-- dump date 20140619_112340 -- class Genbank::misc_feature -- table misc_feature_note -- id note 1216962000001 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 1216962000002 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 1216962000003 ligand binding site [chemical binding]; other site 1216962000004 CHASE3 domain; Region: CHASE3; cl05000 1216962000005 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 1216962000006 FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]; Region: SlpA; COG1047 1216962000007 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 1216962000008 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 1216962000009 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 1216962000010 nucleotide binding pocket [chemical binding]; other site 1216962000011 K-X-D-G motif; other site 1216962000012 catalytic site [active] 1216962000013 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 1216962000014 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 1216962000015 Dimer interface [polypeptide binding]; other site 1216962000016 BRCT sequence motif; other site 1216962000017 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 1216962000018 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 1216962000019 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 1216962000020 active site 1216962000021 phosphorylation site [posttranslational modification] 1216962000022 intermolecular recognition site; other site 1216962000023 dimerization interface [polypeptide binding]; other site 1216962000024 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 1216962000025 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 1216962000026 motif 2; other site 1216962000027 GAD domain; Region: GAD; pfam02938 1216962000028 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 1216962000029 active site 1216962000030 motif 3; other site 1216962000031 adenylate kinase; Reviewed; Region: adk; PRK00279 1216962000032 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 1216962000033 AMP-binding site [chemical binding]; other site 1216962000034 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 1216962000035 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 1216962000036 dimer interface [polypeptide binding]; other site 1216962000037 substrate binding site [chemical binding]; other site 1216962000038 metal binding sites [ion binding]; metal-binding site 1216962000039 anthranilate synthase component I; Provisional; Region: PRK13564 1216962000040 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 1216962000041 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 1216962000042 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 1216962000043 Glutamine amidotransferase class-I; Region: GATase; pfam00117 1216962000044 glutamine binding [chemical binding]; other site 1216962000045 catalytic triad [active] 1216962000046 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1216962000047 AcrB/AcrD/AcrF family; Region: ACR_tran; pfam00873 1216962000048 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1216962000049 HlyD family secretion protein; Region: HlyD_3; pfam13437 1216962000050 type I secretion outer membrane protein, TolC family; Region: type_I_sec_TolC; TIGR01844 1216962000051 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 1216962000052 IHF dimer interface [polypeptide binding]; other site 1216962000053 IHF - DNA interface [nucleotide binding]; other site 1216962000054 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; pfam00044 1216962000055 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 1216962000056 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 1216962000057 Phosphoglycerate kinase (PGK) is a monomeric enzyme which catalyzes the transfer of the high-energy phosphate group of 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate. This reaction represents the first of the two substrate-level...; Region: Phosphoglycerate_kinase; cl00198 1216962000058 ADP binding site [chemical binding]; other site 1216962000059 catalytic site [active] 1216962000060 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 1216962000061 metal ion transporter CorA-like divalent cation transporter superfamily; Region: MIT_CorA-like; cl00459 1216962000062 oligomer interface [polypeptide binding]; other site 1216962000063 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3295 1216962000064 Phosphoglycerate kinase (PGK) is a monomeric enzyme which catalyzes the transfer of the high-energy phosphate group of 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate. This reaction represents the first of the two substrate-level...; Region: Phosphoglycerate_kinase; cl00198 1216962000065 hinge regions; other site 1216962000066 ADP binding site [chemical binding]; other site 1216962000067 catalytic site [active] 1216962000068 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 1216962000069 metal ion transporter CorA-like divalent cation transporter superfamily; Region: MIT_CorA-like; cl00459 1216962000070 oligomer interface [polypeptide binding]; other site 1216962000071 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3295 1216962000072 Glutathionylspermidine synthase [Amino acid transport and metabolism]; Region: Gsp; COG0754 1216962000073 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 1216962000074 Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]; Region: Rpe; COG0036 1216962000075 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 1216962000076 substrate binding site [chemical binding]; other site 1216962000077 hexamer interface [polypeptide binding]; other site 1216962000078 metal binding site [ion binding]; metal-binding site 1216962000079 DNA polymerase III subunit epsilon; Provisional; Region: PRK08517 1216962000080 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 1216962000081 active site 1216962000082 catalytic site [active] 1216962000083 substrate binding site [chemical binding]; other site 1216962000084 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 1216962000085 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1216962000086 dimer interface [polypeptide binding]; other site 1216962000087 putative CheW interface [polypeptide binding]; other site 1216962000088 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 1216962000089 Clp amino terminal domain; Region: Clp_N; pfam02861 1216962000090 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 1216962000091 Walker A motif; other site 1216962000092 ATP binding site [chemical binding]; other site 1216962000093 Walker B motif; other site 1216962000094 arginine finger; other site 1216962000095 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 1216962000096 Walker A motif; other site 1216962000097 ATP binding site [chemical binding]; other site 1216962000098 Walker B motif; other site 1216962000099 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 1216962000100 SurA N-terminal domain; Region: SurA_N; pfam09312 1216962000101 PPIC-type PPIASE domain; Region: Rotamase_2; cl08278 1216962000102 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 1216962000103 binding surface 1216962000104 Tetratricopeptide repeat; Region: TPR_16; pfam13432 1216962000105 TPR motif; other site 1216962000106 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 1216962000107 RNA/DNA hybrid binding site [nucleotide binding]; other site 1216962000108 active site 1216962000109 ribonuclease III; Reviewed; Region: rnc; PRK00102 1216962000110 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 1216962000111 dimerization interface [polypeptide binding]; other site 1216962000112 active site 1216962000113 metal binding site [ion binding]; metal-binding site 1216962000114 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 1216962000115 dsRNA binding site [nucleotide binding]; other site 1216962000116 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 1216962000117 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 1216962000118 Tetramer interface [polypeptide binding]; other site 1216962000119 active site 1216962000120 FMN-binding site [chemical binding]; other site 1216962000121 Protein of unknown function (DUF2603); Region: DUF2603; pfam10788 1216962000122 coproporphyrinogen III oxidase; Provisional; Region: PRK09249 1216962000123 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 1216962000124 FeS/SAM binding site; other site 1216962000125 HemN C-terminal domain; Region: HemN_C; pfam06969 1216962000126 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 1216962000127 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 1216962000128 Cysteine-rich domain; Region: CCG; pfam02754 1216962000129 Cysteine-rich domain; Region: CCG; pfam02754 1216962000130 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1216962000131 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 1216962000132 4Fe-4S binding domain; Region: Fer4_5; pfam12801 1216962000133 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 1216962000134 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 1216962000135 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 1216962000136 Major Facilitator Superfamily; Region: MFS_1; pfam07690 1216962000137 putative substrate translocation pore; other site 1216962000138 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 1216962000139 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1216962000140 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 1216962000141 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1216962000142 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1216962000143 Walker A/P-loop; other site 1216962000144 ATP binding site [chemical binding]; other site 1216962000145 Q-loop/lid; other site 1216962000146 ABC transporter signature motif; other site 1216962000147 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1216962000148 Walker B; other site 1216962000149 D-loop; other site 1216962000150 ABC transporter; Region: ABC_tran_2; pfam12848 1216962000151 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 1216962000152 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1216962000153 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 1216962000154 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 1216962000155 putative active site [active] 1216962000156 putative metal binding site [ion binding]; other site 1216962000157 tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; Region: COG0042 1216962000158 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 1216962000159 FMN binding site [chemical binding]; other site 1216962000160 active site 1216962000161 catalytic residues [active] 1216962000162 substrate binding site [chemical binding]; other site 1216962000163 tRNA CCA-pyrophosphorylase; Provisional; Region: PRK13299 1216962000164 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 1216962000165 active site 1216962000166 NTP binding site [chemical binding]; other site 1216962000167 metal binding triad [ion binding]; metal-binding site 1216962000168 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 1216962000169 tRNA nucleotidyltransferase domain 2 putative; Region: tRNA_NucTran2_2; pfam13735 1216962000170 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 1216962000171 Ligand Binding Site [chemical binding]; other site 1216962000172 chaperone protein DnaJ; Provisional; Region: PRK14299 1216962000173 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 1216962000174 HSP70 interaction site [polypeptide binding]; other site 1216962000175 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 1216962000176 substrate binding site [polypeptide binding]; other site 1216962000177 dimer interface [polypeptide binding]; other site 1216962000178 Helix-Turn-Helix DNA binding domain of the HspR transcription regulator; Region: HTH_HspR; cd04766 1216962000179 Predicted transcriptional regulators [Transcription]; Region: SoxR; COG0789 1216962000180 DNA binding residues [nucleotide binding] 1216962000181 Uncharacterized conserved protein [Function unknown]; Region: COG1565 1216962000182 excinuclease ABC subunit B; Provisional; Region: PRK05298 1216962000183 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 1216962000184 ATP binding site [chemical binding]; other site 1216962000185 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 1216962000186 nucleotide binding region [chemical binding]; other site 1216962000187 ATP-binding site [chemical binding]; other site 1216962000188 Ultra-violet resistance protein B; Region: UvrB; pfam12344 1216962000189 UvrB/uvrC motif; Region: UVR; pfam02151 1216962000190 excinuclease ABC subunit B; Provisional; Region: PRK05298 1216962000191 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 1216962000192 ATP binding site [chemical binding]; other site 1216962000193 primosome assembly protein PriA; Validated; Region: PRK05580 1216962000194 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 1216962000195 ATP binding site [chemical binding]; other site 1216962000196 putative Mg++ binding site [ion binding]; other site 1216962000197 helicase superfamily c-terminal domain; Region: HELICc; smart00490 1216962000198 GMP synthase; Reviewed; Region: guaA; PRK00074 1216962000199 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 1216962000200 AMP/PPi binding site [chemical binding]; other site 1216962000201 candidate oxyanion hole; other site 1216962000202 catalytic triad [active] 1216962000203 potential glutamine specificity residues [chemical binding]; other site 1216962000204 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 1216962000205 ATP Binding subdomain [chemical binding]; other site 1216962000206 Ligand Binding sites [chemical binding]; other site 1216962000207 Dimerization subdomain; other site 1216962000208 heat shock protein 90; Provisional; Region: PRK05218 1216962000209 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 1216962000210 ATP binding site [chemical binding]; other site 1216962000211 Mg2+ binding site [ion binding]; other site 1216962000212 G-X-G motif; other site 1216962000213 Formyltransferase, catalytic core domain; Region: FMT_core; cl00395 1216962000214 active site 1216962000215 substrate binding site [chemical binding]; other site 1216962000216 cosubstrate binding site; other site 1216962000217 catalytic site [active] 1216962000218 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 1216962000219 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 1216962000220 heat shock protein 90; Provisional; Region: PRK05218 1216962000221 Formyltransferase, catalytic core domain; Region: FMT_core; cl00395 1216962000222 active site 1216962000223 substrate binding site [chemical binding]; other site 1216962000224 cosubstrate binding site; other site 1216962000225 catalytic site [active] 1216962000226 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 1216962000227 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 1216962000228 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1216962000229 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1216962000230 ABC transporter signature motif; other site 1216962000231 Walker B; other site 1216962000232 D-loop; other site 1216962000233 H-loop/switch region; other site 1216962000234 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 1216962000235 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 1216962000236 active site 1216962000237 substrate binding site [chemical binding]; other site 1216962000238 metal binding site [ion binding]; metal-binding site 1216962000239 Mycolic acid cyclopropane synthetase; Region: CMAS; pfam02353 1216962000240 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 1216962000241 S-adenosylmethionine binding site [chemical binding]; other site 1216962000242 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 1216962000243 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 1216962000244 dimerization interface [polypeptide binding]; other site 1216962000245 DPS ferroxidase diiron center [ion binding]; other site 1216962000246 ion pore; other site 1216962000247 Domain of unknown function (DUF2018); Region: DUF2018; pfam09442 1216962000248 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 1216962000249 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 1216962000250 substrate binding pocket [chemical binding]; other site 1216962000251 chain length determination region; other site 1216962000252 substrate-Mg2+ binding site; other site 1216962000253 catalytic residues [active] 1216962000254 aspartate-rich region 1; other site 1216962000255 active site lid residues [active] 1216962000256 aspartate-rich region 2; other site 1216962000257 glutamyl-tRNA reductase; Reviewed; Region: hemA; PRK00045 1216962000258 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 1216962000259 tRNA; other site 1216962000260 putative tRNA binding site [nucleotide binding]; other site 1216962000261 putative NADP binding site [chemical binding]; other site 1216962000262 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 1216962000263 prolyl-tRNA synthetase; Provisional; Region: PRK09194 1216962000264 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 1216962000265 dimer interface [polypeptide binding]; other site 1216962000266 motif 1; other site 1216962000267 active site 1216962000268 motif 2; other site 1216962000269 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 1216962000270 putative deacylase active site [active] 1216962000271 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 1216962000272 active site 1216962000273 motif 3; other site 1216962000274 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 1216962000275 anticodon binding site; other site 1216962000276 FxsA cytoplasmic membrane protein; Region: FxsA; cl01148 1216962000277 Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12. HMBS catalyzes the conversion of...; Region: HMBS; cl17708 1216962000278 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 1216962000279 active site 1216962000280 domain interfaces; other site 1216962000281 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 1216962000282 TrkA-N domain; Region: TrkA_N; pfam02254 1216962000283 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 1216962000284 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 1216962000285 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1216962000286 Type II (periplasmic) bacterial L-asparaginase; Region: L-asparaginase_II; cd08964 1216962000287 active site 1216962000288 homodimer interface [polypeptide binding]; other site 1216962000289 homotetramer interface [polypeptide binding]; other site 1216962000290 flagellar protein FliS; Validated; Region: fliS; PRK05685 1216962000291 flagellar capping protein; Validated; Region: fliD; PRK08453 1216962000292 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 1216962000293 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 1216962000294 FlaG protein; Region: FlaG; cl00591 1216962000295 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]; Region: COG4942 1216962000296 Peptidase family M23; Region: Peptidase_M23; pfam01551 1216962000297 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1216962000298 H-loop/switch region; other site 1216962000299 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 1216962000300 S-adenosylmethionine binding site [chemical binding]; other site 1216962000301 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 1216962000302 Interdomain contacts; other site 1216962000303 Cytokine receptor motif; other site 1216962000304 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 1216962000305 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 1216962000306 RNA binding surface [nucleotide binding]; other site 1216962000307 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 1216962000308 active site 1216962000309 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 1216962000310 ferrous iron transporter FeoB; Region: feoB; TIGR00437 1216962000311 G1 box; other site 1216962000312 GTP/Mg2+ binding site [chemical binding]; other site 1216962000313 Switch I region; other site 1216962000314 G2 box; other site 1216962000315 G3 box; other site 1216962000316 Switch II region; other site 1216962000317 G4 box; other site 1216962000318 G5 box; other site 1216962000319 Nucleoside recognition; Region: Gate; pfam07670 1216962000320 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 1216962000321 Nucleoside recognition; Region: Gate; pfam07670 1216962000322 nonheme-containing ferritins; Region: Nonheme_Ferritin; cd01055 1216962000323 Ferritin-like domain; Region: Ferritin; pfam00210 1216962000324 ferroxidase diiron center [ion binding]; other site 1216962000325 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl14958 1216962000326 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 1216962000327 Methyltransferase domain; Region: Methyltransf_26; pfam13659 1216962000328 oligoendopeptidase, pepF/M3 family; Region: M3_fam_3; TIGR02290 1216962000329 Peptidase family M3B Oligopeptidase F (PepF); Region: M3B_PepF_5; cd09610 1216962000330 active site 1216962000331 Zn binding site [ion binding]; other site 1216962000332 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 1216962000333 N-terminal tellurium resistance protein terB-like domain of heat shock DnaJ-like proteins; Region: terB_like_DjlA; cd07316 1216962000334 putative metal binding site [ion binding]; other site 1216962000335 acetate kinase A/propionate kinase 2; Reviewed; Region: PRK00180 1216962000336 propionate/acetate kinase; Provisional; Region: PRK12379 1216962000337 phosphotransacetylase; Reviewed; Region: eutD; PRK09653 1216962000338 Shikimate kinase [Amino acid transport and metabolism]; Region: AroK; COG0703 1216962000339 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 1216962000340 ADP binding site [chemical binding]; other site 1216962000341 magnesium binding site [ion binding]; other site 1216962000342 putative shikimate binding site; other site 1216962000343 Enolase-superfamily, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion; Region: enolase_like; cl17188 1216962000344 substrate binding pocket [chemical binding]; other site 1216962000345 Shikimate kinase [Amino acid transport and metabolism]; Region: AroK; COG0703 1216962000346 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 1216962000347 ADP binding site [chemical binding]; other site 1216962000348 magnesium binding site [ion binding]; other site 1216962000349 putative shikimate binding site; other site 1216962000350 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 1216962000351 Enolase, C-terminal TIM barrel domain; Region: Enolase_C; pfam00113 1216962000352 substrate binding pocket [chemical binding]; other site 1216962000353 dimer interface [polypeptide binding]; other site 1216962000354 metal binding site [ion binding]; metal-binding site 1216962000355 heme oxygenase, HugZ family; Region: heme_ox_HugZ; TIGR04109 1216962000356 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 1216962000357 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 1216962000358 rRNA interaction site [nucleotide binding]; other site 1216962000359 S8 interaction site; other site 1216962000360 putative laminin-1 binding site; other site 1216962000361 Elongation factor TS; Region: EF_TS; pfam00889 1216962000362 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 1216962000363 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 1216962000364 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 1216962000365 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 1216962000366 putative acyl-acceptor binding pocket; other site 1216962000367 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 1216962000368 C-terminal peptidase (prc); Region: prc; TIGR00225 1216962000369 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 1216962000370 protein binding site [polypeptide binding]; other site 1216962000371 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 1216962000372 Catalytic dyad [active] 1216962000373 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 1216962000374 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 1216962000375 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 1216962000376 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 1216962000377 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 1216962000378 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 1216962000379 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 1216962000380 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 1216962000381 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 1216962000382 MoeA family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF), an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoeA; cd00887 1216962000383 dimer interface [polypeptide binding]; other site 1216962000384 putative functional site; other site 1216962000385 putative MPT binding site; other site 1216962000386 flagellar biosynthesis protein FliR; Reviewed; Region: fliR; PRK05701 1216962000387 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 1216962000388 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 1216962000389 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 1216962000390 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 1216962000391 Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]; Region: KsgA; COG0030 1216962000392 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 1216962000393 Metallo-beta-lactamase superfamily; Region: Lactamase_B; pfam00753 1216962000394 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 1216962000395 Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: MsrA; COG0225 1216962000396 methionine sulfoxide reductase B; Provisional; Region: PRK00222 1216962000397 SelR domain; Region: SelR; pfam01641 1216962000398 KpsF/GutQ family protein; Region: kpsF; TIGR00393 1216962000399 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 1216962000400 putative active site [active] 1216962000401 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called...; Region: CBS_pair; cl15354 1216962000402 Protein of unknown function (DUF2443); Region: DUF2443; pfam10398 1216962000403 glucosamine--fructose-6-phosphate aminotransferase; Reviewed; Region: PRK00331 1216962000404 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 1216962000405 glutaminase active site [active] 1216962000406 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 1216962000407 dimer interface [polypeptide binding]; other site 1216962000408 active site 1216962000409 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 1216962000410 dimer interface [polypeptide binding]; other site 1216962000411 active site 1216962000412 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 1216962000413 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 1216962000414 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1216962000415 dimer interface [polypeptide binding]; other site 1216962000416 putative CheW interface [polypeptide binding]; other site 1216962000417 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1216962000418 PAS domain; Region: PAS_9; pfam13426 1216962000419 putative active site [active] 1216962000420 heme pocket [chemical binding]; other site 1216962000421 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 1216962000422 Part of AAA domain; Region: AAA_19; pfam13245 1216962000423 Family description; Region: UvrD_C_2; pfam13538 1216962000424 Uncharacterized conserved protein [Function unknown]; Region: COG1479 1216962000425 Protein of unknown function DUF262; Region: DUF262; pfam03235 1216962000426 Uncharacterized conserved protein [Function unknown]; Region: COG3472 1216962000427 flagellar hook protein FlgE; Validated; Region: flgE; PRK05841 1216962000428 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 1216962000429 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 1216962000430 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 1216962000431 flagellar basal body rod modification protein; Reviewed; Region: flgD; PRK05842 1216962000432 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 1216962000433 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 1216962000434 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 1216962000435 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1216962000436 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 1216962000437 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1216962000438 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cd00596 1216962000439 active site 1216962000440 Zn binding site [ion binding]; other site 1216962000441 3-methyladenine DNA glycosylase; Provisional; Region: PRK13913 1216962000442 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 1216962000443 minor groove reading motif; other site 1216962000444 helix-hairpin-helix signature motif; other site 1216962000445 substrate binding pocket [chemical binding]; other site 1216962000446 active site 1216962000447 The URO-D_CIMS_like protein superfamily includes bacterial and eukaryotic uroporphyrinogen decarboxylases (URO-D), coenzyme M methyltransferases and other putative bacterial methyltransferases, as well as cobalamine (B12) independent methionine synthases; Region: URO-D_CIMS_like; cl00464 1216962000448 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1216962000449 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1216962000450 Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; Region: Tdh; COG1063 1216962000451 NADP(H)-dependent alcohol dehydrogenases; Region: NADP_ADH; cd08285 1216962000452 tetramer interface [polypeptide binding]; other site 1216962000453 catalytic Zn binding site [ion binding]; other site 1216962000454 NADP binding site [chemical binding]; other site 1216962000455 Protein of unknown function DUF262; Region: DUF262; pfam03235 1216962000456 Protein of unknown function DUF262; Region: DUF262; pfam03235 1216962000457 Uncharacterized conserved protein [Function unknown]; Region: COG1479 1216962000458 Putative transposase DNA-binding domain; Region: OrfB_Zn_ribbon; pfam07282 1216962000459 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 1216962000460 Probable transposase; Region: OrfB_IS605; pfam01385 1216962000461 Putative transposase DNA-binding domain; Region: OrfB_Zn_ribbon; pfam07282 1216962000462 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 1216962000463 Probable transposase; Region: OrfB_IS605; pfam01385 1216962000464 Helix-turn-helix domain; Region: HTH_OrfB_IS605; pfam12323 1216962000465 DNA methylase; Region: N6_N4_Mtase; cl17433 1216962000466 MjaII restriction endonuclease; Region: RE_MjaII; pfam09520 1216962000467 histidyl-tRNA synthetase; Region: hisS; TIGR00442 1216962000468 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for...; Region: HisRS-like_core; cd00773 1216962000469 dimer interface [polypeptide binding]; other site 1216962000470 motif 1; other site 1216962000471 active site 1216962000472 motif 2; other site 1216962000473 motif 3; other site 1216962000474 HisRS Histidyl-anticodon binding domain. HisRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is...; Region: HisRS_anticodon; cd00859 1216962000475 anticodon binding site; other site 1216962000476 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 1216962000477 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 1216962000478 Uncharacterized protein conserved in bacteria (DUF2147); Region: DUF2147; pfam09917 1216962000479 Domain of unknown function (DUF386); Region: DUF386; cl01047 1216962000480 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 1216962000481 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 1216962000482 RF-1 domain; Region: RF-1; pfam00472 1216962000483 peptide chain release factor 1; Validated; Region: prfA; PRK00591 1216962000484 This domain is found in peptide chain release factors; Region: PCRF; smart00937 1216962000485 RF-1 domain; Region: RF-1; pfam00472 1216962000486 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 1216962000487 phosphomannomutase CpsG; Provisional; Region: PRK15414 1216962000488 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 1216962000489 active site 1216962000490 substrate binding site [chemical binding]; other site 1216962000491 metal binding site [ion binding]; metal-binding site 1216962000492 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 1216962000493 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 1216962000494 Mechanosensitive ion channel; Region: MS_channel; pfam00924 1216962000495 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 1216962000496 MiaB-like tRNA modifying enzyme; Region: MiaB-like-C; TIGR01579 1216962000497 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 1216962000498 FeS/SAM binding site; other site 1216962000499 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 1216962000500 Walker B motif; other site 1216962000501 arginine finger; other site 1216962000502 Peptidase family M41; Region: Peptidase_M41; pfam01434 1216962000503 Cache domain; Region: Cache_1; pfam02743 1216962000504 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 1216962000505 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 1216962000506 dimerization interface [polypeptide binding]; other site 1216962000507 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1216962000508 dimer interface [polypeptide binding]; other site 1216962000509 putative CheW interface [polypeptide binding]; other site 1216962000510 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 1216962000511 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 1216962000512 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 1216962000513 DNA repair protein RadA; Provisional; Region: PRK11823 1216962000514 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 1216962000515 Walker A motif; other site 1216962000516 ATP binding site [chemical binding]; other site 1216962000517 Walker B motif; other site 1216962000518 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 1216962000519 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 1216962000520 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 1216962000521 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 1216962000522 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dam; COG0338 1216962000523 AlwI restriction endonuclease; Region: RE_AlwI; pfam09491 1216962000524 Initiator Replication protein; Region: Rep_3; pfam01051 1216962000525 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1216962000526 multiple promoter invertase; Provisional; Region: mpi; PRK13413 1216962000527 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 1216962000528 catalytic residues [active] 1216962000529 