] 684950004122 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 684950004123 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 684950004124 active site 684950004125 riboflavin synthase, alpha subunit; Region: ribE; TIGR00187 684950004126 Lumazine binding domain; Region: Lum_binding; pfam00677 684950004127 Lumazine binding domain; Region: Lum_binding; pfam00677 684950004128 flhB C-terminus-related protein; Region: flhB_rel; TIGR00789 684950004129 DL-methionine transporter ATP-binding subunit; Provisional; Region: metN; PRK11153 684950004130 ATP-binding cassette domain of methionine transporter; Region: ABC_MetN_methionine_transporter; cd03258 684950004131 Walker A/P-loop; other site 684950004132 ATP binding site [chemical binding]; other site 684950004133 Q-loop/lid; other site 684950004134 ABC transporter signature motif; other site 684950004135 Walker B; other site 684950004136 D-loop; other site 684950004137 H-loop/switch region; other site 684950004138 NIL domain; Region: NIL; pfam09383 684950004139 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; cl00427 684950004140 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 684950004141 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 684950004142 active site 684950004143 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 684950004144 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 684950004145 Mg++ binding site [ion binding]; other site 684950004146 putative catalytic motif [active] 684950004147 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 684950004148 active site 684950004149 hydrophilic channel; other site 684950004150 dimerization interface [polypeptide binding]; other site 684950004151 catalytic residues [active] 684950004152 active site lid [active] 684950004153 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 684950004154 4-hydroxythreonine-4-phosphate dehydrogenase; Provisional; Region: pdxA; PRK03946 684950004155 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 684950004156 metallohydrolase, glycoprotease/Kae1 family; Region: gcp_kae1; TIGR00329 684950004157 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 684950004158 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 684950004159 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 684950004160 hypothetical protein; Provisional; Region: PRK10236 684950004161 Domain of unknown function (DUF3944); Region: DUF3944; pfam13099 684950004162 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4735