catalytic nucleophile [active] 1216962000530 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1216962000531 multiple promoter invertase; Provisional; Region: mpi; PRK13413 1216962000532 Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and...; Region: SR_ResInv; cd03768 1216962000533 catalytic residues [active] 1216962000534 catalytic nucleophile [active] 1216962000535 HipA-like N-terminal domain; Region: HipA_N; pfam07805 1216962000536 HipA-like C-terminal domain; Region: HipA_C; pfam07804 1216962000537 HipA-like N-terminal domain; Region: HipA_N; pfam07805 1216962000538 Protein of unknown function (DUF3519); Region: DUF3519; pfam12033 1216962000539 T5orf172 domain; Region: T5orf172; pfam10544 1216962000540 ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]; Region: ClpX; COG1219 1216962000541 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 1216962000542 Walker A motif; other site 1216962000543 ATP binding site [chemical binding]; other site 1216962000544 Walker B motif; other site 1216962000545 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 1216962000546 Na(+)/proline cotransporter PutP and related proteins; solute binding domain; Region: SLC5sbd_PutP; cd11475 1216962000547 Na binding site [ion binding]; other site 1216962000548 Proline dehydrogenase; Region: Pro_dh; cl03282 1216962000549 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 1216962000550 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 1216962000551 Glutamate binding site [chemical binding]; other site 1216962000552 NAD binding site [chemical binding]; other site 1216962000553 catalytic residues [active] 1216962000554 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 1216962000555 SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]; Region: LexA; COG1974 1216962000556 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cd00093 1216962000557 non-specific DNA binding site [nucleotide binding]; other site 1216962000558 salt bridge; other site 1216962000559 sequence-specific DNA binding site [nucleotide binding]; other site 1216962000560 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC...; Region: S24_LexA-like; cd06529 1216962000561 Catalytic site [active] 1216962000562 cytochrome c-type protein NapC; Provisional; Region: PRK10617; cl17554 1216962000563 Seven times multi-haem cytochrome CxxCH; Region: Multi-haem_cyto; pfam13447 1216962000564 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 1216962000565 NAD synthase; Region: NAD_synthase; pfam02540 1216962000566 homodimer interface [polypeptide binding]; other site 1216962000567 NAD binding pocket [chemical binding]; other site 1216962000568 ATP binding pocket [chemical binding]; other site 1216962000569 Mg binding site [ion binding]; other site 1216962000570 active-site loop [active] 1216962000571 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 1216962000572 Uncharacterized proteins involved in stress response, homologs of TerZ and putative cAMP-binding protein CABP1 [Signal transduction mechanisms]; Region: TerZ; COG2310 1216962000573 Uncharacterized proteins involved in stress response, similar to tellurium resistance terD; Region: TerD_like; cd06974 1216962000574 putative metal binding site [ion binding]; other site 1216962000575 Uncharacterized proteins involved in stress response, homologs of TerZ and putative cAMP-binding protein CABP1 [Signal transduction mechanisms]; Region: TerZ; COG2310 1216962000576 Uncharacterized proteins involved in stress response, similar to tellurium resistance terD; Region: TerD_like; cd06974 1216962000577 putative metal binding site [ion binding]; other site 1216962000578 Competence protein ComGF [Intracellular trafficking and secretion]; Region: ComGF; COG4940 1216962000579 HD domain; Region: HD_3; pfam13023 1216962000580 chromosome segregation protein SMC, common bacterial type; Region: SMC_prok_B; TIGR02168 1216962000581 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 1216962000582 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 1216962000583 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 1216962000584 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 1216962000585 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 1216962000586 metal binding site [ion binding]; metal-binding site 1216962000587 dimer interface [polypeptide binding]; other site 1216962000588 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1216962000589 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 1216962000590 active site 1216962000591 phosphorylation site [posttranslational modification] 1216962000592 intermolecular recognition site; other site 1216962000593 dimerization interface [polypeptide binding]; other site 1216962000594 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 1216962000595 DNA binding site [nucleotide binding] 1216962000596 arginyl-tRNA synthetase; Reviewed; Region: argS; PRK01611 1216962000597 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 1216962000598 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 1216962000599 active site 1216962000600 HIGH motif; other site 1216962000601 KMSK motif region; other site 1216962000602 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 1216962000603 tRNA binding surface [nucleotide binding]; other site 1216962000604 anticodon binding site; other site 1216962000605 twin arginine translocase protein A; Provisional; Region: tatA; PRK00575 1216962000606 twin arginine translocase protein A; Provisional; Region: tatA; PRK00720 1216962000607 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 1216962000608 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 1216962000609 catalytic site [active] 1216962000610 G-X2-G-X-G-K; other site 1216962000611 Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6, and similar proteins; Region: PLDc_Nuc_like; cd09116 1216962000612 PLD-like domain; Region: PLDc_2; pfam13091 1216962000613 putative active site [active] 1216962000614 catalytic site [active] 1216962000615 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1216962000616 Flagellar L-ring protein; Region: FlgH; cl17277 1216962000617 CMP-NeuAc_Synthase activates N-acetylneuraminic acid by adding CMP moiety; Region: CMP-NeuAc_Synthase; cd02513 1216962000618 ligand binding site; other site 1216962000619 tetramer interface; other site 1216962000620 pseudaminic acid biosynthesis-associated protein PseG; Region: PseG; TIGR03590 1216962000621 pseudaminic acid biosynthesis N-acetyl transferase; Region: PseH; TIGR03585 1216962000622 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 1216962000623 pseudaminic acid synthase; Region: PseI; TIGR03586 1216962000624 NeuB family; Region: NeuB; pfam03102 1216962000625 C-terminal SAF domain of sialic acid synthetase; Region: SAF_NeuB_like; cd11615 1216962000626 NeuB binding interface [polypeptide binding]; other site 1216962000627 putative substrate binding site [chemical binding]; other site 1216962000628 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 1216962000629 metal binding site 2 [ion binding]; metal-binding site 1216962000630 putative DNA binding helix; other site 1216962000631 metal binding site 1 [ion binding]; metal-binding site 1216962000632 dimer interface [polypeptide binding]; other site 1216962000633 structural Zn2+ binding site [ion binding]; other site 1216962000634 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1216962000635 dimer interface [polypeptide binding]; other site 1216962000636 putative CheW interface [polypeptide binding]; other site 1216962000637 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 1216962000638 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 1216962000639 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 1216962000640 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1216962000641 catalytic residue [active] 1216962000642 formamidase; Provisional; Region: amiF; PRK13287 1216962000643 aliphatic amidases (class 2 nitrilases); Region: aliphatic_amidase; cd07565 1216962000644 multimer interface [polypeptide binding]; other site 1216962000645 active site 1216962000646 catalytic triad [active] 1216962000647 dimer interface [polypeptide binding]; other site 1216962000648 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 1216962000649 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 1216962000650 cofactor binding site; other site 1216962000651 DNA binding site [nucleotide binding] 1216962000652 substrate interaction site [chemical binding]; other site 1216962000653 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 1216962000654 Transposase IS200 like; Region: Y1_Tnp; pfam01797 1216962000655 Transposase IS200 like; Region: Y1_Tnp; pfam01797 1216962000656 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1216962000657 RecG-like helicase [DNA replication, recombination, and repair / Transcription]; Region: RecG; COG1200 1216962000658 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 1216962000659 ssDNA binding site; other site 1216962000660 generic binding surface II; other site 1216962000661 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 1216962000662 ATP binding site [chemical binding]; other site 1216962000663 putative Mg++ binding site [ion binding]; other site 1216962000664 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 1216962000665 nucleotide binding region [chemical binding]; other site 1216962000666 ATP-binding site [chemical binding]; other site 1216962000667 cbb3-type cytochrome c oxidase subunit I; Provisional; Region: PRK14488 1216962000668 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 1216962000669 Low-spin heme binding site [chemical binding]; other site 1216962000670 D-pathway; other site 1216962000671 Putative water exit pathway; other site 1216962000672 Binuclear center (active site) [active] 1216962000673 K-pathway; other site 1216962000674 Putative proton exit pathway; other site 1216962000675 cbb3-type cytochrome c oxidase subunit II; Provisional; Region: PRK14487 1216962000676 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 1216962000677 Cytochrome cbb oxidase CcoQ. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction of O2...; Region: cbb3_Oxidase_CcoQ; cl00282 1216962000678 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 1216962000679 Cytochrome c; Region: Cytochrom_C; pfam00034 1216962000680 Cytochrome c, mono- and diheme variants [Energy production and conversion]; Region: CccA; COG2010 1216962000681 Cytochrome C oxidase, cbb3-type, subunit III; Region: Cytochrome_CBB3; pfam13442 1216962000682 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 1216962000683 Cytochrome C oxidase, mono-heme subunit/FixO; Region: FixO; cl01130 1216962000684 Cytochrome cbb oxidase CcoQ. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction of O2...; Region: cbb3_Oxidase_CcoQ; cl00282 1216962000685 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 1216962000686 Cytochrome c; Region: Cytochrom_C; pfam00034 1216962000687 Cytochrome c; Region: Cytochrom_C; pfam00034 1216962000688 Family of unknown function (DUF4006); Region: DUF4006; pfam13179 1216962000689 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1216962000690 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1216962000691 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1216962000692 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1216962000693 Mycoplasma protein of unknown function, DUF285; Region: DUF285; pfam03382 1216962000694 Mycoplasma protein of unknown function, DUF285; Region: DUF285; pfam03382 1216962000695 Mycoplasma protein of unknown function, DUF285; Region: DUF285; pfam03382 1216962000696 Protein of unknown function (DUF1104); Region: DUF1104; pfam06518 1216962000697 Mycoplasma protein of unknown function, DUF285; Region: DUF285; pfam03382 1216962000698 Mycoplasma protein of unknown function, DUF285; Region: DUF285; pfam03382 1216962000699 Protein of unknown function (DUF1104); Region: DUF1104; pfam06518 1216962000700 Mycoplasma protein of unknown function, DUF285; Region: DUF285; pfam03382 1216962000701 Mycoplasma protein of unknown function, DUF285; Region: DUF285; pfam03382 1216962000702 Protein of unknown function (DUF1104); Region: DUF1104; pfam06518 1216962000703 Protein of unknown function (DUF1104); Region: DUF1104; pfam06518 1216962000704 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 1216962000705 Catalase-like heme-binding proteins and protein domains; Region: catalase_like; cl09506 1216962000706 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 1216962000707 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 1216962000708 G1 box; other site 1216962000709 putative GEF interaction site [polypeptide binding]; other site 1216962000710 GTP/Mg2+ binding site [chemical binding]; other site 1216962000711 Switch I region; other site 1216962000712 G2 box; other site 1216962000713 G3 box; other site 1216962000714 Switch II region; other site 1216962000715 G4 box; other site 1216962000716 G5 box; other site 1216962000717 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 1216962000718 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 1216962000719 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK08447 1216962000720 ATP cone domain; Region: ATP-cone; pfam03477 1216962000721 Class I ribonucleotide reductase; Region: RNR_I; cd01679 1216962000722 active site 1216962000723 dimer interface [polypeptide binding]; other site 1216962000724 catalytic residues [active] 1216962000725 effector binding site; other site 1216962000726 R2 peptide binding site; other site 1216962000727 Transposase IS200 like; Region: Y1_Tnp; pfam01797 1216962000728 Transposase IS200 like; Region: Y1_Tnp; pfam01797 1216962000729 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1216962000730 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 1216962000731 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1216962000732 dimer interface [polypeptide binding]; other site 1216962000733 putative CheW interface [polypeptide binding]; other site 1216962000734 Cache domain; Region: Cache_2; cl07034 1216962000735 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1216962000736 Probable transposase; Region: OrfB_IS605; pfam01385 1216962000737 Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining...; Region: Ser_Recombinase; cl02788 1216962000738 Predicted site-specific integrase-resolvase [DNA replication, recombination, and repair]; Region: COG2452 1216962000739 catalytic residues [active] 1216962000740 Uncharacterized protein family (UPF0150); Region: UPF0150; pfam03681 1216962000741 multiple promoter invertase; Provisional; Region: mpi; PRK13413 1216962000742 HipA N-terminal domain; Region: Couple_hipA; cl11853 1216962000743 Alginate Lyase A1-III; enzymatically depolymerizes alginate, a complex copolymer of beta-D-mannuronate and alpha-L-guluronate, by cleaving the beta-(1,4) glycosidic bond; Region: AlgLyase; cl00179 1216962000744 Potential Monad-binding region of RPAP3; Region: RPAP3_C; pfam13877 1216962000745 Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; Region: DNA_polB_like1_exo; cd05782 1216962000746 active site 1216962000747 catalytic site [active] 1216962000748 substrate binding site [chemical binding]; other site 1216962000749 Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; Region: DNA_pol_B_exo2; pfam10108 1216962000750 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1216962000751 Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; Region: DNA_polB_like1_exo; cd05782 1216962000752 active site 1216962000753 catalytic site [active] 1216962000754 substrate binding site [chemical binding]; other site 1216962000755 Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; Region: DNA_pol_B_exo2; pfam10108 1216962000756 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1216962000757 AIR (aminoimidazole ribonucleotide) synthase related protein. This family includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM (formylglycinamidine ribonucleotide) synthase and Selenophosphate synthetase (SelD). The N-terminal domain...; Region: PurM-like; cl10019 1216962000758 dimerization interface [polypeptide binding]; other site 1216962000759 ATP binding site [chemical binding]; other site 1216962000760 AIR (aminoimidazole ribonucleotide) synthase related protein. This family includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM (formylglycinamidine ribonucleotide) synthase and Selenophosphate synthetase (SelD). The N-terminal domain...; Region: PurM-like; cl10019 1216962000761 dimerization interface [polypeptide binding]; other site 1216962000762 ATP binding site [chemical binding]; other site 1216962000763 Anaerobic c4-dicarboxylate membrane transporter; Region: DcuA_DcuB; cl01040 1216962000764 transcription elongation factor NusA; Provisional; Region: nusA; PRK12328 1216962000765 NusA N-terminal domain; Region: NusA_N; pfam08529 1216962000766 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 1216962000767 RNA binding site [nucleotide binding]; other site 1216962000768 homodimer interface [polypeptide binding]; other site 1216962000769 NusA-like KH domain; Region: KH_5; pfam13184 1216962000770 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 1216962000771 G-X-X-G motif; other site 1216962000772 tryptophan synthase alpha subunit; Provisional; Region: trpA; CHL00200 1216962000773 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 1216962000774 substrate binding site [chemical binding]; other site 1216962000775 active site 1216962000776 catalytic residues [active] 1216962000777 heterodimer interface [polypeptide binding]; other site 1216962000778 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 1216962000779 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 1216962000780 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 1216962000781 putative active site [active] 1216962000782 catalytic residue [active] 1216962000783 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 1216962000784 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 1216962000785 5S rRNA interface [nucleotide binding]; other site 1216962000786 CTC domain interface [polypeptide binding]; other site 1216962000787 L16 interface [polypeptide binding]; other site 1216962000788 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1216962000789 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 1216962000790 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 1216962000791 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 1216962000792 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 1216962000793 tonB-system energizer ExbB, group 2; Region: exbB2; TIGR02805 1216962000794 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 1216962000795 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 1216962000796 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 1216962000797 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; pfam00044 1216962000798 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 1216962000799 pyridine nucleotide-disulfide oxidoreductase; Provisional; Region: PRK07251 1216962000800 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1216962000801 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 1216962000802 Protein of unknown function (DUF465); Region: DUF465; cl01070 1216962000803 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 1216962000804 HSP70 interaction site [polypeptide binding]; other site 1216962000805 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA; Region: MATE_MepA_like; cd13143 1216962000806 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 1216962000807 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 1216962000808 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 1216962000809 23S rRNA interface [nucleotide binding]; other site 1216962000810 L3 interface [polypeptide binding]; other site 1216962000811 Restriction endonuclease [Defense mechanisms]; Region: McrA; COG1403 1216962000812 HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085 1216962000813 active site 1216962000814 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 1216962000815 DNA methylase; Region: N6_N4_Mtase; pfam01555 1216962000816 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 1216962000817 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 1216962000818 CoA-binding site [chemical binding]; other site 1216962000819 ATP-binding [chemical binding]; other site 1216962000820 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 1216962000821 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 1216962000822 gamma-glutamyltranspeptidase; Region: g_glut_trans; TIGR00066 1216962000823 DNA polymerase III subunits gamma and tau; Validated; Region: PRK08451 1216962000824 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 1216962000825 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1216962000826 ABC transporter signature motif; other site 1216962000827 Walker B; other site 1216962000828 D-loop; other site 1216962000829 H-loop/switch region; other site 1216962000830 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 1216962000831 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 1216962000832 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 1216962000833 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 1216962000834 Sel1 repeat; Region: Sel1; cl02723 1216962000835 Sel1 repeat; Region: Sel1; cl02723 1216962000836 Uncharacterized conserved protein (DUF2156); Region: DUF2156; cl12090 1216962000837 diaminopimelate decarboxylase; Region: lysA; TIGR01048 1216962000838 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 1216962000839 active site 1216962000840 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 1216962000841 substrate binding site [chemical binding]; other site 1216962000842 catalytic residues [active] 1216962000843 dimer interface [polypeptide binding]; other site 1216962000844 Chorismate mutase type II; Region: CM_2; smart00830 1216962000845 2-oxoglutarate-acceptor oxidoreductase subunit OorC; Reviewed; Region: oorC; PRK08441 1216962000846 2-oxoglutarate ferredoxin oxidoreductase subunit gamma; Validated; Region: PRK08537 1216962000847 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cl01629 1216962000848 2-oxoglutarate-acceptor oxidoreductase subunit OorA; Reviewed; Region: oorA; PRK09627 1216962000849 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 1216962000850 dimer interface [polypeptide binding]; other site 1216962000851 PYR/PP interface [polypeptide binding]; other site 1216962000852 TPP binding site [chemical binding]; other site 1216962000853 substrate binding site [chemical binding]; other site 1216962000854 2-oxoglutarate-acceptor oxidoreductase subunit OorD; Reviewed; Region: oorD; PRK09626 1216962000855 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 1216962000856 YceG-like family; Region: YceG; pfam02618 1216962000857 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 1216962000858 dimerization interface [polypeptide binding]; other site 1216962000859 Protein of unknown function; Region: DUF3971; pfam13116 1216962000860 AsmA-like C-terminal region; Region: AsmA_1; pfam13109 1216962000861 FeoA domain; Region: FeoA; pfam04023 1216962000862 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 1216962000863 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 1216962000864 minor groove reading motif; other site 1216962000865 helix-hairpin-helix signature motif; other site 1216962000866 substrate binding pocket [chemical binding]; other site 1216962000867 active site 1216962000868 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 1216962000869 flagellar motor switch protein; Validated; Region: PRK08433 1216962000870 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 1216962000871 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 1216962000872 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 1216962000873 active site 1216962000874 NTPase/HAM1. This family consists of the HAM1 protein and pyrophosphate-releasing xanthosine/ inosine triphosphatase. HAM1 protects the cell against mutagenesis by the base analog 6-N-hydroxylaminopurine (HAP) in E. Coli and S. cerevisiae. A...; Region: HAM1; cd00515 1216962000875 active site 1216962000876 dimerization interface [polypeptide binding]; other site 1216962000877 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 1216962000878 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypC; COG0298 1216962000879 hydrogenase isoenzymes formation protein HypD; Provisional; Region: PRK15062 1216962000880 hydrogenase expression/formation protein HypD; Region: hypD; TIGR00075 1216962000881 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 1216962000882 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 1216962000883 hypothetical protein; Provisional; Region: PRK08445 1216962000884 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 1216962000885 FeS/SAM binding site; other site 1216962000886 Outer membrane protein/protective antigen OMA87 [Cell envelope biogenesis, outer membrane]; Region: COG4775 1216962000887 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1216962000888 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1216962000889 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 1216962000890 Surface antigen; Region: Bac_surface_Ag; pfam01103 1216962000891 hypothetical protein; Provisional; Region: PRK08444 1216962000892 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 1216962000893 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 1216962000894 FeS/SAM binding site; other site 1216962000895 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 1216962000896 DpnII restriction endonuclease; Region: DpnII; pfam04556 1216962000897 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 1216962000898 DNA methylase; Region: N6_N4_Mtase; pfam01555 1216962000899 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 1216962000900 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 1216962000901 GTP binding site; other site 1216962000902 flagellar biosynthesis protein FlhB; Reviewed; Region: flhB; PRK05702 1216962000903 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257; cl15822 1216962000904 Lysophospholipase [Lipid metabolism]; Region: PldB; COG2267 1216962000905 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 1216962000906 Menaquinone biosynthesis; Region: VitK2_biosynth; cl17475 1216962000907 ICEA Protein; Region: ICEA; pfam05315 1216962000908 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; cl17344 1216962000909 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 1216962000910 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 1216962000911 dimer interface [polypeptide binding]; other site 1216962000912 active site 1216962000913 CoA binding pocket [chemical binding]; other site 1216962000914 putative phosphate acyltransferase; Provisional; Region: PRK05331 1216962000915 Ribosomal L32p protein family; Region: Ribosomal_L32p; cl09115 1216962000916 Uncharacterized ACR, COG1399; Region: DUF177; cl00616 1216962000917 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 1216962000918 active site 1216962000919 multimer interface [polypeptide binding]; other site 1216962000920 Type II (periplasmic) bacterial L-asparaginase; Region: L-asparaginase_II; cd08964 1216962000921 active site 1216962000922 homodimer interface [polypeptide binding]; other site 1216962000923 homotetramer interface [polypeptide binding]; other site 1216962000924 guanosine 5'-monophosphate oxidoreductase; Provisional; Region: PRK05096 1216962000925 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 1216962000926 active site 1216962000927 Nitrate reductase delta subunit; Region: Nitrate_red_del; cl00958 1216962000929 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 1216962000931 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 1216962000932 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 1216962000933 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 1216962000934 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 1216962000935 Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]; Region: BisC; COG0243 1216962000936 Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the...; Region: MopB_CT_Formate-Dh-Na-like; cd02792 1216962000937 molybdopterin cofactor binding site; other site 1216962000938 Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]; Region: HybA; COG0437 1216962000939 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; cl00859 1216962000940 formate dehydrogenase, gamma subunit; Region: formate-DH-gamm; TIGR01583 1216962000941 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 1216962000942 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 1216962000943 Pyridoxal phosphate biosynthetic protein PdxA; Region: PdxA; cl00873 1216962000944 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 1216962000945 active site 1216962000946 hydrophilic channel; other site 1216962000947 dimerization interface [polypeptide binding]; other site 1216962000948 catalytic residues [active] 1216962000949 active site lid [active] 1216962000950 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 1216962000951 This subfamily contains Escherichia coli WecA, Bacillus subtilis TagO and related proteins. WecA is an UDP-N-acetylglucosamine (GlcNAc):undecaprenyl-phosphate (Und-P) GlcNAc-1-phosphate transferase that catalyzes the formation of a phosphodiester bond...; Region: GT_WecA_like; cd06853 1216962000952 Mg++ binding site [ion binding]; other site 1216962000953 putative catalytic motif [active] 1216962000954 substrate binding site [chemical binding]; other site 1216962000955 Glycosyltransferase 4 (GT4) includes both eukaryotic and prokaryotic UDP-D-N-acetylhexosamine:polyprenol phosphate D-N-acetylhexosamine-1-phosphate transferases. They catalyze the transfer of a D-N-acetylhexosamine 1-phosphate to a membrane-bound...; Region: GT_MraY-like; cl10571 1216962000956 Mg++ binding site [ion binding]; other site 1216962000957 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 1216962000958 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 1216962000959 active site 1216962000960 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 1216962000961 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1216962000962 dimer interface [polypeptide binding]; other site 1216962000963 putative CheW interface [polypeptide binding]; other site 1216962000964 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 1216962000965 active site 1216962000966 putative DNA-binding cleft [nucleotide binding]; other site 1216962000967 dimer interface [polypeptide binding]; other site 1216962000968 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 1216962000969 DnaA N-terminal domain; Region: DnaA_N; pfam11638 1216962000970 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 1216962000971 Walker A motif; other site 1216962000972 ATP binding site [chemical binding]; other site 1216962000973 Walker B motif; other site 1216962000974 arginine finger; other site 1216962000975 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 1216962000976 DnaA box-binding interface [nucleotide binding]; other site 1216962000977 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 1216962000978 selenocysteine synthase; Provisional; Region: PRK04311 1216962000979 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 1216962000980 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1216962000981 catalytic residue [active] 1216962000982 arginine decarboxylase; Provisional; Region: PRK05354 1216962000983 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase; Region: PLPDE_III_ADC; cd06830 1216962000984 active site 1216962000985 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 1216962000986 catalytic residues [active] 1216962000987 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 1216962000988 N-carbamoylputrescine amidase; Region: agmatine_aguB; TIGR03381 1216962000989 N-carbamoylputrescine amidohydrolase (CPA) (class 11 nitrilases); Region: CPA; cd07573 1216962000990 putative active site; other site 1216962000991 catalytic triad [active] 1216962000992 putative dimer interface [polypeptide binding]; other site 1216962000993 Predicted permease [General function prediction only]; Region: COG2056 1216962000994 Na+-H+ antiporter family; Region: Na_H_antiport_2; pfam13726 1216962000995 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Thermotoga marina NorM; Region: MATE_NorM_like; cd13137 1216962000996 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 1216962000997 GDP-D-mannose dehydratase [Cell envelope biogenesis, outer membrane]; Region: Gmd; COG1089 1216962000998 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 1216962000999 NADP-binding site; other site 1216962001000 homotetramer interface [polypeptide binding]; other site 1216962001001 substrate binding site [chemical binding]; other site 1216962001002 homodimer interface [polypeptide binding]; other site 1216962001003 active site 1216962001004 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 1216962001005 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 1216962001006 active site 1216962001007 Cupin domain; Region: Cupin_2; cl17218 1216962001008 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 1216962001009 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 1216962001010 active site 1216962001011 HIGH motif; other site 1216962001012 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 1216962001013 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 1216962001014 active site 1216962001015 KMSKS motif; other site 1216962001016 diaminopimelate epimerase; Provisional; Region: dapF; PRK00450 1216962001017 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 1216962001018 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 1216962001019 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 1216962001020 Domain of unknown function DUF20; Region: UPF0118; pfam01594 1216962001021 L-lactate permease [Energy production and conversion]; Region: LldP; COG1620 1216962001022 L-lactate transport; Region: lctP; TIGR00795 1216962001023 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1216962001024 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 1216962001025 active site 1216962001026 pyrophosphate binding site [ion binding]; other site 1216962001027 thiamine phosphate binding site [chemical binding]; other site 1216962001028 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 1216962001029 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 1216962001030 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1216962001031 catalytic residue [active] 1216962001032 bifunctional indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase; Provisional; Region: PRK09427 1216962001033 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 1216962001034 active site 1216962001035 ribulose/triose binding site [chemical binding]; other site 1216962001036 phosphate binding site [ion binding]; other site 1216962001037 substrate (anthranilate) binding pocket [chemical binding]; other site 1216962001038 product (indole) binding pocket [chemical binding]; other site 1216962001039 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 1216962001040 active site 1216962001041 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 1216962001042 anthranilate phosphoribosyltransferase; Provisional; Region: trpD; PRK00188 1216962001043 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 1216962001044 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 1216962001045 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 1216962001046 Predicted membrane protein [Function unknown]; Region: COG2855 1216962001047 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 1216962001048 Sel1 repeat; Region: Sel1; cl02723 1216962001049 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 1216962001050 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 1216962001051 binding surface 1216962001052 TPR motif; other site 1216962001053 GIY-YIG nuclease domain superfamily; Region: GIY-YIG_SF; cl15257 1216962001054 GIY-YIG motif/motif A; other site 1216962001055 active site 1216962001056 catalytic site [active] 1216962001057 metal binding site [ion binding]; metal-binding site 1216962001058 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dam; COG0338 1216962001059 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dam; COG0338 1216962001060 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 1216962001061 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 1216962001062 stacking interactions; other site 1216962001063 hinge regions; other site 1216962001064 ATP/Mg binding site [chemical binding]; other site 1216962001065 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 1216962001066 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 1216962001067 ATP/Mg binding site [chemical binding]; other site 1216962001068 stacking interactions; other site 1216962001069 hinge regions; other site 1216962001070 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 1216962001071 oligomerisation interface [polypeptide binding]; other site 1216962001072 mobile loop; other site 1216962001073 roof hairpin; other site 1216962001074 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 1216962001075 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 1216962001076 Ligand Binding Site [chemical binding]; other site 1216962001078 thiamine monophosphate kinase; Provisional; Region: PRK05731 1216962001079 Selenophosphate synthetase (SelD) catalyzes the conversion of selenium to selenophosphate which is required by a number of bacterial, archaeal and eukaryotic organisms for synthesis of Secys-tRNA, the precursor of selenocysteine in selenoenzymes. The...; Region: SelD; cd02195 1216962001080 dimerization interface [polypeptide binding]; other site 1216962001081 putative ATP binding site [chemical binding]; other site 1216962001082 serine O-acetyltransferase; Region: cysE; TIGR01172 1216962001083 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 1216962001084 trimer interface [polypeptide binding]; other site 1216962001085 active site 1216962001086 substrate binding site [chemical binding]; other site 1216962001087 CoA binding site [chemical binding]; other site 1216962001088 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 1216962001089 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 1216962001090 dimer interface [polypeptide binding]; other site 1216962001091 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1216962001092 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 1216962001093 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 1216962001094 dimer interface [polypeptide binding]; other site 1216962001095 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1216962001096 catalytic residue [active] 1216962001097 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 1216962001098 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 1216962001099 active site 1216962001100 catalytic tetrad [active] 1216962001101 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 1216962001102 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 1216962001103 Walker A motif; other site 1216962001104 ATP binding site [chemical binding]; other site 1216962001105 Walker B motif; other site 1216962001106 arginine finger; other site 1216962001107 DNA gyrase subunit A; Validated; Region: PRK05560 1216962001108 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 1216962001109 CAP-like domain; other site 1216962001110 active site 1216962001111 primary dimer interface [polypeptide binding]; other site 1216962001112 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1216962001113 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1216962001114 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1216962001115 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1216962001116 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1216962001117 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1216962001118 Diacylglycerol kinase [Cell envelope biogenesis, outer membrane]; Region: DgkA; COG0818 1216962001119 Uncharacterized protein conserved in bacteria (DUF2219); Region: DUF2219; cl01409 1216962001120 Uncharacterized protein conserved in bacteria (DUF2219); Region: DUF2219; cl01409 1216962001121 Cation transport protein; Region: TrkH; cl17365 1216962001122 Kef-type K+ transport systems, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: Kch; COG1226 1216962001123 TrkA-N domain; Region: TrkA_N; pfam02254 1216962001124 TrkA-C domain; Region: TrkA_C; pfam02080 1216962001125 Ribosomal L28 family; Region: Ribosomal_L28; cl00367 1216962001126 Cytochrome c peroxidase [Inorganic ion transport and metabolism]; Region: MauG; COG1858 1216962001127 Transcriptional regulatory protein, C terminal; Region: Trans_reg_C; pfam00486 1216962001128 DNA binding site [nucleotide binding] 1216962001129 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1216962001130 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; cl00080 1216962001131 dimer interface [polypeptide binding]; other site 1216962001132 phosphorylation site [posttranslational modification] 1216962001133 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 1216962001134 ATP binding site [chemical binding]; other site 1216962001135 Mg2+ binding site [ion binding]; other site 1216962001136 G-X-G motif; other site 1216962001137 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 1216962001138 Sel1-like repeats; Region: SEL1; smart00671 1216962001139 Sel1-like repeats; Region: SEL1; smart00671 1216962001140 Sel1-like repeats; Region: SEL1; smart00671 1216962001141 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 1216962001142 Sel1-like repeats; Region: SEL1; smart00671 1216962001143 Sel1-like repeats; Region: SEL1; smart00671 1216962001144 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 1216962001145 TPR motif; other site 1216962001146 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 1216962001147 binding surface 1216962001148 Sel1-like repeats; Region: SEL1; smart00671 1216962001149 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 1216962001150 TPR motif; other site 1216962001151 binding surface 1216962001152 Protein of unknown function (DUF330); Region: DUF330; cl01135 1216962001153 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 1216962001154 mce related protein; Region: MCE; pfam02470 1216962001155 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 1216962001156 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 1216962001157 Walker A/P-loop; other site 1216962001158 ATP binding site [chemical binding]; other site 1216962001159 Q-loop/lid; other site 1216962001160 ABC transporter signature motif; other site 1216962001161 Walker B; other site 1216962001162 D-loop; other site 1216962001163 H-loop/switch region; other site 1216962001164 Sulphate Transporter and Anti-Sigma factor antagonist domain found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors; Region: STAS; cl00604 1216962001165 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 1216962001166 conserved hypothetical integral membrane protein; Region: TIGR00056 1216962001167 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1216962001168 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 1216962001169 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 1216962001170 nucleotide binding site/active site [active] 1216962001171 HIT family signature motif; other site 1216962001172 catalytic residue [active] 1216962001173 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 1216962001174 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 1216962001175 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1216962001176 catalytic residue [active] 1216962001177 Protein of unknown function (DUF3972); Region: DUF3972; pfam13118 1216962001178 DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains...; Region: DnaE_OBF; cd04485 1216962001179 generic binding surface II; other site 1216962001180 generic binding surface I; other site 1216962001181 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 1216962001182 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 1216962001183 S17 interaction site [polypeptide binding]; other site 1216962001184 S8 interaction site; other site 1216962001185 16S rRNA interaction site [nucleotide binding]; other site 1216962001186 streptomycin interaction site [chemical binding]; other site 1216962001187 23S rRNA interaction site [nucleotide binding]; other site 1216962001188 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 1216962001189 30S ribosomal protein S7; Validated; Region: PRK05302 1216962001190 elongation factor G; Reviewed; Region: PRK00007 1216962001191 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 1216962001192 G1 box; other site 1216962001193 putative GEF interaction site [polypeptide binding]; other site 1216962001194 GTP/Mg2+ binding site [chemical binding]; other site 1216962001195 Switch I region; other site 1216962001196 G2 box; other site 1216962001197 G3 box; other site 1216962001198 Switch II region; other site 1216962001199 G4 box; other site 1216962001200 G5 box; other site 1216962001201 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 1216962001202 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 1216962001203 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 1216962001204 ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase; Region: ribokinase_pfkB_like; cl00192 1216962001205 T5orf172 domain; Region: T5orf172; pfam10544 1216962001206 Adenine-specific methyltransferase EcoRI; Region: EcoRI_methylase; pfam13651 1216962001207 S-ribosylhomocysteinase; Provisional; Region: PRK02260 1216962001208 cystathionine gamma-synthase/cystathionine beta-lyase; Validated; Region: PRK06176 1216962001209 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 1216962001210 homodimer interface [polypeptide binding]; other site 1216962001211 substrate-cofactor binding pocket; other site 1216962001212 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1216962001213 catalytic residue [active] 1216962001214 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 1216962001215 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 1216962001216 dimer interface [polypeptide binding]; other site 1216962001217 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1216962001218 catalytic residue [active] 1216962001219 ATP-grasp domain; Region: ATP-grasp_4; cl17255 1216962001220 Lecithin retinol acyltransferase; Region: LRAT; pfam04970 1216962001221 Mycoplasma protein of unknown function, DUF285; Region: DUF285; pfam03382 1216962001222 bacterial surface protein 26-residue repeat; Region: Liste_lipo_26; TIGR02167 1216962001223 Mycoplasma protein of unknown function, DUF285; Region: DUF285; pfam03382 1216962001224 bacterial surface protein 26-residue repeat; Region: Liste_lipo_26; TIGR02167 1216962001225 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 1216962001226 DNA methylase; Region: N6_N4_Mtase; pfam01555 1216962001227 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 1216962001228 Nucleotide-binding domain of human HSPA9 and similar proteins; Region: HSPA9-Ssq1-like_NBD; cd10234 1216962001229 nucleotide binding site [chemical binding]; other site 1216962001230 NEF interaction site [polypeptide binding]; other site 1216962001231 SBD interface [polypeptide binding]; other site 1216962001232 GrpE; Region: GrpE; pfam01025 1216962001233 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 1216962001234 dimer interface [polypeptide binding]; other site 1216962001235 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 1216962001236 heat-inducible transcription repressor; Provisional; Region: PRK03911 1216962001237 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 1216962001238 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 1216962001239 active site 1216962001240 homodimer interface [polypeptide binding]; other site 1216962001241 FliW protein; Region: FliW; cl00740 1216962001242 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1216962001243 Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]; Region: FecA; COG4772 1216962001244 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 1216962001245 N-terminal plug; other site 1216962001246 ligand-binding site [chemical binding]; other site 1216962001247 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 1216962001248 Glycosaminoglycan (GAG) polysaccharide lyase family. This family consists of a group of secreted bacterial lyase enzymes capable of acting on glycosaminoglycans, such as hyaluronan and chondroitin, in the extracellular matrix of host tissues; Region: GAG_Lyase; cl17706 1216962001249 substrate binding site [chemical binding]; other site 1216962001250 catalytic residues [active] 1216962001251 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 1216962001252 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 1216962001253 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 1216962001254 Walker A motif; other site 1216962001255 ATP binding site [chemical binding]; other site 1216962001256 TraM recognition site of TraD and TraG; Region: TraG-D_C; cl17375 1216962001257 UDP-N-acetylglucosamine 4,6-dehydratase; Region: PseB; TIGR03589 1216962001258 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 1216962001259 NAD(P) binding site [chemical binding]; other site 1216962001260 homodimer interface [polypeptide binding]; other site 1216962001261 substrate binding site [chemical binding]; other site 1216962001262 active site 1216962001263 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated; Region: PRK05579 1216962001264 Flavoprotein; Region: Flavoprotein; pfam02441 1216962001265 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 1216962001266 Uncharacterized conserved protein [Function unknown]; Region: COG1479 1216962001267 Protein of unknown function DUF262; Region: DUF262; pfam03235 1216962001268 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 1216962001269 Tsp45I type II restriction enzyme; Region: Tsp45I; pfam06300 1216962001270 Tsp45I type II restriction enzyme; Region: Tsp45I; pfam06300 1216962001271 DNA methylase; Region: N6_N4_Mtase; pfam01555 1216962001272 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 1216962001273 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 1216962001274 S-adenosylmethionine binding site [chemical binding]; other site 1216962001275 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 1216962001276 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1216962001277 active site 1216962001278 HIGH motif; other site 1216962001279 nucleotide binding site [chemical binding]; other site 1216962001280 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 1216962001281 active site 1216962001282 KMSKS motif; other site 1216962001283 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 1216962001284 tRNA binding surface [nucleotide binding]; other site 1216962001285 anticodon binding site; other site 1216962001286 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 1216962001287 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 1216962001288 RNA binding surface [nucleotide binding]; other site 1216962001289 Sortases are cysteine transpeptidases, found in gram-positive bacteria, that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. They do so by catalyzing a transpeptidation reaction in which the surface protein substrate is...; Region: Sortase; cl09098 1216962001290 FIST N domain; Region: FIST; pfam08495 1216962001291 FIST C domain; Region: FIST_C; pfam10442 1216962001292 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1216962001293 dimer interface [polypeptide binding]; other site 1216962001294 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 1216962001295 putative CheW interface [polypeptide binding]; other site 1216962001296 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK14359 1216962001297 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 1216962001298 Substrate binding site; other site 1216962001299 Mg++ binding site; other site 1216962001300 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 1216962001301 active site 1216962001302 substrate binding site [chemical binding]; other site 1216962001303 CoA binding site [chemical binding]; other site 1216962001304 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK05699 1216962001305 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1216962001306 Flagellar basal body rod protein [Cell motility and secretion]; Region: FlgG; COG4786 1216962001307 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 1216962001308 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 1216962001309 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 1216962001310 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 1216962001311 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1216962001312 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1216962001313 peptide chain release factor 2; Validated; Region: prfB; PRK00578 1216962001314 This domain is found in peptide chain release factors; Region: PCRF; smart00937 1216962001315 RF-1 domain; Region: RF-1; pfam00472 1216962001316 NAD(P) binding domain of amino acid dehydrogenase-like proteins; Region: NAD_bind_amino_acid_DH; cl17226 1216962001317 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 1216962001318 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1216962001319 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 1216962001320 NAD(P) binding site [chemical binding]; other site 1216962001321 active site 1216962001322 acyl carrier protein; Provisional; Region: acpP; PRK00982 1216962001323 Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the...; Region: cond_enzymes; cl09938 1216962001324 active site 1216962001325 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated; Region: PRK05724 1216962001326 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; pfam03255 1216962001327 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 1216962001328 Sulfatase; Region: Sulfatase; pfam00884 1216962001329 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 1216962001330 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cl09940 1216962001331 RNA binding surface [nucleotide binding]; other site 1216962001332 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 1216962001333 S-adenosylmethionine binding site [chemical binding]; other site 1216962001334 Uncharacterized conserved protein [Function unknown]; Region: COG0062 1216962001335 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 1216962001336 putative substrate binding site [chemical binding]; other site 1216962001337 putative ATP binding site [chemical binding]; other site 1216962001338 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 1216962001339 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 1216962001340 Inactivated superfamily I helicase [DNA replication, recombination, and repair]; Region: COG3893 1216962001341 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 1216962001342 Transketolase [Carbohydrate transport and metabolism]; Region: TktA; COG0021 1216962001343 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 1216962001344 TPP-binding site [chemical binding]; other site 1216962001345 dimer interface [polypeptide binding]; other site 1216962001346 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 1216962001347 PYR/PP interface [polypeptide binding]; other site 1216962001348 dimer interface [polypeptide binding]; other site 1216962001349 TPP binding site [chemical binding]; other site 1216962001350 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 1216962001351 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 1216962001352 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1216962001353 active site 1216962001354 nucleotide binding site [chemical binding]; other site 1216962001355 HIGH motif; other site 1216962001356 KMSKS motif; other site 1216962001357 Riboflavin kinase; Region: Flavokinase; smart00904 1216962001358 GTPase CgtA; Reviewed; Region: obgE; PRK12299 1216962001359 GTP1/OBG; Region: GTP1_OBG; pfam01018 1216962001360 Obg GTPase; Region: Obg; cd01898 1216962001361 G1 box; other site 1216962001362 GTP/Mg2+ binding site [chemical binding]; other site 1216962001363 Switch I region; other site 1216962001364 G2 box; other site 1216962001365 G3 box; other site 1216962001366 Switch II region; other site 1216962001367 G4 box; other site 1216962001368 G5 box; other site 1216962001369 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 1216962001370 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 1216962001371 Walker A/P-loop; other site 1216962001372 ATP binding site [chemical binding]; other site 1216962001373 Q-loop/lid; other site 1216962001374 ABC transporter signature motif; other site 1216962001375 Walker B; other site 1216962001376 D-loop; other site 1216962001377 H-loop/switch region; other site 1216962001378 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 1216962001379 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 1216962001380 Walker A/P-loop; other site 1216962001381 ATP binding site [chemical binding]; other site 1216962001382 Q-loop/lid; other site 1216962001383 ABC transporter signature motif; other site 1216962001384 Walker B; other site 1216962001385 D-loop; other site 1216962001386 H-loop/switch region; other site 1216962001387 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 1216962001388 dipeptide transporter; Provisional; Region: PRK10913 1216962001389 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 1216962001390 dimer interface [polypeptide binding]; other site 1216962001391 conserved gate region; other site 1216962001392 putative PBP binding loops; other site 1216962001393 ABC-ATPase subunit interface; other site 1216962001394 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 1216962001395 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 1216962001396 dimer interface [polypeptide binding]; other site 1216962001397 conserved gate region; other site 1216962001398 putative PBP binding loops; other site 1216962001399 ABC-ATPase subunit interface; other site 1216962001400 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 1216962001401 The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; Region: PBP2_DppA_like; cd08493 1216962001402 peptide binding site [polypeptide binding]; other site 1216962001403 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 1216962001404 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 1216962001405 flagellar hook-associated protein FlgL; Validated; Region: flgL; PRK08412 1216962001406 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 1216962001407 Sulfatase; Region: Sulfatase; pfam00884 1216962001408 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 1216962001409 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 1216962001410 trimer interface [polypeptide binding]; other site 1216962001411 dimer interface [polypeptide binding]; other site 1216962001412 putative active site [active] 1216962001413 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 1216962001414 MPT binding site; other site 1216962001415 trimer interface [polypeptide binding]; other site 1216962001416 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 1216962001417 MoaE homodimer interface [polypeptide binding]; other site 1216962001418 MoaD interaction [polypeptide binding]; other site 1216962001419 active site residues [active] 1216962001420 Molybdopterin converting factor, small subunit [Coenzyme metabolism]; Region: MoaD; COG1977 1216962001421 charged pocket; other site 1216962001422 hydrophobic patch; other site 1216962001423 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 1216962001424 MoeA family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF), an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoeA; cd00887 1216962001425 dimer interface [polypeptide binding]; other site 1216962001426 putative functional site; other site 1216962001427 putative MPT binding site; other site 1216962001428 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 1216962001429 dimerization interface [polypeptide binding]; other site 1216962001430 active site 1216962001431 Domain of unknown function (DUF3943); Region: DUF3943; pfam13084 1216962001432 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 1216962001433 Sel1-like repeats; Region: SEL1; smart00671 1216962001434 Sel1-like repeats; Region: SEL1; smart00671 1216962001435 Sel1-like repeats; Region: SEL1; smart00671 1216962001436 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 1216962001437 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 1216962001438 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 1216962001439 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 1216962001440 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cl14786 1216962001441 minor groove reading motif; other site 1216962001442 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 1216962001443 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 1216962001444 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 1216962001445 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 1216962001446 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 1216962001447 minor groove reading motif; other site 1216962001448 helix-hairpin-helix signature motif; other site 1216962001449 substrate binding pocket [chemical binding]; other site 1216962001450 active site 1216962001451 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 1216962001452 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 1216962001453 DNA binding and oxoG recognition site [nucleotide binding] 1216962001454 HNH endonuclease; Region: HNH_2; pfam13391 1216962001455 C-5 cytosine-specific DNA methylase; Region: DNA_methylase; pfam00145 1216962001456 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 1216962001457 cofactor binding site; other site 1216962001458 DNA binding site [nucleotide binding] 1216962001459 substrate interaction site [chemical binding]; other site 1216962001460 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 1216962001461 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 1216962001462 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 1216962001463 ATP-grasp domain; Region: ATP-grasp_4; cl17255 1216962001464 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 1216962001465 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 1216962001466 ATP-grasp domain; Region: ATP-grasp_4; cl17255 1216962001467 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 1216962001468 IMP binding site; other site 1216962001469 dimer interface [polypeptide binding]; other site 1216962001470 interdomain contacts; other site 1216962001471 partial ornithine binding site; other site 1216962001472 NAD kinase [Coenzyme metabolism]; Region: nadF; COG0061 1216962001473 ATP-NAD kinase; Region: NAD_kinase; pfam01513 1216962001474 Autotransporter beta-domain; Region: Autotransporter; pfam03797 1216962001475 FG-GAP repeat; Region: FG-GAP_2; pfam14312 1216962001476 flagellar hook protein FlgE; Validated; Region: flgE; PRK08425 1216962001477 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 1216962001478 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 1216962001479 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 1216962001480 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 1216962001481 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 1216962001482 Hydrogenase expression/synthesis hypA family; Region: HypA; pfam01155 1216962001483 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 1216962001484 lipid-A-disaccharide synthase; Region: lpxB; TIGR00215 1216962001485 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 1216962001486 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 1216962001487 Cytochrome c1 [Energy production and conversion]; Region: CYT1; COG2857 1216962001488 Cytochrome c; Region: Cytochrom_C; pfam00034 1216962001489 Cytochrome b subunit of the bc complex [Energy production and conversion]; Region: QcrB; COG1290 1216962001490 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 1216962001491 intrachain domain interface; other site 1216962001492 interchain domain interface [polypeptide binding]; other site 1216962001493 heme bH binding site [chemical binding]; other site 1216962001494 Qi binding site; other site 1216962001495 heme bL binding site [chemical binding]; other site 1216962001496 Qo binding site; other site 1216962001497 interchain domain interface [polypeptide binding]; other site 1216962001498 intrachain domain interface; other site 1216962001499 Qi binding site; other site 1216962001500 Cytochrome b(C-terminal)/b6/petD; Region: Cytochrom_B_C; pfam00032 1216962001501 Qo binding site; other site 1216962001502 Rieske Fe-S protein [Energy production and conversion]; Region: QcrA; COG0723 1216962001503 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 1216962001504 iron-sulfur cluster [ion binding]; other site 1216962001505 [2Fe-2S] cluster binding site [ion binding]; other site 1216962001506 DNA polymerase I; Provisional; Region: PRK05755 1216962001507 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 1216962001508 active site 1216962001509 metal binding site 1 [ion binding]; metal-binding site 1216962001510 putative 5' ssDNA interaction site; other site 1216962001511 metal binding site 3; metal-binding site 1216962001512 metal binding site 2 [ion binding]; metal-binding site 1216962001513 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 1216962001514 putative DNA binding site [nucleotide binding]; other site 1216962001515 putative metal binding site [ion binding]; other site 1216962001516 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 1216962001517 active site 1216962001518 DNA binding site [nucleotide binding] 1216962001519 catalytic site [active] 1216962001520 FAD-dependent thymidylate synthase; Reviewed; Region: thyX; PRK00847 1216962001521 DDE superfamily endonuclease; Region: DDE_5; cl17874 1216962001522 aspartate ammonia-lyase; Provisional; Region: aspA; PRK12273 1216962001523 Aspartase; Region: Aspartase; cd01357 1216962001524 active sites [active] 1216962001525 tetramer interface [polypeptide binding]; other site 1216962001526 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 1216962001527 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 1216962001528 carboxyltransferase (CT) interaction site; other site 1216962001529 biotinylation site [posttranslational modification]; other site 1216962001530 biotin carboxylase; Validated; Region: PRK08462 1216962001531 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 1216962001532 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 1216962001533 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 1216962001534 aspartate aminotransferase; Provisional; Region: PRK05764 1216962001535 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 1216962001536 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1216962001537 homodimer interface [polypeptide binding]; other site 1216962001538 catalytic residue [active] 1216962001539 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 1216962001540 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 1216962001541 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 1216962001542 alphaNTD homodimer interface [polypeptide binding]; other site 1216962001543 alphaNTD - beta interaction site [polypeptide binding]; other site 1216962001544 alphaNTD - beta' interaction site [polypeptide binding]; other site 1216962001545 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 1216962001546 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 1216962001547 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 1216962001548 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 1216962001549 RNA binding surface [nucleotide binding]; other site 1216962001550 30S ribosomal protein S11; Validated; Region: PRK05309 1216962001551 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 1216962001552 30S ribosomal protein S13; Region: bact_S13; TIGR03631 1216962001553 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 1216962001554 rRNA binding site [nucleotide binding]; other site 1216962001555 predicted 30S ribosome binding site; other site 1216962001556 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 1216962001557 active site 1216962001558 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 1216962001559 SecY translocase; Region: SecY; pfam00344 1216962001560 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 1216962001561 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 1216962001562 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 1216962001563 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 1216962001564 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 1216962001565 5S rRNA interface [nucleotide binding]; other site 1216962001566 L27 interface [polypeptide binding]; other site 1216962001567 23S rRNA interface [nucleotide binding]; other site 1216962001568 L5 interface [polypeptide binding]; other site 1216962001569 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 1216962001570 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 1216962001571 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 1216962001572 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08061 1216962001573 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 1216962001574 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 1216962001575 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 1216962001576 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 1216962001577 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 1216962001578 RNA binding site [nucleotide binding]; other site 1216962001579 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 1216962001580 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 1216962001581 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 1216962001582 putative translocon interaction site; other site 1216962001583 23S rRNA interface [nucleotide binding]; other site 1216962001584 signal recognition particle (SRP54) interaction site; other site 1216962001585 L23 interface [polypeptide binding]; other site 1216962001586 trigger factor interaction site; other site 1216962001587 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 1216962001588 23S rRNA interface [nucleotide binding]; other site 1216962001589 5S rRNA interface [nucleotide binding]; other site 1216962001590 putative antibiotic binding site [chemical binding]; other site 1216962001591 L25 interface [polypeptide binding]; other site 1216962001592 L27 interface [polypeptide binding]; other site 1216962001593 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 1216962001594 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 1216962001595 G-X-X-G motif; other site 1216962001596 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 1216962001597 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 1216962001598 putative translocon binding site; other site 1216962001599 protein-rRNA interface [nucleotide binding]; other site 1216962001600 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 1216962001601 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 1216962001602 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 1216962001603 Ribosomal protein L4/L1 family; Region: Ribosomal_L4; cl00325 1216962001604 Ribosomal protein L3; Region: Ribosomal_L3; cl00324 1216962001605 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 1216962001606 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 1216962001607 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 1216962001608 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 1216962001609 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 1216962001610 Tetrahydrodipicolinate N-succinyltransferase [Amino acid transport and metabolism]; Region: DapD; COG2171 1216962001611 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 1216962001612 putative trimer interface [polypeptide binding]; other site 1216962001613 putative CoA binding site [chemical binding]; other site 1216962001614 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 1216962001615 Sel1-like repeats; Region: SEL1; smart00671 1216962001616 Sel1-like repeats; Region: SEL1; smart00671 1216962001617 Sel1-like repeats; Region: SEL1; smart00671 1216962001618 Sel1-like repeats; Region: SEL1; smart00671 1216962001619 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 1216962001620 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 1216962001621 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 1216962001622 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 1216962001623 active site 1216962001624 HslU subunit interaction site [polypeptide binding]; other site 1216962001625 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 1216962001626 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 1216962001627 Walker A motif; other site 1216962001628 ATP binding site [chemical binding]; other site 1216962001629 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 1216962001630 Walker B motif; other site 1216962001631 arginine finger; other site 1216962001632 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 1216962001633 GTPase Era; Reviewed; Region: era; PRK00089 1216962001634 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3034 1216962001635 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 1216962001636 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 1216962001637 Glycosyltransferase family 10 (fucosyltransferase); Region: Glyco_transf_10; pfam00852 1216962001638 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 1216962001639 Sel1-like repeats; Region: SEL1; smart00671 1216962001640 Sel1-like repeats; Region: SEL1; smart00671 1216962001641 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 1216962001642 Uncharacterized membrane protein, putative virulence factor [General function prediction only]; Region: MviN; COG0728 1216962001643 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 1216962001644 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 1216962001645 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1216962001646 active site 1216962001647 HIGH motif; other site 1216962001648 nucleotide binding site [chemical binding]; other site 1216962001649 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 1216962001650 KMSKS motif; other site 1216962001651 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 1216962001652 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 1216962001653 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 1216962001654 Walker A/P-loop; other site 1216962001655 ATP binding site [chemical binding]; other site 1216962001656 Q-loop/lid; other site 1216962001657 ABC transporter signature motif; other site 1216962001658 Walker B; other site 1216962001659 D-loop; other site 1216962001660 H-loop/switch region; other site 1216962001661 DNA polymerase III subunit beta; Validated; Region: PRK05643 1216962001662 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 1216962001663 putative DNA binding surface [nucleotide binding]; other site 1216962001664 dimer interface [polypeptide binding]; other site 1216962001665 beta-clamp/clamp loader binding surface; other site 1216962001666 beta-clamp/translesion DNA polymerase binding surface; other site 1216962001667 Domain of unknown function (DUF814); Region: DUF814; pfam05670 1216962001668 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 1216962001669 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1216962001670 Walker A/P-loop; other site 1216962001671 ATP binding site [chemical binding]; other site 1216962001672 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1216962001673 Walker B; other site 1216962001674 D-loop; other site 1216962001675 H-loop/switch region; other site 1216962001676 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 1216962001677 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 1216962001678 Walker A motif; other site 1216962001679 ATP binding site [chemical binding]; other site 1216962001680 Walker B motif; other site 1216962001681 arginine finger; other site 1216962001682 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 1216962001683 Elongation factor Tu GTP binding domain; Region: GTP_EFTU; pfam00009 1216962001684 G1 box; other site 1216962001685 GTP/Mg2+ binding site [chemical binding]; other site 1216962001686 Switch I region; other site 1216962001687 G2 box; other site 1216962001688 G3 box; other site 1216962001689 Switch II region; other site 1216962001690 G4 box; other site 1216962001691 G5 box; other site 1216962001692 GTP-binding protein Der; Reviewed; Region: PRK00093 1216962001693 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 1216962001694 G1 box; other site 1216962001695 GTP/Mg2+ binding site [chemical binding]; other site 1216962001696 Switch I region; other site 1216962001697 G2 box; other site 1216962001698 Switch II region; other site 1216962001699 G3 box; other site 1216962001700 G4 box; other site 1216962001701 G5 box; other site 1216962001702 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 1216962001703 G1 box; other site 1216962001704 GTP/Mg2+ binding site [chemical binding]; other site 1216962001705 Switch I region; other site 1216962001706 G2 box; other site 1216962001707 G3 box; other site 1216962001708 Switch II region; other site 1216962001709 G4 box; other site 1216962001710 G5 box; other site 1216962001711 Transglycosylase; Region: Transgly; pfam00912 1216962001712 penicillin-binding protein, 1A family; Region: PBP_1a_fam; TIGR02074 1216962001713 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 1216962001714 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 1216962001715 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1216962001716 dimer interface [polypeptide binding]; other site 1216962001717 putative CheW interface [polypeptide binding]; other site 1216962001718 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 1216962001719 putative CheA interaction surface; other site 1216962001720 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 1216962001721 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 1216962001722 putative binding surface; other site 1216962001723 active site 1216962001724 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 1216962001725 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 1216962001726 ATP binding site [chemical binding]; other site 1216962001727 Mg2+ binding site [ion binding]; other site 1216962001728 G-X-G motif; other site 1216962001729 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 1216962001730 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 1216962001731 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 1216962001732 active site 1216962001733 phosphorylation site [posttranslational modification] 1216962001734 intermolecular recognition site; other site 1216962001735 dimerization interface [polypeptide binding]; other site 1216962001736 Chemotaxis signal transduction protein [Cell motility and secretion / Signal transduction mechanisms]; Region: CheW; COG0835 1216962001737 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 1216962001738 Response regulator receiver domain; Region: Response_reg; pfam00072 1216962001739 active site 1216962001740 phosphorylation site [posttranslational modification] 1216962001741 intermolecular recognition site; other site 1216962001742 dimerization interface [polypeptide binding]; other site 1216962001743 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 1216962001744 putative active site [active] 1216962001745 putative metal binding site [ion binding]; other site 1216962001746 ThiaminS ubiquitin-like sulfur carrier protein; Region: ThiS; cd00565 1216962001747 thiS-thiF/thiG interaction site; other site 1216962001748 Short chain fatty acid transporter; Region: SCFA_trans; cl17380 1216962001749 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 1216962001750 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 2 [Coenzyme metabolism]; Region: ThiF; COG0476 1216962001751 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 1216962001752 ATP binding site [chemical binding]; other site 1216962001753 substrate interface [chemical binding]; other site 1216962001754 flagellar motor protein MotA; Validated; Region: PRK08456 1216962001755 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 1216962001756 flagellar motor protein MotB; Reviewed; Region: motB; PRK08457 1216962001757 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 1216962001758 ligand binding site [chemical binding]; other site 1216962001759 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 1216962001760 glutamine synthetase, type I; Region: GlnA; TIGR00653 1216962001761 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 1216962001762 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 1216962001763 Carbon starvation protein CstA; Region: CstA; pfam02554 1216962001764 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 1216962001765 Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20...; Region: PGRP; cd06583 1216962001766 amidase catalytic site [active] 1216962001767 Zn binding residues [ion binding]; other site 1216962001768 substrate binding site [chemical binding]; other site 1216962001769 catabolite control protein A; Region: ccpA; TIGR01481 1216962001770 Homeodomain-like domain; Region: HTH_23; pfam13384 1216962001771 Phage virion morphogenesis family; Region: Phage_tail_S; cl02089 1216962001772 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dam; COG0338 1216962001773 ribonucleoside-diphosphate reductase, alpha chain; Region: NrdE-prime; TIGR02510 1216962001774 Phage Mu protein F like protein; Region: Phage_Mu_F; cl10072 1216962001775 Protein of unknown function (DUF935); Region: DUF935; pfam06074 1216962001776 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4487 1216962001777 Uncharacterized protein conserved in bacteria (DUF2130); Region: DUF2130; pfam09903 1216962001778 HipA-like C-terminal domain; Region: HipA_C; pfam07804 1216962001780 crystallin beta/gamma motif-containing protein; Region: PHA00657 1216962001781 Phage portal protein, SPP1 Gp6-like; Region: Phage_prot_Gp6; pfam05133 1216962001782 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 1216962001783 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 1216962001784 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5410 1216962001785 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 1216962001786 G4 box; other site 1216962001787 G5 box; other site 1216962001788 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 1216962001789 G4 box; other site 1216962001790 G5 box; other site 1216962001791 Protein of unknown function (DUF4043); Region: DUF4043; pfam13252 1216962001792 CHC2 zinc finger; Region: zf-CHC2; cl17510 1216962001793 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 1216962001794 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 1216962001795 active site 1216962001796 metal binding site [ion binding]; metal-binding site 1216962001797 interdomain interaction site; other site 1216962001798 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 1216962001799 Walker A motif; other site 1216962001800 ATP binding site [chemical binding]; other site 1216962001801 Walker B motif; other site 1216962001802 PNGase/UBA or UBX (PUB) domain of p97 adaptor proteins; Region: PUB; cl15262 1216962001803 peptide binding site [polypeptide binding]; other site 1216962001804 Domain of unknown function (DUF3596); Region: DUF3596; pfam12167 1216962001805 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 1216962001806 phiLC3 phage and phage-related integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes various bacterial (mainly gram positive) and phage integrases, including those similar to Lactococcus...; Region: INT_phiLC3_C; cd01189 1216962001807 Int/Topo IB signature motif; other site 1216962001808 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 1216962001809 Domain of unknown function (DUF3596); Region: DUF3596; pfam12167 1216962001810 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 1216962001811 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 1216962001812 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 1216962001813 CrcB-like protein; Region: CRCB; cl09114 1216962001814 phosphogluconate dehydratase; Validated; Region: PRK09054 1216962001815 6-phosphogluconate dehydratase; Region: edd; TIGR01196 1216962001816 Initiator Replication protein; Region: Rep_3; pfam01051 1216962001817 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 1216962001818 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 1216962001819 binding surface 1216962001820 TPR motif; other site 1216962001821 type I site-specific deoxyribonuclease, HsdR family; Region: hsdR; TIGR00348 1216962001822 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 1216962001823 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 1216962001824 ATP binding site [chemical binding]; other site 1216962001825 putative Mg++ binding site [ion binding]; other site 1216962001826 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 1216962001827 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 1216962001828 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 1216962001829 ATP binding site [chemical binding]; other site 1216962001830 putative Mg++ binding site [ion binding]; other site 1216962001831 RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; Region: Rel-Spo_like; cl11966 1216962001832 metal binding triad [ion binding]; metal-binding site 1216962001833 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 1216962001834 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 1216962001835 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 1216962001836 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 1216962001837 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 1216962001838 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 1216962001839 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 1216962001840 active site 1216962001841 carbon storage regulator; Provisional; Region: PRK00568 1216962001842 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: PRK04181 1216962001843 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 1216962001844 SmpB-tmRNA interface; other site 1216962001845 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; pfam01618 1216962001846 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 1216962001847 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 1216962001848 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 1216962001849 Ribonuclease P; Region: Ribonuclease_P; pfam00825 1216962001850 Ribonuclease P; Region: Ribonuclease_P; pfam00825 1216962001851 Haemolytic domain; Region: Haemolytic; pfam01809 1216962001852 membrane protein insertase; Provisional; Region: PRK01318 1216962001853 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 1216962001854 Predicted RNA-binding protein [General function prediction only]; Region: Jag; COG1847 1216962001855 jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta...; Region: jag_KH; cd02414 1216962001856 G-X-X-G motif; other site 1216962001857 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 1216962001858 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 1216962001859 Circularly permuted YlqF-related GTPases; Region: YlqF_related_GTPase; cl17249 1216962001860 GTP/Mg2+ binding site [chemical binding]; other site 1216962001861 G5 box; other site 1216962001862 trmE is a tRNA modification GTPase; Region: trmE; cd04164 1216962001863 G1 box; other site 1216962001864 G1 box; other site 1216962001865 GTP/Mg2+ binding site [chemical binding]; other site 1216962001866 Switch I region; other site 1216962001867 Switch I region; other site 1216962001868 G2 box; other site 1216962001869 G2 box; other site 1216962001870 Switch II region; other site 1216962001871 G3 box; other site 1216962001872 G4 box; other site 1216962001873 G5 box; other site 1216962001874 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 1216962001875 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1216962001876 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 1216962001877 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1216962001878 Walker A/P-loop; other site 1216962001879 ATP binding site [chemical binding]; other site 1216962001880 Q-loop/lid; other site 1216962001881 ABC transporter signature motif; other site 1216962001882 Walker B; other site 1216962001883 D-loop; other site 1216962001884 H-loop/switch region; other site 1216962001885 Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II); Region: Aldolase_II; cl00214 1216962001886 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 1216962001887 ATP-binding cassette domain of multidrug resistance protein-like transporters; Region: ABCC_MRP_Like; cd03228 1216962001888 Walker A/P-loop; other site 1216962001889 ATP binding site [chemical binding]; other site 1216962001890 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 1216962001891 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 1216962001892 dimer interface [polypeptide binding]; other site 1216962001893 decamer (pentamer of dimers) interface [polypeptide binding]; other site 1216962001894 catalytic triad [active] 1216962001895 peroxidatic and resolving cysteines [active] 1216962001896 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1216962001897 ATP-binding cassette domain of multidrug resistance protein-like transporters; Region: ABCC_MRP_Like; cd03228 1216962001898 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 1216962001899 Walker A/P-loop; other site 1216962001900 ATP binding site [chemical binding]; other site 1216962001901 Q-loop/lid; other site 1216962001902 ABC transporter signature motif; other site 1216962001903 Walker B; other site 1216962001904 D-loop; other site 1216962001905 H-loop/switch region; other site 1216962001906 Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl...; Region: CIS_IPPS; cl00230 1216962001907 Undecaprenyl pyrophosphate synthase [Lipid metabolism]; Region: UppS; COG0020 1216962001908 catalytic residue [active] 1216962001909 putative FPP diphosphate binding site; other site 1216962001910 putative FPP binding hydrophobic cleft; other site 1216962001911 dimer interface [polypeptide binding]; other site 1216962001912 putative IPP diphosphate binding site; other site 1216962001913 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 1216962001914 FAD binding domain; Region: FAD_binding_4; pfam01565 1216962001915 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 1216962001916 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 1216962001917 active site residue [active] 1216962001918 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 1216962001919 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 1216962001920 active site 1216962001921 CrcB-like protein; Region: CRCB; cl09114 1216962001922 Etoposide-induced protein 2.4 (EI24); Region: EI24; pfam07264 1216962001923 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 1216962001924 active site 1216962001925 CrcB-like protein; Region: CRCB; cl09114 1216962001926 Etoposide-induced protein 2.4 (EI24); Region: EI24; pfam07264 1216962001927 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 1216962001928 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 1216962001929 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 1216962001930 intersubunit interface [polypeptide binding]; other site 1216962001931 active site 1216962001932 zinc binding site [ion binding]; other site 1216962001933 Na+ binding site [ion binding]; other site 1216962001934 elongation factor P; Validated; Region: PRK00529 1216962001935 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 1216962001936 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 1216962001937 RNA binding site [nucleotide binding]; other site 1216962001938 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 1216962001939 RNA binding site [nucleotide binding]; other site 1216962001940 tumor necrosis factor alpha-inducing protein; Reviewed; Region: PRK12303 1216962001941 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 1216962001942 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 1216962001943 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 1216962001944 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 1216962001945 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 1216962001946 HlyD family secretion protein; Region: HlyD_3; pfam13437 1216962001947 Outer membrane efflux protein; Region: OEP; pfam02321 1216962001948 Outer membrane efflux protein; Region: OEP; pfam02321 1216962001949 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 1216962001950 Domain of unknown function DUF21; Region: DUF21; pfam01595 1216962001951 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 1216962001952 Transporter associated domain; Region: CorC_HlyC; smart01091 1216962001953 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 1216962001954 Phosphate transporter family; Region: PHO4; cl00396 1216962001955 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 1216962001956 active site 1216962001957 ATP binding site [chemical binding]; other site 1216962001958 substrate binding site [chemical binding]; other site 1216962001959 activation loop (A-loop); other site 1216962001960 Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of...; Region: vWFA; cl00057 1216962001961 metal ion-dependent adhesion site (MIDAS); other site 1216962001962 Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence...; Region: PP2Cc; cl00120 1216962001963 Protein phosphatase 2C; Region: PP2C_2; pfam13672 1216962001964 NifU-like domain; Region: NifU; pfam01106 1216962001965 putative manganese-dependent inorganic pyrophosphatase; Provisional; Region: PRK14869 1216962001966 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 1216962001967 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1216962001968 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1216962001969 Class I aldolases; Region: Aldolase_Class_I; cl17187 1216962001970 transaldolase; Provisional; Region: PRK03903 1216962001971 catalytic residue [active] 1216962001972 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 1216962001973 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 1216962001974 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 1216962001975 threonine/serine transporter TdcC; Provisional; Region: PRK13629; cl17672 1216962001976 Putative transposase DNA-binding domain; Region: OrfB_Zn_ribbon; pfam07282 1216962001977 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 1216962001978 Probable transposase; Region: OrfB_IS605; pfam01385 1216962001979 Helix-turn-helix domain; Region: HTH_OrfB_IS605; pfam12323 1216962001980 Putative transposase DNA-binding domain; Region: OrfB_Zn_ribbon; pfam07282 1216962001981 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 1216962001982 Probable transposase; Region: OrfB_IS605; pfam01385 1216962001983 Helix-turn-helix domain; Region: HTH_OrfB_IS605; pfam12323 1216962001984 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 1216962001985 threonine/serine transporter TdcC; Provisional; Region: PRK13629; cl17672 1216962001986 fumarate hydratase; Reviewed; Region: fumC; PRK00485 1216962001987 Class II fumarases; Region: Fumarase_classII; cd01362 1216962001988 active site 1216962001989 tetramer interface [polypeptide binding]; other site 1216962001990 YtkA-like; Region: YtkA; pfam13115 1216962001991 Outer membrane efflux protein; Region: OEP; pfam02321 1216962001992 Outer membrane efflux protein; Region: OEP; pfam02321 1216962001993 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 1216962001994 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 1216962001995 E3 interaction surface; other site 1216962001996 lipoyl attachment site [posttranslational modification]; other site 1216962001997 HlyD family secretion protein; Region: HlyD_3; pfam13437 1216962001998 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 1216962001999 fumarate reductase iron-sulfur subunit; Provisional; Region: frdB; PRK13552 1216962002000 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 1216962002001 catalytic loop [active] 1216962002002 iron binding site [ion binding]; other site 1216962002003 fumarate reductase flavoprotein subunit; Provisional; Region: PRK08626 1216962002004 L-aspartate oxidase; Provisional; Region: PRK06175 1216962002005 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 1216962002006 fumarate reductase cytochrome b-556 subunit; Provisional; Region: PRK13553 1216962002007 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 1216962002008 Iron-sulfur protein interface; other site 1216962002009 proximal heme binding site [chemical binding]; other site 1216962002010 distal heme binding site [chemical binding]; other site 1216962002011 dimer interface [polypeptide binding]; other site 1216962002012 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 1216962002013 substrate binding site [chemical binding]; other site 1216962002014 dimer interface [polypeptide binding]; other site 1216962002015 catalytic triad [active] 1216962002016 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 1216962002017 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 1216962002018 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 1216962002019 trimer interface [polypeptide binding]; other site 1216962002020 active site 1216962002021 UDP-GlcNAc binding site [chemical binding]; other site 1216962002022 lipid binding site [chemical binding]; lipid-binding site 1216962002023 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 1216962002024 metabolite-proton symporter; Region: 2A0106; TIGR00883 1216962002025 putative substrate translocation pore; other site 1216962002026 Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_1; cd09111 1216962002027 PLD-like domain; Region: PLDc_2; pfam13091 1216962002028 putative active site [active] 1216962002029 catalytic site [active] 1216962002030 Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_2; cd09113 1216962002031 PLD-like domain; Region: PLDc_2; pfam13091 1216962002032 putative active site [active] 1216962002033 catalytic site [active] 1216962002034 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 1216962002035 NADPH:quinone reductase and related Zn-dependent oxidoreductases [Energy production and conversion / General function prediction only]; Region: Qor; COG0604 1216962002036 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 1216962002037 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 1216962002038 MraW methylase family; Region: Methyltransf_5; cl17771 1216962002039 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2604 1216962002040 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 1216962002041 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 1216962002042 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 1216962002043 protein binding site [polypeptide binding]; other site 1216962002044 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 1216962002045 protein binding site [polypeptide binding]; other site 1216962002046 Amino acid transporters [Amino acid transport and metabolism]; Region: LysP; COG0833 1216962002047 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3399 1216962002048 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 1216962002049 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 1216962002050 tandem repeat interface [polypeptide binding]; other site 1216962002051 oligomer interface [polypeptide binding]; other site 1216962002052 active site residues [active] 1216962002053 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 1216962002054 Major Facilitator Superfamily; Region: MFS_1; pfam07690 1216962002055 putative substrate translocation pore; other site 1216962002056 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3014 1216962002057 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 1216962002058 RNA methyltransferase, RsmE family; Region: TIGR00046 1216962002059 Catalase-like heme-binding proteins similar to the uncharacterized srpA; Region: srpA_like; cd08153 1216962002060 putative heme binding pocket [chemical binding]; other site 1216962002061 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1216962002062 Integral membrane protein TerC family; Region: TerC; cl10468 1216962002063 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 1216962002064 Ligand Binding Site [chemical binding]; other site 1216962002065 NADH dehydrogenase subunit A; Validated; Region: PRK08489 1216962002066 NADH dehydrogenase subunit B; Validated; Region: PRK06411 1216962002067 NADH dehydrogenase subunit C; Provisional; Region: PRK08491 1216962002068 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; cl16917 1216962002069 NADH dehydrogenase subunit D; Validated; Region: PRK06075 1216962002070 NADH dehydrogenase I, D subunit; Region: NuoD; TIGR01962 1216962002071 NADH dehydrogenase subunit G; Validated; Region: PRK08493 1216962002072 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 1216962002073 catalytic loop [active] 1216962002074 iron binding site [ion binding]; other site 1216962002075 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 1216962002076 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 1216962002077 molybdopterin cofactor binding site; other site 1216962002078 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 1216962002079 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 1216962002080 NADH-quinone oxidoreductase, chain I; Region: NuoI; TIGR01971 1216962002081 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 1216962002082 4Fe-4S binding domain; Region: Fer4; pfam00037 1216962002083 NADH:ubiquinone oxidoreductase subunit 6 (chain J) [Energy production and conversion]; Region: NuoJ; COG0839 1216962002084 NADH dehydrogenase subunit J; Provisional; Region: PRK06433 1216962002085 NADH dehydrogenase subunit 6; Provisional; Region: ND6; MTH00213 1216962002086 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 1216962002087 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 1216962002088 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 1216962002089 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1216962002090 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 1216962002091 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1216962002092 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 1216962002093 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 1216962002094 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 1216962002095 N-acetylneuraminate synthase; Region: NeuB_NnaB; TIGR03569 1216962002096 NeuB family; Region: NeuB; pfam03102 1216962002097 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 1216962002098 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 1216962002099 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 1216962002100 Alpha-2,3-sialyltransferase (CST-I); Region: CST-I; pfam06002 1216962002101 replicative DNA helicase; Provisional; Region: PRK08506 1216962002102 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 1216962002103 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 1216962002104 Walker A motif; other site 1216962002105 ATP binding site [chemical binding]; other site 1216962002106 Walker B motif; other site 1216962002107 DNA binding loops [nucleotide binding] 1216962002108 Competence protein; Region: Competence; cl00471 1216962002109 prenyltransferase; Reviewed; Region: ubiA; PRK12874 1216962002110 UbiA prenyltransferase family; Region: UbiA; pfam01040 1216962002111 Helix-turn-helix domain; Region: HTH_28; pfam13518 1216962002112 Phosphatidylserine decarboxylase; Region: PS_Dcarbxylase; cl03656 1216962002113 quinolinate synthetase; Provisional; Region: PRK09375 1216962002114 nicotinate-nucleotide pyrophosphorylase; Provisional; Region: PRK05848 1216962002115 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 1216962002116 dimerization interface [polypeptide binding]; other site 1216962002117 active site 1216962002118 thiamine monophosphate kinase; Provisional; Region: PRK05731 1216962002119 ThiL (Thiamine-monophosphate kinase) plays a dual role in de novo biosynthesis and in salvage of exogenous thiamine. Thiamine salvage occurs in two steps, with thiamine kinase catalyzing the formation of thiamine phosphate, and ThiL catalyzing the...; Region: ThiL; cd02194 1216962002120 ATP binding site [chemical binding]; other site 1216962002121 dimerization interface [polypeptide binding]; other site 1216962002122 Putative F0F1-ATPase subunit (ATPase_gene1); Region: ATPase_gene1; pfam09527 1216962002123 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 1216962002124 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 1216962002125 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 1216962002126 inhibitor-cofactor binding pocket; inhibition site 1216962002127 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1216962002128 catalytic residue [active] 1216962002129 YceI-like domain; Region: YceI; cl01001 1216962002130 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 1216962002131 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD1; cd05283 1216962002132 putative NAD(P) binding site [chemical binding]; other site 1216962002133 putative substrate binding site [chemical binding]; other site 1216962002134 catalytic Zn binding site [ion binding]; other site 1216962002135 structural Zn binding site [ion binding]; other site 1216962002136 dimer interface [polypeptide binding]; other site 1216962002137 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 1216962002138 Esterase/lipase [Lipid metabolism]; Region: Aes; COG0657 1216962002139 Sulfatase; Region: Sulfatase; cl17466 1216962002140 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 1216962002141 Sulfatase; Region: Sulfatase; cl17466 1216962002142 Predicted neuraminidase (sialidase) [Carbohydrate transport and metabolism]; Region: COG4692 1216962002143 BNR repeat-like domain; Region: BNR_2; pfam13088 1216962002144 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 1216962002145 Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; Region: FDH_GDH_like; cl17240 1216962002146 NAD binding site [chemical binding]; other site 1216962002147 Arginase family; Region: Arginase; cd09989 1216962002148 active site 1216962002149 Mn binding site [ion binding]; other site 1216962002150 oligomer interface [polypeptide binding]; other site 1216962002151 Solute carrier families 5 and 6-like; solute binding domain; Region: SLC5-6-like_sbd; cl00456 1216962002152 Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; Region: FDH_GDH_like; cl17240 1216962002153 NAD binding site [chemical binding]; other site 1216962002154 Arginase family; Region: Arginase; cd09989 1216962002155 active site 1216962002156 Mn binding site [ion binding]; other site 1216962002157 oligomer interface [polypeptide binding]; other site 1216962002158 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 1216962002159 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain; Region: SLC5sbd_u4; cd11480 1216962002160 Na binding site [ion binding]; other site 1216962002161 Protein of unknown function, DUF485; Region: DUF485; pfam04341 1216962002162 Protein of unknown function, DUF485; Region: DUF485; pfam04341 1216962002163 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 1216962002164 Mechanosensitive ion channel; Region: MS_channel; pfam00924 1216962002165 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 1216962002166 active site 1216962002167 dimer interface [polypeptide binding]; other site 1216962002168 metal binding site [ion binding]; metal-binding site 1216962002169 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3400 1216962002170 TrkA-C domain; Region: TrkA_C; pfam02080 1216962002171 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 1216962002172 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 1216962002173 cell division protein FtsZ; Validated; Region: PRK09330 1216962002174 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 1216962002175 nucleotide binding site [chemical binding]; other site 1216962002176 SulA interaction site; other site 1216962002177 cell division protein FtsA; Region: ftsA; TIGR01174 1216962002178 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 1216962002179 nucleotide binding site [chemical binding]; other site 1216962002180 SHS2 domain inserted in FTSA; Region: SHS2_FTSA; pfam02491 1216962002181 Cell division protein FtsA; Region: FtsA; pfam14450 1216962002182 SurA N-terminal domain; Region: SurA_N_3; cl07813 1216962002183 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 1216962002184 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 1216962002185 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK05964 1216962002186 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 1216962002187 inhibitor-cofactor binding pocket; inhibition site 1216962002188 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1216962002189 catalytic residue [active] 1216962002190 Amino Acid Kinases (AAK) superfamily, catalytic domain; present in such enzymes like N-acetylglutamate kinase (NAGK), carbamate kinase (CK), aspartokinase (AK), glutamate-5-kinase (G5K) and UMP kinase (UMPK). The AAK superfamily includes kinases that...; Region: AAK; cl00452 1216962002191 nucleotide binding site [chemical binding]; other site 1216962002192 DNA-directed RNA polymerase subunit omega; Reviewed; Region: rpoZ; PRK00392 1216962002193 (p)ppGpp synthetase, RelA/SpoT family; Region: spoT_relA; TIGR00691 1216962002194 HD domain; Region: HD_4; pfam13328 1216962002195 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 1216962002196 synthetase active site [active] 1216962002197 NTP binding site [chemical binding]; other site 1216962002198 metal binding site [ion binding]; metal-binding site 1216962002199 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 1216962002200 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 1216962002201 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 1216962002202 active site 1216962002203 HIGH motif; other site 1216962002204 dimer interface [polypeptide binding]; other site 1216962002205 KMSKS motif; other site 1216962002206 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 1216962002207 RNA binding surface [nucleotide binding]; other site 1216962002208 Nitronate monooxygenase; Region: NMO; pfam03060 1216962002209 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 1216962002210 FMN binding site [chemical binding]; other site 1216962002211 substrate binding site [chemical binding]; other site 1216962002212 putative catalytic residue [active] 1216962002213 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 1216962002214 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 1216962002215 active site 1216962002216 metal binding site [ion binding]; metal-binding site 1216962002217 Menaquinone biosynthesis; Region: VitK2_biosynth; cl17475 1216962002218 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated; Region: PRK09238 1216962002219 Aconitase B swivel domain. Aconitate hydratase B is involved in energy metabolism as part of the TCA cycle. It catalyses the formation of cis-aconitate from citrate. This is the aconitase swivel domain, which undergoes swivelling conformational change in...; Region: AcnB_Swivel; cd01576 1216962002220 substrate binding site [chemical binding]; other site 1216962002221 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 1216962002222 substrate binding site [chemical binding]; other site 1216962002223 ligand binding site [chemical binding]; other site 1216962002224 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 1216962002225 dimer interface [polypeptide binding]; other site 1216962002226 conserved gate region; other site 1216962002227 putative PBP binding loops; other site 1216962002228 ABC-ATPase subunit interface; other site 1216962002229 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 1216962002230 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 1216962002231 dimer interface [polypeptide binding]; other site 1216962002232 conserved gate region; other site 1216962002233 putative PBP binding loops; other site 1216962002234 ABC-ATPase subunit interface; other site 1216962002235 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 1216962002236 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 1216962002237 Walker A/P-loop; other site 1216962002238 ATP binding site [chemical binding]; other site 1216962002239 Q-loop/lid; other site 1216962002240 ABC transporter signature motif; other site 1216962002241 Walker B; other site 1216962002242 D-loop; other site 1216962002243 H-loop/switch region; other site 1216962002244 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 1216962002245 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 1216962002246 substrate binding pocket [chemical binding]; other site 1216962002247 membrane-bound complex binding site; other site 1216962002248 hinge residues; other site 1216962002249 Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; Region: FDH_GDH_like; cl17240 1216962002250 2-hydroxyacid dehydrogenase; Provisional; Region: PRK08410 1216962002251 NAD binding site [chemical binding]; other site 1216962002252 Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; Region: FDH_GDH_like; cl17240 1216962002253 NAD binding site [chemical binding]; other site 1216962002254 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; cl00248 1216962002255 dimerization interface [polypeptide binding]; other site 1216962002256 substrate binding site [chemical binding]; other site 1216962002257 active site 1216962002258 calcium binding site [ion binding]; other site 1216962002259 Solute carrier families 5 and 6-like; solute binding domain; Region: SLC5-6-like_sbd; cl00456 1216962002260 Na binding site [ion binding]; other site 1216962002261 Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; Region: FDH_GDH_like; cl17240 1216962002262 NAD binding site [chemical binding]; other site 1216962002263 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; cl00248 1216962002264 dimerization interface [polypeptide binding]; other site 1216962002265 substrate binding site [chemical binding]; other site 1216962002266 active site 1216962002267 calcium binding site [ion binding]; other site 1216962002268 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 1216962002269 Na2 binding site [ion binding]; other site 1216962002270 putative substrate binding site 1 [chemical binding]; other site 1216962002271 Na binding site 1 [ion binding]; other site 1216962002272 putative substrate binding site 2 [chemical binding]; other site 1216962002273 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 1216962002274 putative substrate binding site 2 [chemical binding]; other site 1216962002275 putative substrate binding site 1 [chemical binding]; other site 1216962002276 Na binding site 1 [ion binding]; other site 1216962002277 Na2 binding site [ion binding]; other site 1216962002278 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 1216962002279 active site 1216962002280 Protein of unknown function (DUF493); Region: DUF493; pfam04359 1216962002281 Disulfide bond formation protein DsbB; Region: DsbB; cl00649 1216962002282 Protein of unknown function (DUF507); Region: DUF507; pfam04368 1216962002283 carbamoyl-phosphate synthase, small subunit; Region: CPSaseIIsmall; TIGR01368 1216962002284 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; cl03056 1216962002285 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 1216962002286 catalytic site [active] 1216962002287 subunit interface [polypeptide binding]; other site 1216962002288 V-type ATP synthase subunit I; Validated; Region: PRK05771 1216962002289 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl14958 1216962002290 type II restriction m6 adenine DNA methyltransferase, Alw26I/Eco31I/Esp3I family; Region: met_A_Alw26; TIGR02987 1216962002291 Eco57I restriction-modification methylase; Region: Eco57I; pfam07669 1216962002292 Uncharacterized conserved protein [Function unknown]; Region: COG4278 1216962002293 Protein of unknown function DUF262; Region: DUF262; pfam03235 1216962002294 Alginate Lyase A1-III; enzymatically depolymerizes alginate, a complex copolymer of beta-D-mannuronate and alpha-L-guluronate, by cleaving the beta-(1,4) glycosidic bond; Region: AlgLyase; cl00179 1216962002295 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 1216962002296 Saccharopine dehydrogenase and related proteins [Amino acid transport and metabolism]; Region: LYS9; COG1748 1216962002297 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 1216962002298 sodium--glutamate symport carrier (gltS); Region: gltS; TIGR00210 1216962002299 riboflavin biosynthesis protein RibD; Region: eubact_ribD; TIGR00326 1216962002300 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 1216962002301 catalytic motif [active] 1216962002302 Zn binding site [ion binding]; other site 1216962002303 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 1216962002304 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 1216962002305 S-adenosylmethionine binding site [chemical binding]; other site 1216962002306 Putative metal-binding domain of cation transport ATPase; Region: ATPase-cat_bd; pfam12156 1216962002307 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 1216962002308 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 1216962002309 metal-binding site [ion binding] 1216962002310 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 1216962002311 Soluble P-type ATPase [General function prediction only]; Region: COG4087 1216962002312 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 1216962002313 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 1216962002314 inhibitor-cofactor binding pocket; inhibition site 1216962002315 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1216962002316 catalytic residue [active] 1216962002317 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl17548 1216962002318 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 1216962002319 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 1216962002320 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 1216962002321 nucleotide binding region [chemical binding]; other site 1216962002322 ATP-binding site [chemical binding]; other site 1216962002323 SEC-C motif; Region: SEC-C; pfam02810 1216962002324 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 1216962002325 FtsX-like permease family; Region: FtsX; pfam02687 1216962002326 RNA recognition motif (RRM) superfamily; Region: RRM_SF; cl17169 1216962002327 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 1216962002328 GIY-YIG motif/motif A; other site 1216962002329 active site 1216962002330 catalytic site [active] 1216962002331 putative DNA binding site [nucleotide binding]; other site 1216962002332 metal binding site [ion binding]; metal-binding site 1216962002333 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 1216962002334 hypothetical protein; Provisional; Region: PRK05839 1216962002335 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 1216962002336 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1216962002337 homodimer interface [polypeptide binding]; other site 1216962002338 catalytic residue [active] 1216962002339 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 1216962002340 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1216962002341 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1216962002342 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1216962002343 recombination and DNA strand exchange inhibitor protein; Reviewed; Region: PRK00409 1216962002344 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1216962002345 Walker A/P-loop; other site 1216962002346 ATP binding site [chemical binding]; other site 1216962002347 Q-loop/lid; other site 1216962002348 ABC transporter signature motif; other site 1216962002349 Walker B; other site 1216962002350 D-loop; other site 1216962002351 H-loop/switch region; other site 1216962002352 Smr domain; Region: Smr; pfam01713 1216962002353 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 1216962002354 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 1216962002355 Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]; Region: AbgB; COG1473 1216962002356 M20 Peptidase Aminoacylase 1 subfamily; Region: M20_Acy1_like1; cd05666 1216962002357 metal binding site [ion binding]; metal-binding site 1216962002358 putative dimer interface [polypeptide binding]; other site 1216962002359 Nitrate and nitrite sensing; Region: NIT; pfam08376 1216962002360 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 1216962002361 HAMP domain; Region: HAMP; pfam00672 1216962002362 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1216962002363 dimer interface [polypeptide binding]; other site 1216962002364 putative CheW interface [polypeptide binding]; other site 1216962002365 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 1216962002366 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 1216962002367 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 1216962002368 tetramer interfaces [polypeptide binding]; other site 1216962002369 binuclear metal-binding site [ion binding]; other site 1216962002370 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1216962002371 FOG: PAS/PAC domain [Signal transduction mechanisms]; Region: AtoS; COG2202 1216962002372 putative active site [active] 1216962002373 heme pocket [chemical binding]; other site 1216962002374 PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; Region: PAS; cd00130 1216962002375 putative active site [active] 1216962002376 heme pocket [chemical binding]; other site 1216962002377 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1216962002378 dimer interface [polypeptide binding]; other site 1216962002379 putative CheW interface [polypeptide binding]; other site 1216962002380 Cellular and retroviral pepsin-like aspartate proteases; Region: pepsin_retropepsin_like; cl11403 1216962002381 aspartate aminotransferase; Provisional; Region: PRK06225 1216962002382 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 1216962002383 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 1216962002384 LytB protein; Region: LYTB; pfam02401 1216962002385 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 1216962002386 conserved cys residue [active] 1216962002387 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 1216962002388 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 1216962002389 hinge; other site 1216962002390 active site 1216962002391 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 1216962002392 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 1216962002393 putative tRNA-binding site [nucleotide binding]; other site 1216962002394 tRNA synthetase B5 domain; Region: B5; smart00874 1216962002395 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 1216962002396 dimer interface [polypeptide binding]; other site 1216962002397 motif 1; other site 1216962002398 motif 3; other site 1216962002399 motif 2; other site 1216962002400 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; smart00896 1216962002401 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 1216962002402 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 1216962002403 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 1216962002404 dimer interface [polypeptide binding]; other site 1216962002405 motif 1; other site 1216962002406 active site 1216962002407 motif 2; other site 1216962002408 motif 3; other site 1216962002409 Predicted phosphohydrolase (DHH superfamily) [General function prediction only]; Region: COG2404 1216962002410 DHH family; Region: DHH; pfam01368 1216962002411 Flagellar biosynthesis pathway, component FlhA [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FlhA; cl07980 1216962002412 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 1216962002413 16S/18S rRNA binding site [nucleotide binding]; other site 1216962002414 S13e-L30e interaction site [polypeptide binding]; other site 1216962002415 25S rRNA binding site [nucleotide binding]; other site 1216962002416 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 1216962002417 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 1216962002418 thymidylate kinase; Validated; Region: tmk; PRK00698 1216962002419 TMP-binding site; other site 1216962002420 ATP-binding site [chemical binding]; other site 1216962002421 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 1216962002422 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 1216962002423 active site 1216962002424 (T/H)XGH motif; other site 1216962002425 SAF-like; Region: SAF_2; pfam13144 1216962002426 Domains similar to fish antifreeze type III protein; Region: SAF; cl00555 1216962002427 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 1216962002428 Part of AAA domain; Region: AAA_19; pfam13245 1216962002429 Family description; Region: UvrD_C_2; pfam13538 1216962002430 TPR repeat; Region: TPR_11; pfam13414 1216962002431 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 1216962002432 TPR motif; other site 1216962002433 binding surface 1216962002434 seryl-tRNA synthetase; Provisional; Region: PRK05431 1216962002435 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 1216962002436 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 1216962002437 dimer interface [polypeptide binding]; other site 1216962002438 active site 1216962002439 motif 1; other site 1216962002440 motif 2; other site 1216962002441 motif 3; other site 1216962002442 Predicted amidohydrolase [General function prediction only]; Region: COG0388 1216962002443 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cd07197 1216962002444 active site 1216962002445 catalytic triad [active] 1216962002446 dimer interface [polypeptide binding]; other site 1216962002447 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 1216962002448 Uncharacterized protein family (UPF0093); Region: UPF0093; pfam03653 1216962002449 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 1216962002450 META domain; Region: META; cl01245 1216962002451 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 1216962002452 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 1216962002453 Mg++ binding site [ion binding]; other site 1216962002454 putative catalytic motif [active] 1216962002455 putative substrate binding site [chemical binding]; other site 1216962002456 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK03815 1216962002457 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1216962002458 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1216962002459 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 1216962002460 Mechanosensitive ion channel; Region: MS_channel; pfam00924 1216962002461 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1216962002462 dimer interface [polypeptide binding]; other site 1216962002463 putative CheW interface [polypeptide binding]; other site 1216962002464 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 1216962002465 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 1216962002466 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK14593 1216962002467 RimM N-terminal domain; Region: RimM; pfam01782 1216962002468 Predicted RNA-binding protein (contains KH domain) [General function prediction only]; Region: COG1837 1216962002469 KH domain; Region: KH_4; pfam13083 1216962002470 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 1216962002471 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 1216962002472 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 1216962002473 NAD(P) binding site [chemical binding]; other site 1216962002474 Flavodoxin-like fold; Region: Flavodoxin_2; pfam02525 1216962002475 Maltose O-acetyltransferase (MAT) and Galactoside O-acetyltransferase (GAT): MAT and GAT catalyze the CoA-dependent acetylation of the 6-hydroxyl group of their respective sugar substrates. MAT acetylates maltose and glucose exclusively at the C6...; Region: LbH_MAT_GAT; cd03357 1216962002476 active site 1216962002477 substrate binding site [chemical binding]; other site 1216962002478 trimer interface [polypeptide binding]; other site 1216962002479 CoA binding site [chemical binding]; other site 1216962002480 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 1216962002481 Carboxymuconolactone decarboxylase family; Region: CMD; pfam02627 1216962002482 Uncharacterized homolog of gamma-carboxymuconolactone decarboxylase subunit [Function unknown]; Region: COG0599 1216962002483 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 1216962002484 DNA methylase; Region: N6_N4_Mtase; pfam01555 1216962002485 Restriction endonuclease BglII; Region: Endonuc-BglII; pfam09195 1216962002486 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 1216962002487 DNA-methyltransferase (dcm); Region: dcm; TIGR00675 1216962002488 cofactor binding site; other site 1216962002489 DNA binding site [nucleotide binding] 1216962002490 substrate interaction site [chemical binding]; other site 1216962002491 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 1216962002492 Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial...; Region: Aldo_ket_red; cd06660 1216962002493 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 1216962002494 active site 1216962002495 catalytic tetrad [active] 1216962002496 Cache domain; Region: Cache_1; pfam02743 1216962002497 LabA_like proteins; Region: LabA_like; cd06167 1216962002498 Uncharacterized conserved protein [Function unknown]; Region: COG1432 1216962002499 putative metal binding site [ion binding]; other site 1216962002500 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1216962002501 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 1216962002502 This family is most closely related to the GT1 family of glycosyltransferases. wcfI in Bacteroides fragilis has been shown to be involved in the capsular polysaccharide biosynthesis; Region: GT1_wcfI_like; cd03825 1216962002503 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1216962002504 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 1216962002505 WfgS and WfeV are involved in O-antigen biosynthesis; Region: GT_2_WfgS_like; cd06433 1216962002506 metal-binding site 1216962002507 HAD-superfamily hydrolase, subfamily IIIA; Region: HAD-SF-IIIA; TIGR01662 1216962002508 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 1216962002509 active site 1216962002510 motif I; other site 1216962002511 motif II; other site 1216962002512 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 1216962002513 Sel1-like repeats; Region: SEL1; smart00671 1216962002514 Sel1 repeat; Region: Sel1; cl02723 1216962002515 DOPA decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to DOPA/tyrosine decarboxylase (DDC), histidine decarboxylase (HDC), and...; Region: DOPA_deC_like; cd06450 1216962002516 tyrosine decarboxylase MnfA; Region: tyr_de_CO2_Arch; TIGR03812 1216962002517 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1216962002518 catalytic residue [active] 1216962002519 Bacterial protein of unknown function (YtfJ_HI0045); Region: YtfJ_HI0045; pfam09695 1216962002520 dihydrodipicolinate reductase; Provisional; Region: PRK00048 1216962002521 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 1216962002522 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 1216962002523 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 1216962002524 hypothetical protein; Reviewed; Region: PRK12497 1216962002525 Homoserine dehydrogenase [Amino acid transport and metabolism]; Region: ThrA; COG0460 1216962002526 Homoserine dehydrogenase, NAD binding domain; Region: NAD_binding_3; pfam03447 1216962002527 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 1216962002528 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 1216962002529 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1216962002530 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 1216962002531 active site 1216962002532 phosphorylation site [posttranslational modification] 1216962002533 intermolecular recognition site; other site 1216962002534 dimerization interface [polypeptide binding]; other site 1216962002535 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 1216962002536 DNA binding site [nucleotide binding] 1216962002537 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 1216962002538 HAMP domain; Region: HAMP; pfam00672 1216962002539 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 1216962002540 dimer interface [polypeptide binding]; other site 1216962002541 phosphorylation site [posttranslational modification] 1216962002542 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 1216962002543 ATP binding site [chemical binding]; other site 1216962002544 Mg2+ binding site [ion binding]; other site 1216962002545 G-X-G motif; other site 1216962002546 Glutamine amidotransferases class-II (GATase). The glutaminase domain catalyzes an amide nitrogen transfer from glutamine to the appropriate substrate. In this process, glutamine is hydrolyzed to glutamic acid and ammonia. This domain is related to...; Region: Gn_AT_II; cl00319 1216962002547 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1216962002548 active site 1216962002549 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 1216962002550 dimer interface [polypeptide binding]; other site 1216962002551 active site 1216962002552 Schiff base residues; other site 1216962002553 hypothetical protein; Provisional; Region: PRK12378 1216962002554 Holliday junction resolvase-like protein; Reviewed; Region: PRK00109 1216962002555 DNA protecting protein DprA; Region: dprA; TIGR00732 1216962002556 DNA recombination-mediator protein A; Region: DNA_processg_A; pfam02481 1216962002557 Septum formation topological specificity factor MinE; Region: MinE; cl00538 1216962002558 Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]; Region: MinD; COG2894 1216962002559 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 1216962002560 Switch I; other site 1216962002561 Switch II; other site 1216962002562 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 1216962002563 Phosphoenolpyruvate carboxylase; Region: PEPcase; cl17418 1216962002564 Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]; Region: FecA; COG4772 1216962002565 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 1216962002566 N-terminal plug; other site 1216962002567 ligand-binding site [chemical binding]; other site 1216962002568 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 1216962002569 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 1216962002570 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 1216962002571 Uncharacterized protein conserved in bacteria (DUF2219); Region: DUF2219; cl01409 1216962002572 1-deoxy-D-xylulose-5-phosphate synthase; Region: dxs; TIGR00204 1216962002573 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 1216962002574 TPP-binding site; other site 1216962002575 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 1216962002576 PYR/PP interface [polypeptide binding]; other site 1216962002577 dimer interface [polypeptide binding]; other site 1216962002578 TPP binding site [chemical binding]; other site 1216962002579 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 1216962002580 flagellar assembly protein H; Validated; Region: fliH; PRK06669 1216962002581 Flagellar assembly protein FliH; Region: FliH; pfam02108 1216962002582 flagellar motor switch protein FliG; Region: fliG; TIGR00207 1216962002583 FliG C-terminal domain; Region: FliG_C; pfam01706 1216962002584 flagellar MS-ring protein; Reviewed; Region: fliF; PRK06007 1216962002585 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; cl01907 1216962002586 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 1216962002587 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 1216962002588 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 1216962002589 active site 1216962002590 nitrate reductase catalytic subunit; Provisional; Region: PRK13532 1216962002591 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 1216962002592 molybdopterin cofactor binding site; other site 1216962002593 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 1216962002594 Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol...; Region: MopB_CT_Nitrate-R-NapA-like; cd02791 1216962002595 molybdopterin cofactor binding site; other site 1216962002596 quinol dehydrogenase periplasmic component; Provisional; Region: napG; PRK09476 1216962002597 quinol dehydrogenase membrane component; Provisional; Region: napH; PRK09477 1216962002598 4Fe-4S binding domain; Region: Fer4_5; pfam12801 1216962002599 H+/citrate symporter [Energy production and conversion]; Region: CitM; COG2851 1216962002600 Citrate transporter; Region: CitMHS; pfam03600 1216962002601 tumor necrosis factor alpha-inducing protein; Reviewed; Region: PRK12303 1216962002602 flavodoxin FldA; Validated; Region: PRK09267 1216962002603 Protein of unknown function (DUF2393); Region: DUF2393; pfam09624 1216962002604 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 1216962002605 SPFH domain / Band 7 family; Region: Band_7; pfam01145 1216962002606 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 1216962002607 branched-chain amino acid aminotransferase; Validated; Region: PRK06606 1216962002608 homodimer interface [polypeptide binding]; other site 1216962002609 substrate-cofactor binding pocket; other site 1216962002610 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1216962002611 catalytic residue [active] 1216962002612 helicase 45; Provisional; Region: PTZ00424 1216962002613 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 1216962002614 ATP binding site [chemical binding]; other site 1216962002615 Mg++ binding site [ion binding]; other site 1216962002616 motif III; other site 1216962002617 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 1216962002618 nucleotide binding region [chemical binding]; other site 1216962002619 ATP-binding site [chemical binding]; other site 1216962002620 Cytochrome c biogenesis protein [Posttranslational modification, protein turnover, chaperones]; Region: CcdA; COG0785 1216962002621 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; cl15788 1216962002622 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 1216962002623 dihydroorotase; Provisional; Region: PRK08417 1216962002624 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 1216962002625 active site 1216962002626 chlorohydrolase; Provisional; Region: PRK08418 1216962002627 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 1216962002628 active site 1216962002629 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 1216962002630 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14339 1216962002631 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 1216962002632 FeS/SAM binding site; other site 1216962002633 TRAM domain; Region: TRAM; pfam01938 1216962002634 Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis; Region: LPLAT; cl17185 1216962002635 Predicted Fe-S-cluster oxidoreductase [General function prediction only]; Region: COG0727 1216962002636 putative PEP-CTERM system TPR-repeat lipoprotein; Region: PEP_TPR_lipo; TIGR02917 1216962002637 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 1216962002638 Thiamine pyrophosphate (TPP) family, PDC_IPDC subfamily, TPP-binding module; composed of proteins similar to pyruvate decarboxylase (PDC) and indolepyruvate decarboxylase (IPDC). PDC, a key enzyme in alcoholic fermentation, catalyzes the conversion of...; Region: TPP_PDC_IPDC; cd02005 1216962002639 TPP-binding site [chemical binding]; other site 1216962002640 dimer interface [polypeptide binding]; other site 1216962002641 flagellin A; Reviewed; Region: PRK12584 1216962002642 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 1216962002643 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 1216962002644 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 1216962002645 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 1216962002646 coproporphyrinogen III oxidase; Provisional; Region: PRK08446 1216962002647 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 1216962002648 FeS/SAM binding site; other site 1216962002649 HemN C-terminal domain; Region: HemN_C; pfam06969 1216962002650 Cytochrome c; Region: Cytochrom_C; cl11414 1216962002651 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 1216962002652 putative active site [active] 1216962002653 Ap4A binding site [chemical binding]; other site 1216962002654 nudix motif; other site 1216962002655 putative metal binding site [ion binding]; other site 1216962002656 aspartate kinase; Reviewed; Region: PRK06635 1216962002657 AAK_AK-DapG-like: Amino Acid Kinase Superfamily (AAK), AK-DapG-like; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the diaminopimelate-sensitive aspartokinase isoenzyme AKI (DapG), a monofunctional enzymes found in Bacilli; Region: AAK_AK-DapG-like; cd04246 1216962002658 putative catalytic residues [active] 1216962002659 putative nucleotide binding site [chemical binding]; other site 1216962002660 putative aspartate binding site [chemical binding]; other site 1216962002661 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 1216962002662 putative allosteric regulatory site; other site 1216962002663 ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related domains; Region: ACT_AK-LysC-DapG-like_2; cd04923 1216962002664 DNA replication regulator; Region: HobA; pfam12163 1216962002665 DNA polymerase III subunit delta'; Validated; Region: PRK08485 1216962002666 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 1216962002667 dihydropteroate synthase; Region: DHPS; TIGR01496 1216962002668 substrate binding pocket [chemical binding]; other site 1216962002669 dimer interface [polypeptide binding]; other site 1216962002670 inhibitor binding site; inhibition site 1216962002671 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 1216962002672 threonine/serine transporter TdcC; Provisional; Region: PRK13629; cl17672 1216962002673 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 1216962002674 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 1216962002675 Serine dehydratase alpha chain; Region: SDH_alpha; pfam03313 1216962002676 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 1216962002677 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 1216962002678 catalytic residues [active] 1216962002679 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 1216962002680 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 1216962002681 Ligand binding site; other site 1216962002682 oligomer interface; other site 1216962002683 P-type DNA transfer ATPase VirB11; Region: VirB11; TIGR02788 1216962002684 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 1216962002685 Walker A motif; other site 1216962002686 hexamer interface [polypeptide binding]; other site 1216962002687 ATP binding site [chemical binding]; other site 1216962002688 Walker B motif; other site 1216962002689 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 1216962002690 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 1216962002691 isocitrate dehydrogenase; Validated; Region: PRK07362 1216962002692 isocitrate dehydrogenase; Reviewed; Region: PRK07006 1216962002693 Uncharacterized protein/domain associated with GTPases [Function unknown]; Region: COG3597 1216962002694 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 1216962002695 dimer interface [polypeptide binding]; other site 1216962002696 Citrate synthase; Region: Citrate_synt; pfam00285 1216962002697 active site 1216962002698 citrylCoA binding site [chemical binding]; other site 1216962002699 NADH binding [chemical binding]; other site 1216962002700 cationic pore residues; other site 1216962002701 oxalacetate/citrate binding site [chemical binding]; other site 1216962002702 coenzyme A binding site [chemical binding]; other site 1216962002703 catalytic triad [active] 1216962002704 lipid A phosphoethanolamine transferase; Reviewed; Region: PRK09598 1216962002705 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 1216962002706 Sulfatase; Region: Sulfatase; pfam00884 1216962002707 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 1216962002708 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 1216962002709 active site 1216962002710 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 1216962002711 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 1216962002712 putative active site [active] 1216962002713 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 1216962002714 Dihydroneopterin aldolase; Region: FolB; pfam02152 1216962002715 active site 1216962002716 putative glycerol-3-phosphate acyltransferase PlsY; Provisional; Region: PRK00220 1216962002717 Isochorismatase family; Region: Isochorismatase; pfam00857 1216962002718 YcaC related amidohydrolases; E.coli YcaC is an homooctameric hydrolase with unknown specificity. Despite its weak sequence similarity, it is structurally related to other amidohydrolases and shares conserved active site residues with them; Region: YcaC_related; cd01012 1216962002719 catalytic triad [active] 1216962002720 dimer interface [polypeptide binding]; other site 1216962002721 conserved cis-peptide bond; other site 1216962002722 ATP synthase subunit C; Region: ATP-synt_C; cl00466 1216962002723 Isochorismatase family; Region: Isochorismatase; pfam00857 1216962002724 YcaC related amidohydrolases; E.coli YcaC is an homooctameric hydrolase with unknown specificity. Despite its weak sequence similarity, it is structurally related to other amidohydrolases and shares conserved active site residues with them; Region: YcaC_related; cd01012 1216962002725 catalytic triad [active] 1216962002726 dimer interface [polypeptide binding]; other site 1216962002727 conserved cis-peptide bond; other site 1216962002728 F0F1 ATP synthase subunit C; Validated; Region: PRK08482 1216962002729 K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has...; Region: vigilin_like_KH; cd02394 1216962002730 putative nucleic acid binding region [nucleotide binding]; other site 1216962002731 G-X-X-G motif; other site 1216962002732 Ribosomal protein S1-like RNA-binding domain; Region: S1; smart00316 1216962002733 RNA binding site [nucleotide binding]; other site 1216962002734 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1216962002735 active site 1216962002736 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 1216962002737 Organic solvent tolerance protein; Region: OstA_C; pfam04453 1216962002738 RDD family; Region: RDD; pfam06271 1216962002739 phosphoribosylamine--glycine ligase; Provisional; Region: PRK00885 1216962002740 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 1216962002741 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 1216962002742 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 1216962002743 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 1216962002744 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 1216962002745 dimerization interface 3.5A [polypeptide binding]; other site 1216962002746 active site 1216962002747 Predicted permeases [General function prediction only]; Region: COG0795 1216962002748 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 1216962002749 protein-L-isoaspartate O-methyltransferase; Reviewed; Region: pcm; PRK00312 1216962002750 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 1216962002751 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 1216962002752 active site 1216962002753 Predicted permeases [General function prediction only]; Region: COG0795 1216962002754 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 1216962002755 protein-L-isoaspartate O-methyltransferase; Reviewed; Region: pcm; PRK00312 1216962002756 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 1216962002757 S-adenosylmethionine binding site [chemical binding]; other site 1216962002758 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 1216962002759 dimer interface [polypeptide binding]; other site 1216962002760 putative radical transfer pathway; other site 1216962002761 diiron center [ion binding]; other site 1216962002762 tyrosyl radical; other site 1216962002763 short chain dehydrogenase; Validated; Region: PRK06182 1216962002764 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 1216962002765 NADP binding site [chemical binding]; other site 1216962002766 active site 1216962002767 steroid binding site; other site 1216962002768 UDP-glucose-4-epimerase GalE; Region: galE; TIGR01179 1216962002769 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 1216962002770 NAD binding site [chemical binding]; other site 1216962002771 homodimer interface [polypeptide binding]; other site 1216962002772 active site 1216962002773 substrate binding site [chemical binding]; other site 1216962002774 DNA Topoisomerase I (eukaryota); Region: TOPEUc; smart00435 1216962002775 hydroxyglutarate oxidase; Provisional; Region: PRK11728 1216962002776 hydroxyglutarate oxidase; Provisional; Region: PRK11728 1216962002777 hydroxyglutarate oxidase; Provisional; Region: PRK11728 1216962002778 succinic semialdehyde dehydrogenase; Region: PLN02278 1216962002779 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 1216962002780 tetramerization interface [polypeptide binding]; other site 1216962002781 NAD(P) binding site [chemical binding]; other site 1216962002782 catalytic residues [active] 1216962002783 4-aminobutyrate aminotransferase; Provisional; Region: PRK06777 1216962002784 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 1216962002785 inhibitor-cofactor binding pocket; inhibition site 1216962002786 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1216962002787 catalytic residue [active] 1216962002788 Class-II DAHP synthetase family; Region: DAHP_synth_2; pfam01474 1216962002789 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 1216962002790 RuvA N terminal domain; Region: RuvA_N; pfam01330 1216962002791 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 1216962002792 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 1216962002793 RuvA N terminal domain; Region: RuvA_N; pfam01330 1216962002794 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 1216962002795 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 1216962002796 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1216962002797 ATP-binding cassette domain of multidrug resistance protein-like transporters; Region: ABCC_MRP_Like; cd03228 1216962002798 ABC transporter signature motif; other site 1216962002799 ABC transporter signature motif; other site 1216962002800 Walker B; other site 1216962002801 Walker B; other site 1216962002802 D-loop; other site 1216962002803 D-loop; other site 1216962002804 H-loop/switch region; other site 1216962002805 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 1216962002806 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 1216962002807 ATP-binding cassette domain of multidrug resistance protein-like transporters; Region: ABCC_MRP_Like; cd03228 1216962002808 Walker A/P-loop; other site 1216962002809 ATP binding site [chemical binding]; other site 1216962002810 Q-loop/lid; other site 1216962002811 ABC transporter signature motif; other site 1216962002812 Walker B; other site 1216962002813 D-loop; other site 1216962002814 H-loop/switch region; other site 1216962002815 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 1216962002816 metal-binding site [ion binding] 1216962002817 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 1216962002818 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 1216962002819 metal-binding site [ion binding] 1216962002820 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 1216962002821 Soluble P-type ATPase [General function prediction only]; Region: COG4087 1216962002822 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 1216962002823 CDP-diacylglycerol--serine O-phosphatidyltransferase; Region: pssA; TIGR00473 1216962002824 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 1216962002825 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 1216962002826 Walker A motif; other site 1216962002827 ATP binding site [chemical binding]; other site 1216962002828 Walker B motif; other site 1216962002829 arginine finger; other site 1216962002830 Peptidase family M41; Region: Peptidase_M41; pfam01434 1216962002831 Ribosomal protein L11 methylase [Translation, ribosomal structure and biogenesis]; Region: PrmA; COG2264 1216962002832 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 1216962002833 S-adenosylmethionine binding site [chemical binding]; other site 1216962002834 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 1216962002835 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 1216962002836 active site 1216962002837 phosphorylation site [posttranslational modification] 1216962002838 intermolecular recognition site; other site 1216962002839 dimerization interface [polypeptide binding]; other site 1216962002840 Adenine-specific methyltransferase EcoRI; Region: EcoRI_methylase; pfam13651 1216962002841 Nitrate reductase cytochrome c-type subunit (NapB); Region: NapB; cl01153 1216962002842 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 1216962002843 FeS/SAM binding site; other site 1216962002844 Radical SAM superfamily; Region: Radical_SAM; pfam04055 1216962002845 DNA topoisomerase I; Validated; Region: PRK05582 1216962002846 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 1216962002847 active site 1216962002848 interdomain interaction site; other site 1216962002849 putative metal-binding site [ion binding]; other site 1216962002850 nucleotide binding site [chemical binding]; other site 1216962002851 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 1216962002852 domain I; other site 1216962002853 DNA binding groove [nucleotide binding] 1216962002854 phosphate binding site [ion binding]; other site 1216962002855 domain II; other site 1216962002856 domain III; other site 1216962002857 nucleotide binding site [chemical binding]; other site 1216962002858 catalytic site [active] 1216962002859 domain IV; other site 1216962002860 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 1216962002861 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 1216962002862 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 1216962002863 flagellin B; Provisional; Region: PRK13588 1216962002864 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 1216962002865 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 1216962002866 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 1216962002867 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 1216962002868 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2604 1216962002869 RIP metalloprotease RseP; Region: TIGR00054 1216962002870 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 1216962002871 active site 1216962002872 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 1216962002873 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 1216962002874 7-alpha-hydroxysteroid dehydrogenase; Provisional; Region: PRK08416 1216962002875 1-cyclohexenylcarbonyl_coenzyme A_reductase (ChcA)_like, classical (c) SDRs; Region: ChcA_like_SDR_c; cd05359 1216962002876 putative NAD(P) binding site [chemical binding]; other site 1216962002877 active site 1216962002878 Class I aldolases; Region: Aldolase_Class_I; cl17187 1216962002879 catalytic residue [active] 1216962002880 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 1216962002881 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 1216962002882 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 1216962002883 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 1216962002884 dihydroorotate dehydrogenase 2; Reviewed; Region: PRK05286 1216962002885 quinone interaction residues [chemical binding]; other site 1216962002886 active site 1216962002887 catalytic residues [active] 1216962002888 FMN binding site [chemical binding]; other site 1216962002889 substrate binding site [chemical binding]; other site 1216962002890 polyphosphate kinase; Provisional; Region: PRK05443 1216962002891 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 1216962002892 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 1216962002893 Catalytic domain of phospholipase D superfamily proteins; Region: PLDc_SF; cl15239 1216962002894 putative active site [active] 1216962002895 catalytic site [active] 1216962002896 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 1216962002897 putative domain interface [polypeptide binding]; other site 1216962002898 putative active site [active] 1216962002899 catalytic site [active] 1216962002900 RDD family; Region: RDD; pfam06271 1216962002901 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1216962002902 active site 1216962002903 ribosome recycling factor; Reviewed; Region: frr; PRK00083 1216962002904 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 1216962002905 hinge region; other site 1216962002906 Preprotein translocase subunit SecG [Intracellular trafficking and secretion]; Region: SecG; COG1314 1216962002907 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 1216962002908 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 1216962002909 S-adenosylmethionine binding site [chemical binding]; other site 1216962002910 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 1216962002911 KMSKS motif; other site 1216962002912 The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like; cl01709 1216962002913 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4174 1216962002914 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 1216962002915 dimer interface [polypeptide binding]; other site 1216962002916 conserved gate region; other site 1216962002917 ABC-ATPase subunit interface; other site 1216962002918 phosphoribosylaminoimidazole synthetase; Provisional; Region: PRK05385 1216962002919 PurM (Aminoimidazole Ribonucleotide [AIR] synthetase), one of eleven enzymes required for purine biosynthesis, catalyzes the conversion of formylglycinamide ribonucleotide (FGAM) and ATP to AIR, ADP, and Pi, the fifth step in de novo purine biosynthesis; Region: PurM; cd02196 1216962002920 dimerization interface [polypeptide binding]; other site 1216962002921 putative ATP binding site [chemical binding]; other site 1216962002922 Bacterial SH3 domain; Region: SH3_3; pfam08239 1216962002923 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 1216962002924 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 1216962002925 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 1216962002926 shikimate binding site; other site 1216962002927 NAD(P) binding site [chemical binding]; other site 1216962002928 Methyltransferase domain; Region: Methyltransf_26; pfam13659 1216962002929 R.Pab1 restriction endonuclease; Region: RE_R_Pab1; pfam09522 1216962002930 DNA polymerase III subunit delta; Validated; Region: PRK08487 1216962002931 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 1216962002932 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 1216962002933 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 1216962002934 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 1216962002935 dimer interface [polypeptide binding]; other site 1216962002936 ssDNA binding site [nucleotide binding]; other site 1216962002937 tetramer (dimer of dimers) interface [polypeptide binding]; other site 1216962002938 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 1216962002939 Protein of unknown function (DUF3897); Region: DUF3897; pfam13036 1216962002940 Protein of unknown function (DUF3897); Region: DUF3897; cl17494 1216962002941 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 1216962002942 ligand binding site [chemical binding]; other site 1216962002943 active site 1216962002944 UGI interface [polypeptide binding]; other site 1216962002945 catalytic site [active] 1216962002946 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 1216962002947 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 1216962002948 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1216962002949 dimer interface [polypeptide binding]; other site 1216962002950 putative CheW interface [polypeptide binding]; other site 1216962002951 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 1216962002952 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 1216962002953 putative active site [active] 1216962002954 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 1216962002955 DEAD-like helicases superfamily; Region: DEXDc; smart00487 1216962002956 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 1216962002957 ATP binding site [chemical binding]; other site 1216962002958 putative Mg++ binding site [ion binding]; other site 1216962002959 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 1216962002960 nucleotide binding region [chemical binding]; other site 1216962002961 ATP-binding site [chemical binding]; other site 1216962002962 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 1216962002963 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 1216962002964 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 1216962002965 Peptidase family M23; Region: Peptidase_M23; pfam01551 1216962002966 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 1216962002967 Peptidase family M23; Region: Peptidase_M23; pfam01551 1216962002968 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 1216962002969 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1216962002970 Lipopolysaccharide-assembly; Region: LptE; pfam04390 1216962002971 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 1216962002972 Protein export membrane protein; Region: SecD_SecF; pfam02355 1216962002973 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 1216962002974 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 1216962002975 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 1216962002976 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 1216962002977 putative recombination protein RecB; Provisional; Region: PRK13909 1216962002978 Family description; Region: UvrD_C_2; pfam13538 1216962002979 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 1216962002980 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 1216962002981 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 1216962002982 conserved cys residue [active] 1216962002983 cystine transporter subunit; Provisional; Region: PRK11260 1216962002984 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 1216962002985 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 1216962002986 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 1216962002987 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 1216962002988 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 1216962002989 Sodium:alanine symporter family; Region: Na_Ala_symp; cl00548 1216962002990 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 1216962002991 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 1216962002992 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 1216962002993 homotrimer interaction site [polypeptide binding]; other site 1216962002994 putative active site [active] 1216962002995 Sporulation related domain; Region: SPOR; pfam05036 1216962002996 Domain of unknown function (DUF1882); Region: DUF1882; pfam08966 1216962002997 tRNA synthetases class II (D, K and N); Region: tRNA-synt_2; pfam00152 1216962002998 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 1216962002999 motif 1; other site 1216962003000 active site 1216962003001 motif 2; other site 1216962003002 motif 3; other site 1216962003003 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 1216962003004 Colicin V production protein; Region: Colicin_V; pfam02674 1216962003005 apolipoprotein N-acyltransferase; Reviewed; Region: PRK12291 1216962003006 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cl11424 1216962003007 active site 1216962003008 catalytic triad [active] 1216962003009 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 1216962003010 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1216962003011 Walker A/P-loop; other site 1216962003012 ATP binding site [chemical binding]; other site 1216962003013 Q-loop/lid; other site 1216962003014 ABC transporter signature motif; other site 1216962003015 Walker B; other site 1216962003016 D-loop; other site 1216962003017 H-loop/switch region; other site 1216962003018 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 1216962003019 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 1216962003020 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 1216962003021 Mg2+ binding site [ion binding]; other site 1216962003022 G-X-G motif; other site 1216962003023 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 1216962003024 anchoring element; other site 1216962003025 dimer interface [polypeptide binding]; other site 1216962003026 ATP binding site [chemical binding]; other site 1216962003027 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 1216962003028 active site 1216962003029 putative metal-binding site [ion binding]; other site 1216962003030 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 1216962003031 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 1216962003032 DnaA N-terminal domain; Region: DnaA_N; pfam11638 1216962003033 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 1216962003034 Walker A motif; other site 1216962003035 ATP binding site [chemical binding]; other site 1216962003036 Walker B motif; other site 1216962003037 arginine finger; other site 1216962003038 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 1216962003039 DnaA box-binding interface [nucleotide binding]; other site 1216962003040 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 1216962003041 active site 1216962003042 putative DNA-binding cleft [nucleotide binding]; other site 1216962003043 dimer interface [polypeptide binding]; other site 1216962003044 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 1216962003045 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1216962003046 dimer interface [polypeptide binding]; other site 1216962003047 putative CheW interface [polypeptide binding]; other site 1216962003048 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 1216962003049 Protein of unknown function (DUF1104); Region: DUF1104; pfam06518 1216962003050 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 1216962003051 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 1216962003052 Soluble P-type ATPase [General function prediction only]; Region: COG4087 1216962003053 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 1216962003054 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 1216962003055 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 1216962003056 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 1216962003057 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 1216962003058 active site 1216962003059 catalytic residues [active] 1216962003060 metal binding site [ion binding]; metal-binding site 1216962003061 Clp protease; Region: CLP_protease; pfam00574 1216962003062 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 1216962003063 oligomer interface [polypeptide binding]; other site 1216962003064 active site residues [active] 1216962003065 Caseinolytic protease (ClpP) is an ATP-dependent protease; Region: Clp_protease_like; cl15763 1216962003066 trigger factor; Provisional; Region: tig; PRK01490 1216962003067 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 1216962003068 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 1216962003069 flagellum-specific ATP synthase; Validated; Region: fliI; PRK08472 1216962003070 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 1216962003071 Walker A motif/ATP binding site; other site 1216962003072 Walker B motif; other site 1216962003073 Glycosyl transferases group 1; Region: Glyco_trans_1_2; pfam13524 1216962003074 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 1216962003075 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 1216962003076 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1216962003077 catalytic residue [active] 1216962003078 Fe-S cluster assembly protein NifU; Region: NifU_proper; TIGR02000 1216962003079 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 1216962003080 trimerization site [polypeptide binding]; other site 1216962003081 active site 1216962003082 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 1216962003083 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 1216962003084 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 1216962003085 Four helix bundle sensory module for signal transduction; Region: 4HB_MCP_1; pfam12729 1216962003086 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 1216962003087 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 1216962003088 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1216962003089 dimer interface [polypeptide binding]; other site 1216962003090 putative CheW interface [polypeptide binding]; other site 1216962003091 Dehydroquinase class II; Region: DHquinase_II; pfam01220 1216962003092 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 1216962003093 trimer interface [polypeptide binding]; other site 1216962003094 active site 1216962003095 dimer interface [polypeptide binding]; other site 1216962003096 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 1216962003097 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 1216962003098 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 1216962003099 active site 1216962003100 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 1216962003101 catalytic center binding site [active] 1216962003102 ATP binding site [chemical binding]; other site 1216962003103 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK05703 1216962003104 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 1216962003105 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 1216962003106 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 1216962003107 P-loop; other site 1216962003108 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 1216962003109 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 1216962003110 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1216962003111 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 1216962003112 DNA binding residues [nucleotide binding] 1216962003113 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 1216962003114 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 1216962003115 flagellar motor switch protein FliY; Validated; Region: PRK08432 1216962003116 flagellar motor switch protein FliN; Region: fliN; TIGR02480 1216962003117 chaperone protein DnaJ; Region: DnaJ_bact; TIGR02349 1216962003118 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 1216962003119 HSP70 interaction site [polypeptide binding]; other site 1216962003120 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 1216962003121 substrate binding site [polypeptide binding]; other site 1216962003122 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 1216962003123 Zn binding sites [ion binding]; other site 1216962003124 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 1216962003125 dimer interface [polypeptide binding]; other site 1216962003126 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 1216962003127 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 1216962003128 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 1216962003129 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 1216962003130 active site 1216962003131 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 1216962003132 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 1216962003133 hypothetical protein; Provisional; Region: PRK10621 1216962003134 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 1216962003135 Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Ape1-like_AP-endo; cd09087 1216962003136 active site 1216962003137 putative catalytic site [active] 1216962003138 DNA binding site [nucleotide binding] 1216962003139 putative phosphate binding site [ion binding]; other site 1216962003140 metal binding site A [ion binding]; metal-binding site 1216962003141 AP binding site [nucleotide binding]; other site 1216962003142 metal binding site B [ion binding]; metal-binding site 1216962003143 ferredoxin-type protein; Provisional; Region: PRK10194 1216962003144 4Fe-4S binding domain; Region: Fer4; pfam00037 1216962003145 NapD protein; Region: NapD; cl01163 1216962003146 Type IV secretory pathway, TrbL components [Intracellular trafficking and secretion]; Region: TrbL; COG3846 1216962003147 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 1216962003148 Protein of unknown function (DUF779); Region: DUF779; cl01432 1216962003149 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 1216962003150 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 1216962003151 NAD(P) binding site [chemical binding]; other site 1216962003152 catalytic residues [active] 1216962003153 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 1216962003154 Restriction endonuclease EcoRI; Region: EcoRI; pfam02963 1216962003155 Restriction endonuclease EcoRI; Region: EcoRI; pfam02963 1216962003156 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 1216962003157 DNA methylase; Region: N6_N4_Mtase; pfam01555 1216962003158 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 1216962003159 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 1216962003160 Walker A/P-loop; other site 1216962003161 ATP binding site [chemical binding]; other site 1216962003162 Q-loop/lid; other site 1216962003163 ABC transporter signature motif; other site 1216962003164 Walker B; other site 1216962003165 D-loop; other site 1216962003166 H-loop/switch region; other site 1216962003167 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 1216962003168 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 1216962003169 Walker A/P-loop; other site 1216962003170 ATP binding site [chemical binding]; other site 1216962003171 Q-loop/lid; other site 1216962003172 ABC transporter signature motif; other site 1216962003173 Walker B; other site 1216962003174 D-loop; other site 1216962003175 H-loop/switch region; other site 1216962003176 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 1216962003177 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4239 1216962003178 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 1216962003179 dimer interface [polypeptide binding]; other site 1216962003180 conserved gate region; other site 1216962003181 putative PBP binding loops; other site 1216962003182 ABC-ATPase subunit interface; other site 1216962003183 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 1216962003184 Bpu10I restriction endonuclease; Region: RE_Bpu10I; pfam09549 1216962003185 Bpu10I restriction endonuclease; Region: RE_Bpu10I; pfam09549 1216962003186 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 1216962003187 trimer interface [polypeptide binding]; other site 1216962003188 active site 1216962003189 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 1216962003190 Radical SAM superfamily; Region: Radical_SAM; pfam04055 1216962003191 FeS/SAM binding site; other site 1216962003192 rod shape-determining protein MreC; Region: MreC; pfam04085 1216962003193 rod shape-determining protein MreB; Provisional; Region: PRK13927 1216962003194 MreB and similar proteins; Region: MreB_like; cd10225 1216962003195 nucleotide binding site [chemical binding]; other site 1216962003196 Mg binding site [ion binding]; other site 1216962003197 putative protofilament interaction site [polypeptide binding]; other site 1216962003198 RodZ interaction site [polypeptide binding]; other site 1216962003199 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 1216962003200 ClpX C4-type zinc finger; Region: zf-C4_ClpX; smart00994 1216962003201 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 1216962003202 Walker A motif; other site 1216962003203 ATP binding site [chemical binding]; other site 1216962003204 Walker B motif; other site 1216962003205 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 1216962003206 acyl-[acyl-carrier-protein]--UDP-N- acetylglucosamine O-acyltransferase; Region: lipid_A_lpxA; TIGR01852 1216962003207 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 1216962003208 active site 1216962003209 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 1216962003210 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 1216962003211 substrate binding site [chemical binding]; other site 1216962003212 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 1216962003213 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 1216962003214 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 1216962003215 Uncharacterized conserved protein [Function unknown]; Region: COG2353 1216962003216 elongation factor Tu; Reviewed; Region: PRK00049 1216962003217 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 1216962003218 G1 box; other site 1216962003219 GEF interaction site [polypeptide binding]; other site 1216962003220 GTP/Mg2+ binding site [chemical binding]; other site 1216962003221 Switch I region; other site 1216962003222 G2 box; other site 1216962003223 G3 box; other site 1216962003224 Switch II region; other site 1216962003225 G4 box; other site 1216962003226 G5 box; other site 1216962003227 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 1216962003228 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 1216962003229 Antibiotic Binding Site [chemical binding]; other site 1216962003230 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 1216962003231 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 1216962003232 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 1216962003233 putative homodimer interface [polypeptide binding]; other site 1216962003234 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 1216962003235 heterodimer interface [polypeptide binding]; other site 1216962003236 homodimer interface [polypeptide binding]; other site 1216962003237 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 1216962003238 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 1216962003239 23S rRNA interface [nucleotide binding]; other site 1216962003240 L7/L12 interface [polypeptide binding]; other site 1216962003241 putative thiostrepton binding site; other site 1216962003242 L25 interface [polypeptide binding]; other site 1216962003243 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 1216962003244 mRNA/rRNA interface [nucleotide binding]; other site 1216962003245 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 1216962003246 23S rRNA interface [nucleotide binding]; other site 1216962003247 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 1216962003248 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 1216962003249 L11 interface [polypeptide binding]; other site 1216962003250 putative EF-Tu interaction site [polypeptide binding]; other site 1216962003251 putative EF-G interaction site [polypeptide binding]; other site 1216962003252 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 1216962003253 RPB11 interaction site [polypeptide binding]; other site 1216962003254 RPB12 interaction site [polypeptide binding]; other site 1216962003255 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 1216962003256 RPB1 interaction site [polypeptide binding]; other site 1216962003257 RNA polymerase Rpb2, domain 7; Region: RNA_pol_Rpb2_7; pfam04560 1216962003258 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 1216962003259 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 1216962003260 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 1216962003261 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 1216962003262 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 1216962003263 RNA polymerase Rpb1, domain 5; Region: RNA_pol_Rpb1_5; pfam04998 1216962003264 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 1216962003265 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 1216962003266 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 1216962003267 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 1216962003268 DNA binding site [nucleotide binding] 1216962003269 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 1216962003270 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 1216962003271 clamp; other site 1216962003272 Rpb1 - Rpb2 interaction site [polypeptide binding]; other site 1216962003273 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 1216962003274 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 1216962003275 active site 1216962003276 zinc binding site [ion binding]; other site 1216962003277 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; cl17639 1216962003279 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1216962003280 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 1216962003281 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 1216962003282 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 1216962003283 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 1216962003284 Ligand Binding Site [chemical binding]; other site 1216962003285 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 1216962003286 Ligand Binding Site [chemical binding]; other site 1216962003287 Uncharacterized conserved protein [Function unknown]; Region: COG3334 1216962003288 Uncharacterized conserved protein [Function unknown]; Region: COG3334 1216962003289 Flagellar FliJ protein; Region: FliJ; pfam02050 1216962003290 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 1216962003291 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 1216962003292 GDP-binding site [chemical binding]; other site 1216962003293 ACT binding site; other site 1216962003294 IMP binding site; other site 1216962003295 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1216962003296 active site 1216962003297 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 1216962003298 nucleotide binding site/active site [active] 1216962003299 HIT family signature motif; other site 1216962003300 catalytic residue [active] 1216962003301 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1216962003302 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 1216962003303 D-alanyl-alanine synthetase A; Reviewed; Region: ddl; PRK01966 1216962003304 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 1216962003305 ATP-grasp domain; Region: ATP-grasp_4; cl17255 1216962003306 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 1216962003307 D-alanyl-alanine synthetase A; Reviewed; Region: ddl; PRK01966 1216962003308 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 1216962003309 ATP-grasp domain; Region: ATP-grasp_4; cl17255 1216962003310 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 1216962003311 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 1216962003312 S-adenosylmethionine binding site [chemical binding]; other site 1216962003313 carboxynorspermidine decarboxylase; Region: nspC; TIGR01047 1216962003314 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Carboxynorspermidine Decarboxylase; Region: PLPDE_III_CANSDC; cd06829 1216962003315 dimer interface [polypeptide binding]; other site 1216962003316 active site 1216962003317 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 1216962003318 catalytic residues [active] 1216962003319 substrate binding site [chemical binding]; other site 1216962003320 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 1216962003321 Response regulator receiver domain; Region: Response_reg; pfam00072 1216962003322 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 1216962003323 active site 1216962003324 phosphorylation site [posttranslational modification] 1216962003325 intermolecular recognition site; other site 1216962003326 dimerization interface [polypeptide binding]; other site 1216962003327 GTP-binding protein YchF; Reviewed; Region: PRK09601 1216962003328 YchF GTPase; Region: YchF; cd01900 1216962003329 G1 box; other site 1216962003330 GTP/Mg2+ binding site [chemical binding]; other site 1216962003331 Switch I region; other site 1216962003332 G2 box; other site 1216962003333 Switch II region; other site 1216962003334 G3 box; other site 1216962003335 G4 box; other site 1216962003336 G5 box; other site 1216962003337 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 1216962003338 multifunctional aminopeptidase A; Provisional; Region: PRK00913 1216962003339 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 1216962003340 interface (dimer of trimers) [polypeptide binding]; other site 1216962003341 Substrate-binding/catalytic site; other site 1216962003342 Zn-binding sites [ion binding]; other site 1216962003343 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 1216962003344 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 1216962003345 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1216962003346 active site 1216962003347 Regulator of replication initiation timing [Replication, recombination, and repair]; Region: COG4467; cl01853 1216962003348 ribose-5-phosphate isomerase B; Provisional; Region: PRK05571 1216962003349 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 1216962003350 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 1216962003351 Catalytic site [active] 1216962003352 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 1216962003353 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 1216962003354 homodimer interface [polypeptide binding]; other site 1216962003355 NADP binding site [chemical binding]; other site 1216962003356 substrate binding site [chemical binding]; other site 1216962003357 thiamine biosynthesis protein ThiC; Region: thiC; TIGR00190 1216962003358 ThiC family; Region: ThiC; pfam01964 1216962003359 bifunctional 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase/2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase protein; Provisional; Region: ispDF; PRK09382 1216962003360 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 1216962003361 substrate binding site; other site 1216962003362 dimer interface; other site 1216962003363 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 1216962003364 homotrimer interaction site [polypeptide binding]; other site 1216962003365 zinc binding site [ion binding]; other site 1216962003366 CDP-binding sites; other site 1216962003367 Response regulator receiver domain; Region: Response_reg; pfam00072 1216962003368 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 1216962003369 active site 1216962003370 phosphorylation site [posttranslational modification] 1216962003371 dimerization interface [polypeptide binding]; other site 1216962003372 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 1216962003373 HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain; Region: HAMP; smart00304 1216962003374 dimerization interface [polypeptide binding]; other site 1216962003375 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 1216962003376 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 1216962003377 dimer interface [polypeptide binding]; other site 1216962003378 putative CheW interface [polypeptide binding]; other site 1216962003379 UGMP family protein; Validated; Region: PRK09604 1216962003380 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 1216962003381 Peptidylarginine deiminase and related enzymes [Amino acid transport and metabolism]; Region: COG2957; cl01113 1216962003382 Porphyromonas-type peptidyl-arginine deiminase; Region: PAD_porph; pfam04371 1216962003383 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypF; COG0068 1216962003384 Telomere recombination; Region: Sua5_yciO_yrdC; pfam01300 1216962003385 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 1216962003386 dimerization interface [polypeptide binding]; other site 1216962003387 hydrogenase expression/formation protein HypE; Region: hypE; TIGR02124 1216962003388 ATP binding site [chemical binding]; other site 1216962003389 acylamide amidohydrolase; Provisional; Region: amiE; PRK13286 1216962003390 aliphatic amidases (class 2 nitrilases); Region: aliphatic_amidase; cd07565 1216962003391 multimer interface [polypeptide binding]; other site 1216962003392 active site 1216962003393 catalytic triad [active] 1216962003394 dimer interface [polypeptide binding]; other site 1216962003395 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional; Region: PRK05447 1216962003396 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 1216962003397 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 1216962003398 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 1216962003399 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 1216962003400 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 1216962003401 Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices...; Region: ArsB_NhaD_permease; cl17221 1216962003402 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 1216962003403 LPP20 lipoprotein; Region: LPP20; cl15824 1216962003404 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3018 1216962003405 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 1216962003406 ABC-type sulfate transport system, permease component [Posttranslational modification, protein turnover, chaperones]; Region: CysU; COG0555 1216962003407 dimer interface [polypeptide binding]; other site 1216962003408 conserved gate region; other site 1216962003409 ABC-ATPase subunit interface; other site 1216962003410 Bacterial extracellular solute-binding protein; Region: SBP_bac_11; pfam13531 1216962003411 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 1216962003412 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional; Region: PRK09314 1216962003413 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; pfam00926 1216962003414 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 1216962003415 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 1216962003416 Sel1-like repeats; Region: SEL1; smart00671 1216962003417 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1216962003418 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 1216962003419 S-adenosylmethionine binding site [chemical binding]; other site 1216962003420 Thiazole synthase (ThiG) is the tetrameric enzyme that is involved in the formation of the thiazole moiety of thiamin pyrophosphate, an essential ubiquitous cofactor that plays an important role in carbohydrate and amino acid metabolism. ThiG catalyzes...; Region: ThiG; cd04728 1216962003421 ThiS interaction site; other site 1216962003422 putative active site [active] 1216962003423 tetramer interface [polypeptide binding]; other site 1216962003424 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 1216962003425 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 1216962003426 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 1216962003427 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; cd01983 1216962003428 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 1216962003429 Ligand Binding Site [chemical binding]; other site 1216962003430 ATP-dependent Clp protease ATP-binding subunit clpA; Region: ClpA; TIGR02639 1216962003431 Clp amino terminal domain; Region: Clp_N; pfam02861 1216962003432 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 1216962003433 Walker A motif; other site 1216962003434 ATP binding site [chemical binding]; other site 1216962003435 Walker B motif; other site 1216962003436 arginine finger; other site 1216962003437 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 1216962003438 Walker A motif; other site 1216962003439 ATP binding site [chemical binding]; other site 1216962003440 Walker B motif; other site 1216962003441 arginine finger; other site 1216962003442 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 1216962003443 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 1216962003444 tetramerization interface [polypeptide binding]; other site 1216962003445 active site 1216962003446 hypothetical protein; Provisional; Region: PRK03762 1216962003447 PDZ domain; Region: PDZ_2; pfam13180 1216962003448 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 1216962003449 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 1216962003450 substrate binding pocket [chemical binding]; other site 1216962003451 chain length determination region; other site 1216962003452 substrate-Mg2+ binding site; other site 1216962003453 catalytic residues [active] 1216962003454 aspartate-rich region 1; other site 1216962003455 active site lid residues [active] 1216962003456 aspartate-rich region 2; other site 1216962003457 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 1216962003458 6-pyruvoyl tetrahydropterin synthase; Region: PTPS; pfam01242 1216962003459 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 1216962003460 putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE; Region: rSAM_QueE_Ecoli; TIGR04322 1216962003461 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 1216962003462 DHH family; Region: DHH; pfam01368 1216962003463 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 1216962003464 Putative transposase DNA-binding domain; Region: OrfB_Zn_ribbon; pfam07282 1216962003465 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 1216962003466 riboflavin synthase subunit alpha; Provisional; Region: PRK09289 1216962003467 Lumazine binding domain; Region: Lum_binding; pfam00677 1216962003468 Lumazine binding domain; Region: Lum_binding; pfam00677 1216962003469 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 1216962003470 active site 1216962003471 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 1216962003472 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1216962003473 catalytic residue [active] 1216962003474 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 1216962003475 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 1216962003476 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 1216962003477 Sporulation related domain; Region: SPOR; pfam05036 1216962003478 lipopolysaccharide transport periplasmic protein LptA; Region: outer_YhbN_LptA; TIGR03002 1216962003479 OstA-like protein; Region: OstA; pfam03968 1216962003480 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 1216962003481 G1 box; other site 1216962003482 GTP/Mg2+ binding site [chemical binding]; other site 1216962003483 Switch I region; other site 1216962003484 G2 box; other site 1216962003485 G3 box; other site 1216962003486 Switch II region; other site 1216962003487 G4 box; other site 1216962003488 G5 box; other site 1216962003489 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 1216962003490 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 1216962003491 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 1216962003492 phosphoserine phosphatase SerB; Region: serB; TIGR00338 1216962003493 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 1216962003494 motif II; other site 1216962003495 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 1216962003496 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 1216962003497 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 1216962003498 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 1216962003499 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 1216962003500 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 1216962003501 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1216962003502 GDP-fucose synthetase, extended (e) SDRs; Region: GDP_FS_SDR_e; cd05239 1216962003503 GDP-4-keto-6-deoxymannose-3, 5-epimerase-4-reductase; Region: PLN02725 1216962003504 NADP binding site [chemical binding]; other site 1216962003505 active site 1216962003506 putative substrate binding site [chemical binding]; other site 1216962003507 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 1216962003508 putative substrate-binding site; other site 1216962003509 nickel binding site [ion binding]; other site 1216962003510 Ni/Fe-hydrogenase, b-type cytochrome subunit; Region: CytB-hydogenase; TIGR02125 1216962003511 Ni,Fe-hydrogenase I large subunit [Energy production and conversion]; Region: HyaB; COG0374 1216962003512 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; pfam00374 1216962003513 hydrogenase (NiFe) small subunit (hydA); Region: hydA; TIGR00391 1216962003514 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 1216962003515 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 1216962003516 pyruvate flavodoxin oxidoreductase subunit gamma; Validated; Region: PRK05844 1216962003517 pyruvate/ketoisovalerate ferredoxin oxidoreductase subunit gamma; Provisional; Region: PRK14029 1216962003518 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 1216962003519 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 1216962003520 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 1216962003521 substrate binding site [chemical binding]; other site 1216962003522 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 1216962003523 Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and...; Region: TPP_enzymes; cl01629 1216962003524 TPP-binding site [chemical binding]; other site 1216962003525 adenylosuccinate lyase; Provisional; Region: PRK08470 1216962003526 Adenylsuccinate lyase (ASL)_subgroup 1; Region: Adenylsuccinate_lyase_1; cd01360 1216962003527 tetramer interface [polypeptide binding]; other site 1216962003528 active site 1216962003529 Adenylosuccinate lyase C-terminus; Region: ADSL_C; smart00998 1216962003530 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 1216962003531 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 1216962003532 DNA binding site [nucleotide binding] 1216962003533 active site 1216962003534 FAD binding domain; Region: FAD_binding_4; pfam01565 1216962003535 glycolate oxidase, subunit GlcD; Region: glcD; TIGR00387 1216962003536 Protein of unknown function (DUF1682); Region: DUF1682; pfam07946 1216962003537 nudix-type nucleoside diphosphatase, YffH/AdpP family; Region: TIGR00052 1216962003538 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 1216962003539 dimer interface [polypeptide binding]; other site 1216962003540 ADP-ribose binding site [chemical binding]; other site 1216962003541 active site 1216962003542 nudix motif; other site 1216962003543 metal binding site [ion binding]; metal-binding site 1216962003544 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 1216962003545 Peptidase family M23; Region: Peptidase_M23; pfam01551 1216962003546 Anti-sigma-28 factor, FlgM; Region: FlgM; pfam04316 1216962003547 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 1216962003548 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 1216962003549 DNA-methyltransferase (dcm); Region: dcm; TIGR00675 1216962003550 cofactor binding site; other site 1216962003551 DNA binding site [nucleotide binding] 1216962003552 substrate interaction site [chemical binding]; other site 1216962003553 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 1216962003554 cofactor binding site; other site 1216962003555 N-methylhydantoinase B/acetone carboxylase, alpha subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuB; COG0146 1216962003556 Hydantoinase B/oxoprolinase; Region: Hydantoinase_B; pfam02538 1216962003557 N-methylhydantoinase A/acetone carboxylase, beta subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuA; COG0145 1216962003558 Hydantoinase/oxoprolinase; Region: Hydantoinase_A; pfam01968 1216962003559 Acetone carboxylase gamma subunit; Region: Acetone_carb_G; pfam08882 1216962003560 Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcxC; COG4647 1216962003561 N-methylhydantoinase A/acetone carboxylase, beta subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuA; COG0145 1216962003562 Hydantoinase/oxoprolinase N-terminal region; Region: Hydant_A_N; pfam05378 1216962003563 Hydantoinase/oxoprolinase; Region: Hydantoinase_A; pfam01968 1216962003564 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 1216962003565 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 1216962003566 putative acyltransferase; Provisional; Region: PRK05790 1216962003567 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 1216962003568 dimer interface [polypeptide binding]; other site 1216962003569 active site 1216962003570 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 1216962003571 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 1216962003572 flagellar assembly protein FliW; Provisional; Region: PRK13282 1216962003573 DNA uptake lipoprotein [General function prediction only]; Region: ComL; COG4105 1216962003574 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 1216962003575 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 1216962003576 Walker A motif; other site 1216962003577 ATP binding site [chemical binding]; other site 1216962003578 Walker B motif; other site 1216962003579 arginine finger; other site 1216962003580 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 1216962003581 prephenate dehydrogenase; Validated; Region: PRK08507 1216962003582 Prephenate dehydrogenase; Region: PDH; pfam02153 1216962003583 flagellar biosynthesis protein FliQ; Validated; Region: fliQ; PRK05700 1216962003584 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13904 1216962003585 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 1216962003586 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl17341 1216962003587 prephenate dehydrogenase; Validated; Region: PRK08507 1216962003588 Prephenate dehydrogenase [Amino acid transport and metabolism]; Region: TyrA; COG0287 1216962003589 flagellar biosynthesis protein FliQ; Validated; Region: fliQ; PRK05700 1216962003590 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13904 1216962003591 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 1216962003592 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl17341 1216962003593 Predicted dehydrogenase [General function prediction only]; Region: COG0579 1216962003594 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 1216962003595 NlpC/P60 family; Region: NLPC_P60; cl17555 1216962003596 Low molecular weight phosphatase family; Region: LMWPc; cd00115 1216962003597 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 1216962003598 active site 1216962003599 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 1216962003600 RNA polymerase sigma factor RpoD, C-terminal domain; Region: RpoD_Cterm; TIGR02393 1216962003601 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1216962003602 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 1216962003603 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 1216962003604 DNA binding residues [nucleotide binding] 1216962003605 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 1216962003606 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 1216962003607 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 1216962003608 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 1216962003609 rRNA small subunit methyltransferase G; Region: GidB; pfam02527 1216962003610 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 1216962003611 urease subunit alpha; Reviewed; Region: ureC; PRK13207 1216962003612 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 1216962003613 subunit interactions [polypeptide binding]; other site 1216962003614 active site 1216962003615 flap region; other site 1216962003616 AmiS/UreI family transporter; Region: AmiS_UreI; pfam02293 1216962003617 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 1216962003618 urease accessory protein UreE; Provisional; Region: ureE; PRK13261 1216962003619 dimer interface [polypeptide binding]; other site 1216962003620 catalytic residues [active] 1216962003621 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 1216962003622 AmiS/UreI family transporter; Region: AmiS_UreI; pfam02293 1216962003623 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 1216962003624 urease accessory protein UreE; Provisional; Region: ureE; PRK13261 1216962003625 dimer interface [polypeptide binding]; other site 1216962003626 catalytic residues [active] 1216962003627 Urease accessory protein UreF [Posttranslational modification, protein turnover, chaperones]; Region: UreF; COG0830 1216962003628 UreF; Region: UreF; pfam01730 1216962003629 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cd00882 1216962003630 G1 box; other site 1216962003631 GTP/Mg2+ binding site [chemical binding]; other site 1216962003632 G2 box; other site 1216962003633 Switch I region; other site 1216962003634 G3 box; other site 1216962003635 Switch II region; other site 1216962003636 G4 box; other site 1216962003637 G5 box; other site 1216962003638 UreD urease accessory protein; Region: UreD; cl00530 1216962003639 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 1216962003640 Sel1-like repeats; Region: SEL1; smart00671 1216962003641 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 1216962003642 TPR motif; other site 1216962003643 binding surface 1216962003644 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 1216962003645 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 1216962003646 DNA methylase; Region: N6_N4_Mtase; pfam01555 1216962003647 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 1216962003648 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 1216962003649 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 1216962003650 C4-dicarboxylate transporter [Energy production and conversion]; Region: DcuC; cl17322 1216962003651 fructose-1,6-bisphosphatase; Provisional; Region: PRK09293 1216962003652 active site 1216962003653 Mn2+ and Fe2+ transporters of the NRAMP family [Inorganic ion transport and metabolism]; Region: MntH; cl15845 1216962003654 Allophanate hydrolase subunit 1; Region: AHS1; pfam02682 1216962003655 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]; Region: DUR1; COG2049 1216962003656 Allophanate hydrolase subunit 2; Region: AHS2; pfam02626 1216962003657 phosphoglyceromutase; Provisional; Region: PRK05434 1216962003658 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 1216962003659 Allophanate hydrolase subunit 1; Region: AHS1; pfam02682 1216962003660 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]; Region: DUR1; COG2049 1216962003661 Allophanate hydrolase subunit 2; Region: AHS2; pfam02626 1216962003662 BPG-independent PGAM N-terminus (iPGM_N); Region: iPGM_N; cl17463 1216962003663 Allophanate hydrolase subunit 1; Region: AHS1; pfam02682 1216962003664 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]; Region: DUR1; COG2049 1216962003665 Allophanate hydrolase subunit 2; Region: AHS2; pfam02626 1216962003666 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 1216962003667 phosphoglyceromutase; Provisional; Region: PRK05434 1216962003668 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 1216962003669 Outer membrane efflux protein; Region: OEP; pfam02321 1216962003670 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 1216962003671 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 1216962003672 HlyD family secretion protein; Region: HlyD_3; pfam13437 1216962003673 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 1216962003674 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 1216962003675 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 1216962003676 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 1216962003677 glycyl-tRNA synthetase subunit alpha; Validated; Region: glyQ; PRK09348 1216962003678 motif 1; other site 1216962003679 dimer interface [polypeptide binding]; other site 1216962003680 active site 1216962003681 motif 2; other site 1216962003682 motif 3; other site 1216962003683 Uncharacterized conserved protein [Function unknown]; Region: COG0327 1216962003684 NIF3 (NGG1p interacting factor 3); Region: NIF3; pfam01784 1216962003685 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]; Region: COG1579 1216962003686 Putative zinc ribbon domain; Region: DUF164; pfam02591 1216962003687 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 1216962003688 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 1216962003689 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 1216962003690 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 1216962003691 active site 1216962003692 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 1216962003693 nickel responsive regulator; Provisional; Region: PRK00630 1216962003694 Ribbon-helix-helix protein, copG family; Region: RHH_1; pfam01402 1216962003695 NikR C terminal nickel binding domain; Region: NikR_C; pfam08753 1216962003696 nicotinic acid mononucleotide adenylyltransferase; Provisional; Region: nadD; PRK00071 1216962003697 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 1216962003698 active site 1216962003699 (T/H)XGH motif; other site 1216962003700 iojap-like ribosome-associated protein; Region: iojap_ybeB; TIGR00090 1216962003701 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 1216962003702 tRNA dimethylallyltransferase; Region: miaA; TIGR00174 1216962003703 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 1216962003704 active site 1216962003705 zinc binding site [ion binding]; other site 1216962003706 Maf_Ham1. Maf, a nucleotide binding protein, has been implicated in inhibition of septum formation in eukaryotes, bacteria and archaea. A Ham1-related protein from Methanococcus jannaschii is a novel NTPase that has been shown to hydrolyze nonstandard...; Region: Maf_Ham1; cl00276 1216962003707 putative active site [active] 1216962003708 Maf_Ham1. Maf, a nucleotide binding protein, has been implicated in inhibition of septum formation in eukaryotes, bacteria and archaea. A Ham1-related protein from Methanococcus jannaschii is a novel NTPase that has been shown to hydrolyze nonstandard...; Region: Maf_Ham1; cl00276 1216962003709 putative active site [active] 1216962003710 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Validated; Region: PRK05584 1216962003711 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 1216962003712 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1216962003713 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 1216962003714 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 1216962003715 active site 1216962003716 KMSKS motif; other site 1216962003717 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 1216962003718 tRNA binding surface [nucleotide binding]; other site 1216962003719 anticodon binding site; other site 1216962003720 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 1216962003721 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]; Region: COG0075 1216962003722 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1216962003723 catalytic residue [active] 1216962003724 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1216962003725 active site 1216962003726 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 1216962003727 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 1216962003728 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 1216962003729 FeS/SAM binding site; other site 1216962003730 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 1216962003731 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1216962003732 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 1216962003733 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 1216962003734 catalytic triad [active] 1216962003735 Uncharacterized conserved protein [Function unknown]; Region: COG1556 1216962003736 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 1216962003737 4Fe-4S dicluster domain; Region: Fer4_8; pfam13183 1216962003738 Domain of unknown function (DUF3390); Region: DUF3390; pfam11870 1216962003739 Uncharacterized conserved protein containing a ferredoxin-like domain [Energy production and conversion]; Region: COG1139 1216962003740 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 1216962003741 Domain of unknown function (DUF3390); Region: DUF3390; pfam11870 1216962003742 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 1216962003743 Cysteine-rich domain; Region: CCG; pfam02754 1216962003744 Cysteine-rich domain; Region: CCG; pfam02754 1216962003745 Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion]; Region: VirB10; COG2948 1216962003746 Type IV secretory pathway, VirB9 components [Intracellular trafficking and secretion]; Region: VirB9; COG3504 1216962003747 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 1216962003748 VirB7 interaction site; other site 1216962003749 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 1216962003750 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 1216962003751 Rod binding protein; Region: Rod-binding; cl01626 1216962003752 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 1216962003753 dimer interface [polypeptide binding]; other site 1216962003754 phosphorylation site [posttranslational modification] 1216962003755 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 1216962003756 ATP binding site [chemical binding]; other site 1216962003757 Mg2+ binding site [ion binding]; other site 1216962003758 G-X-G motif; other site 1216962003759 methionyl-tRNA synthetase; Reviewed; Region: PRK12267 1216962003760 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 1216962003761 active site 1216962003762 HIGH motif; other site 1216962003763 KMSKS motif; other site 1216962003764 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 1216962003765 tRNA binding surface [nucleotide binding]; other site 1216962003766 anticodon binding site; other site 1216962003767 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 1216962003768 dimer interface [polypeptide binding]; other site 1216962003769 putative tRNA-binding site [nucleotide binding]; other site 1216962003770 Methyltransferase domain; Region: Methyltransf_31; pfam13847 1216962003771 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 1216962003772 S-adenosylmethionine binding site [chemical binding]; other site 1216962003773 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cl00509 1216962003774 active site 2 [active] 1216962003775 active site 1 [active] 1216962003776 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 1216962003777 Protein of unknown function (DUF511); Region: DUF511; cl01114 1216962003778 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 1216962003779 phosphate binding site [ion binding]; other site 1216962003780 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase [Cell envelope biogenesis, outer membrane]; Region: KdsA; cl17225 1216962003781 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 1216962003782 homopentamer interface [polypeptide binding]; other site 1216962003783 active site 1216962003784 transcription antitermination protein NusB; Reviewed; Region: nusB; PRK00202 1216962003785 putative RNA binding site [nucleotide binding]; other site 1216962003786 Virulence factor BrkB; Region: Virul_fac_BrkB; cl07918 1216962003787 biotin synthase; Provisional; Region: PRK08508 1216962003788 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 1216962003789 FeS/SAM binding site; other site 1216962003790 Biotin and Thiamin Synthesis associated domain; Region: BATS; pfam06968 1216962003791 R3H domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. R3H domains are found in proteins together with ATPase domains, SF1 helicase domains, SF2 DEAH helicase domains, Cys-rich...; Region: R3H; cd02325 1216962003792 RxxxH motif; other site 1216962003793 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 1216962003794 23S rRNA binding site [nucleotide binding]; other site 1216962003795 L21 binding site [polypeptide binding]; other site 1216962003796 L13 binding site [polypeptide binding]; other site 1216962003797 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 1216962003798 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 1216962003799 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 1216962003800 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 1216962003801 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK12305 1216962003802 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; pfam07973 1216962003803 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 1216962003804 active site 1216962003805 dimer interface [polypeptide binding]; other site 1216962003806 motif 1; other site 1216962003807 motif 2; other site 1216962003808 motif 3; other site 1216962003809 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 1216962003810 anticodon binding site; other site 1216962003811 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 1216962003812 recombinase A; Provisional; Region: recA; PRK09354 1216962003813 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 1216962003814 hexamer interface [polypeptide binding]; other site 1216962003815 Walker A motif; other site 1216962003816 ATP binding site [chemical binding]; other site 1216962003817 Walker B motif; other site 1216962003818 AMIN domain; Region: AMIN; pfam11741 1216962003819 CTP synthetase; Validated; Region: pyrG; PRK05380 1216962003820 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 1216962003821 Catalytic site [active] 1216962003822 active site 1216962003823 UTP binding site [chemical binding]; other site 1216962003824 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 1216962003825 active site 1216962003826 putative oxyanion hole; other site 1216962003827 catalytic triad [active] 1216962003828 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 1216962003829 active site 1216962003830 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 1216962003831 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 1216962003832 active site 1216962003833 putative oxyanion hole; other site 1216962003834 catalytic triad [active] 1216962003835 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 1216962003836 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 1216962003837 active site 1216962003838 High-affinity nickel permease [Inorganic ion transport and metabolism]; Region: HoxN; COG3376 1216962003839 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 1216962003840 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 1216962003841 Walker A motif; other site 1216962003842 ATP binding site [chemical binding]; other site 1216962003843 Walker B motif; other site 1216962003844 arginine finger; other site 1216962003845 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 1216962003846 Members of the ICL/PEPM_KPHMT enzyme superfamily catalyze the formation and cleavage of either P-C or C-C bonds. Typical members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate...; Region: ICL_KPHMT; cl00435 1216962003847 metal binding site [ion binding]; metal-binding site 1216962003848 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1216962003849 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 1216962003850 Peptidase family M23; Region: Peptidase_M23; pfam01551 1216962003851 septum formation inhibitor; Reviewed; Region: minC; PRK00556 1216962003852 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 1216962003853 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 1216962003854 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 1216962003855 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 1216962003856 homoserine kinase; Provisional; Region: PRK01212 1216962003857 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 1216962003858 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 1216962003859 Ylxr homologs; group of conserved hypothetical bacterial proteins of unknown function; structure revealed putative RNA binding cleft; proteins are encoded by an operon that includes other proteins involved in transcription and/or translation; Region: YlxR; cl00189 1216962003860 putative RNA binding cleft [nucleotide binding]; other site 1216962003861 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 1216962003862 G4 box; other site 1216962003863 G5 box; other site 1216962003864 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 1216962003865 Translation-initiation factor 2; Region: IF-2; pfam11987 1216962003866 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 1216962003867 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 1216962003868 Sm and related proteins; Region: Sm_like; cl00259 1216962003869 Uncharacterized BCR, YhbC family COG0779; Region: DUF150; pfam02576 1216962003870 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 1216962003871 putative oligomer interface [polypeptide binding]; other site 1216962003872 putative RNA binding site [nucleotide binding]; other site 1216962003873 Uncharacterized protein, 4-oxalocrotonate tautomerase homolog [General function prediction only]; Region: COG1942 1216962003874 active site 1 [active] 1216962003875 dimer interface [polypeptide binding]; other site 1216962003876 hexamer interface [polypeptide binding]; other site 1216962003877 active site 2 [active] 1216962003878 Ribosomal protein L31; Region: Ribosomal_L31; pfam01197 1216962003879 Predicted methyltransferases [General function prediction only]; Region: COG0313 1216962003880 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 1216962003881 putative SAM binding site [chemical binding]; other site 1216962003882 putative homodimer interface [polypeptide binding]; other site 1216962003883 rRNA methylase, putative, group 3; Region: rRNA_methyl_3; TIGR00186 1216962003884 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 1216962003885 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 1216962003886 Selenocysteine-specific translation elongation factor [Translation, ribosomal structure and biogenesis]; Region: SelB; COG3276 1216962003887 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 1216962003888 G1 box; other site 1216962003889 GTP/Mg2+ binding site [chemical binding]; other site 1216962003890 G2 box; other site 1216962003891 Switch I region; other site 1216962003892 G3 box; other site 1216962003893 Switch II region; other site 1216962003894 G4 box; other site 1216962003895 G5 box; other site 1216962003896 selB_II: this subfamily represents the domain of elongation factor SelB, homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several...; Region: selB_II; cd03696 1216962003897 Domain III of Elongation factor (EF) Tu (EF-TU) and EF-G. Elongation factors (EF) EF-Tu and EF-G participate in the elongation phase during protein biosynthesis on the ribosome. Their functional cycles depend on GTP binding and its hydrolysis. The EF-Tu...; Region: Translation_factor_III; cl02786 1216962003898 Elongation factor SelB, winged helix; Region: SelB-wing_3; pfam09107 1216962003899 Gluconolactonase [Carbohydrate transport and metabolism]; Region: COG3386 1216962003900 Strictosidine synthase; Region: Str_synth; pfam03088 1216962003901 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 1216962003902 Sel1-like repeats; Region: SEL1; smart00671 1216962003903 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 1216962003904 Sel1-like repeats; Region: SEL1; smart00671 1216962003905 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 1216962003906 Sel1 repeat; Region: Sel1; cl02723 1216962003907 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 1216962003908 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 1216962003909 TPR motif; other site 1216962003910 binding surface 1216962003911 Sel1-like repeats; Region: SEL1; smart00671 1216962003912 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 1216962003913 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 1216962003914 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 1216962003915 Predicted membrane protein [Function unknown]; Region: COG1289 1216962003916 Fusaric acid resistance protein-like; Region: FUSC_2; pfam13515 1216962003917 Domain of unknown function DUF59; Region: DUF59; pfam01883 1216962003918 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 1216962003919 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 1216962003920 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 1216962003921 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 1216962003922 flagellar hook-basal body protein FliE; Reviewed; Region: fliE; PRK03907 1216962003923 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 1216962003924 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK05680 1216962003925 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK07182 1216962003926 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 1216962003927 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 1216962003928 tRNA pseudouridine synthase D; Reviewed; Region: truD; PRK00984 1216962003929 Pseudouridine synthase, similar to Escherichia coli TruD; Region: PseudoU_synth_EcTruD; cd02575 1216962003930 Permutation of conserved domain; other site 1216962003931 active site 1216962003932 Putative NADPH-quinone reductase (modulator of drug activity B) [General function prediction only]; Region: MdaB; COG2249 1216962003933 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 1216962003934 FMN binding site [chemical binding]; other site 1216962003935 dimer interface [polypeptide binding]; other site 1216962003936 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 1216962003937 Ligand Binding Site [chemical binding]; other site 1216962003938 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 1216962003939 Methyltransferase domain; Region: Methyltransf_26; pfam13659 1216962003940 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 1216962003941 acetyl-CoA carboxylase subunit beta; Validated; Region: PRK05654 1216962003942 RNA polymerases M/15 Kd subunit; Region: RNA_POL_M_15KD; cl02717 1216962003943 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 1216962003944 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 1216962003945 putative substrate translocation pore; other site 1216962003946 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 1216962003947 CfrBI restriction endonuclease; Region: RE_CfrBI; pfam09516 1216962003948 Alpha amylase catalytic domain family; Region: AmyAc_family; cl07893 1216962003949 CfrBI restriction endonuclease; Region: RE_CfrBI; pfam09516 1216962003950 RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; Region: Rel-Spo_like; cl11966 1216962003951 metal binding triad [ion binding]; metal-binding site 1216962003952 metallophosphatase superfamily, metallophosphatase domain; Region: MPP_superfamily; cl13995 1216962003953 active site 1216962003954 metal binding site [ion binding]; metal-binding site 1216962003955 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 1216962003956 GTP-binding protein LepA; Provisional; Region: PRK05433 1216962003957 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 1216962003958 G1 box; other site 1216962003959 putative GEF interaction site [polypeptide binding]; other site 1216962003960 GTP/Mg2+ binding site [chemical binding]; other site 1216962003961 Switch I region; other site 1216962003962 G2 box; other site 1216962003963 G3 box; other site 1216962003964 Switch II region; other site 1216962003965 G4 box; other site 1216962003966 G5 box; other site 1216962003967 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 1216962003968 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 1216962003969 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 1216962003970 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 1216962003971 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 1216962003972 Flagellar basal body-associated protein FliL; Region: FliL; cl00681 1216962003973 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 1216962003974 putative inner membrane protein; Provisional; Region: PRK11099 1216962003975 heme oxygenase, HugZ family; Region: heme_ox_HugZ; TIGR04109 1216962003976 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 1216962003977 glutamylglutaminyl-tRNA synthetase; Provisional; Region: PRK12410 1216962003978 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 1216962003979 active site 1216962003980 KMSKS motif; other site 1216962003981 YGGT family; Region: YGGT; pfam02325 1216962003982 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 1216962003983 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 1216962003984 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1216962003985 catalytic residue [active] 1216962003986 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 1216962003987 dTDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]; Region: RfbA; COG1209 1216962003988 active site 1216962003989 tetramer interface; other site 1216962003990 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 1216962003991 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 1216962003992 hinge; other site 1216962003993 active site 1216962003994 phosphodiesterase; Provisional; Region: PRK12704 1216962003995 KH domain; Region: KH_1; pfam00013 1216962003996 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 1216962003997 Zn2+ binding site [ion binding]; other site 1216962003998 Mg2+ binding site [ion binding]; other site 1216962003999 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212; cl00360 1216962004000 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212; cl00360 1216962004001 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 1216962004002 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 1216962004003 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 1216962004004 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 1216962004005 trimer interface [polypeptide binding]; other site 1216962004006 active site 1216962004007 PQQ-like domain; Region: PQQ_2; pfam13360 1216962004008 pantothenate kinase; Reviewed; Region: PRK13333 1216962004009 Family description; Region: DsbD_2; pfam13386 1216962004010 histidinol-phosphate phosphatase family domain; Region: Histidinol-ppas; TIGR01656 1216962004011 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 1216962004012 active site 1216962004013 motif I; other site 1216962004014 motif II; other site 1216962004015 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1216962004016 ADP-L-glycero-D-manno-heptose-6-epimerase; Region: heptose_epim; TIGR02197 1216962004017 NAD(P) binding site [chemical binding]; other site 1216962004018 active site 1216962004019 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 1216962004020 ADP-heptose synthase, bifunctional sugar kinase/adenylyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaE; COG2870 1216962004021 putative ribose interaction site [chemical binding]; other site 1216962004022 putative ADP binding site [chemical binding]; other site 1216962004023 rfaE bifunctional protein, domain II; Region: rfaE_dom_II; TIGR02199 1216962004024 active site 1216962004025 HIGH motif; other site 1216962004026 nucleotide binding site [chemical binding]; other site 1216962004027 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 1216962004028 dimer interface [polypeptide binding]; other site 1216962004029 active site 1216962004030 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 1216962004031 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 1216962004032 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 1216962004033 Putative transposase DNA-binding domain; Region: OrfB_Zn_ribbon; pfam07282 1216962004034 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG0675 1216962004035 Probable transposase; Region: OrfB_IS605; pfam01385 1216962004036 Helix-turn-helix domain; Region: HTH_OrfB_IS605; pfam12323 1216962004037 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 1216962004038 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 1216962004039 Walker A/P-loop; other site 1216962004040 ATP binding site [chemical binding]; other site 1216962004041 Q-loop/lid; other site 1216962004042 ABC transporter signature motif; other site 1216962004043 Walker B; other site 1216962004044 D-loop; other site 1216962004045 H-loop/switch region; other site 1216962004046 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 1216962004047 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 1216962004048 Walker A/P-loop; other site 1216962004049 ATP binding site [chemical binding]; other site 1216962004050 Q-loop/lid; other site 1216962004051 ABC transporter signature motif; other site 1216962004052 Walker B; other site 1216962004053 D-loop; other site 1216962004054 H-loop/switch region; other site 1216962004055 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 1216962004056 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 1216962004057 ABC-ATPase subunit interface; other site 1216962004058 putative PBP binding loops; other site 1216962004059 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 1216962004060 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 1216962004061 dimer interface [polypeptide binding]; other site 1216962004062 conserved gate region; other site 1216962004063 putative PBP binding loops; other site 1216962004064 ABC-ATPase subunit interface; other site 1216962004065 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 1216962004066 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_19; cd08518 1216962004067 L-fucose transporter; Provisional; Region: PRK10133; cl17665 1216962004068 SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars; Region: SIS; cl00389 1216962004069 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 1216962004070 dimer interface [polypeptide binding]; other site 1216962004071 active site 1216962004072 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 1216962004073 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 1216962004074 active site 1216962004075 dimer interface [polypeptide binding]; other site 1216962004076 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 1216962004077 dimer interface [polypeptide binding]; other site 1216962004078 active site 1216962004079 glucokinase; Provisional; Region: glk; PRK00292 1216962004080 glucokinase, proteobacterial type; Region: glk; TIGR00749 1216962004081 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 1216962004082 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 1216962004083 putative active site [active] 1216962004084 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 1216962004085 Glucokinase; Region: Glucokinase; cl17310 1216962004086 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 1216962004087 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 1216962004088 putative active site [active] 1216962004089 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 1216962004090 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 1216962004091 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 1216962004092 Dehydratase family; Region: ILVD_EDD; cl00340 1216962004093 keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase; Provisional; Region: PRK05718 1216962004094 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 1216962004095 active site 1216962004096 intersubunit interface [polypeptide binding]; other site 1216962004097 catalytic residue [active] 1216962004098 LysE type translocator; Region: LysE; cl00565 1216962004099 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 1216962004100 Methyltransferase domain; Region: Methyltransf_26; pfam13659 1216962004101 glutamate racemase; Provisional; Region: PRK00865 1216962004102 transcription termination factor Rho; Provisional; Region: rho; PRK09376 1216962004103 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 1216962004104 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 1216962004105 RNA binding site [nucleotide binding]; other site 1216962004106 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 1216962004107 multimer interface [polypeptide binding]; other site 1216962004108 Walker A motif; other site 1216962004109 ATP binding site [chemical binding]; other site 1216962004110 Walker B motif; other site 1216962004111 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 1216962004112 cytochrome c-type biogenesis protein CcsB; Region: cytochr_II_ccsB; TIGR03144 1216962004113 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 1216962004114 catalytic residues [active] 1216962004115 ferrochelatase; Reviewed; Region: hemH; PRK00035 1216962004116 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 1216962004117 C-terminal domain interface [polypeptide binding]; other site 1216962004118 active site 1216962004119 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 1216962004120 active site 1216962004121 N-terminal domain interface [polypeptide binding]; other site 1216962004122 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 1216962004123 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 1216962004124 GatB domain; Region: GatB_Yqey; smart00845 1216962004125 VirB8 protein; Region: VirB8; cl01500 1216962004126 Pirin-related protein [General function prediction only]; Region: COG1741 1216962004127 Pirin; Region: Pirin; pfam02678 1216962004128 Pirin C-terminal cupin domain; Region: Pirin_C; pfam05726 1216962004129 MmgE/PrpD family; Region: MmgE_PrpD; cl00912 1216962004130 MmgE/PrpD family; Region: MmgE_PrpD; cl00912 1216962004131 2-methylcitrate dehydratase; Region: prpD; TIGR02330 1216962004132 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 1216962004133 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 1216962004134 catalytic residue [active] 1216962004135 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 1216962004136 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 1216962004137 D-3-phosphoglycerate dehydrogenase; Provisional; Region: PRK13581 1216962004138 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_4; cd12173 1216962004139 ligand binding site [chemical binding]; other site 1216962004140 NAD binding site [chemical binding]; other site 1216962004141 dimerization interface [polypeptide binding]; other site 1216962004142 catalytic site [active] 1216962004143 C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH); Region: ACT_3PGDH-xct; cd04902 1216962004144 putative L-serine binding site [chemical binding]; other site 1216962004145 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 1216962004146 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture...; Region: S1_RPS1_repeat_ec1_hs1; cd05687 1216962004147 RNA binding site [nucleotide binding]; other site 1216962004148 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 1216962004149 RNA binding site [nucleotide binding]; other site 1216962004150 Ribosomal protein S1-like RNA-binding domain; Region: S1; smart00316 1216962004151 RNA binding site [nucleotide binding]; other site 1216962004152 S1 RNA binding domain; Region: S1; pfam00575 1216962004153 RNA binding site [nucleotide binding]; other site 1216962004154 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 1216962004155 RNA binding site [nucleotide binding]; other site 1216962004156 Glycosyltransferase like family 2; Region: Glyco_tranf_2_2; pfam10111 1216962004157 N-terminal domain of Chondroitin polymerase functions as a GalNAc transferase; Region: GT2_Chondriotin_Pol_N; cd06420 1216962004158 Substrate binding site; other site 1216962004159 metal-binding site 1216962004160 LPP20 lipoprotein; Region: LPP20; pfam02169 1216962004161 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3014 1216962004162 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 1216962004163 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 1216962004164 putative active site [active] 1216962004165 substrate binding site [chemical binding]; other site 1216962004166 putative cosubstrate binding site; other site 1216962004167 catalytic site [active] 1216962004168 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 1216962004169 substrate binding site [chemical binding]; other site 1216962004170 biotin--protein ligase; Provisional; Region: PRK08477 1216962004171 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 1216962004172 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl17192 1216962004173 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 1216962004174 F0F1 ATP synthase subunit B; Validated; Region: PRK08475 1216962004175 F0F1-type ATP synthase, delta subunit (mitochondrial oligomycin sensitivity protein) [Energy production and conversion]; Region: AtpH; cl17210 1216962004176 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 1216962004177 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 1216962004178 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 1216962004179 beta subunit interaction interface [polypeptide binding]; other site 1216962004180 Walker A motif; other site 1216962004181 ATP binding site [chemical binding]; other site 1216962004182 Walker B motif; other site 1216962004183 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 1216962004184 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 1216962004185 core domain interface [polypeptide binding]; other site 1216962004186 delta subunit interface [polypeptide binding]; other site 1216962004187 epsilon subunit interface [polypeptide binding]; other site 1216962004188 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 1216962004189 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 1216962004190 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 1216962004191 alpha subunit interaction interface [polypeptide binding]; other site 1216962004192 Walker A motif; other site 1216962004193 ATP binding site [chemical binding]; other site 1216962004194 Walker B motif; other site 1216962004195 inhibitor binding site; inhibition site 1216962004196 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 1216962004197 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK00571 1216962004198 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 1216962004199 gamma subunit interface [polypeptide binding]; other site 1216962004200 epsilon subunit interface [polypeptide binding]; other site 1216962004201 LBP interface [polypeptide binding]; other site 1216962004202 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; pfam01618 1216962004203 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 1216962004204 TolR protein; Region: tolR; TIGR02801 1216962004205 Gram-negative bacterial tonB protein; Region: TonB; cl10048 1216962004206 translocation protein TolB; Provisional; Region: tolB; PRK04043 1216962004207 TolB amino-terminal domain; Region: TolB_N; pfam04052