-- dump date 20140618_184116 -- class Genbank::misc_feature -- table misc_feature_note -- id note 441768000001 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 441768000002 DnaA N-terminal domain; Region: DnaA_N; pfam11638 441768000003 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 441768000004 Walker A motif; other site 441768000005 ATP binding site [chemical binding]; other site 441768000006 Walker B motif; other site 441768000007 arginine finger; other site 441768000008 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 441768000009 DnaA box-binding interface [nucleotide binding]; other site 441768000010 Transposase DDE domain; Region: DDE_Tnp_1; pfam01609 441768000011 S4 domain; Region: S4_2; pfam13275 441768000012 Recombinational DNA repair ATPase (RecF pathway) [DNA replication, recombination, and repair]; Region: RecF; COG1195 441768000013 ATP-binding cassette domain of RecF; Region: ABC_RecF; cd03242 441768000014 Walker A/P-loop; other site 441768000015 ATP binding site [chemical binding]; other site 441768000016 Q-loop/lid; other site 441768000017 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 441768000018 ABC transporter signature motif; other site 441768000019 Walker B; other site 441768000020 D-loop; other site 441768000021 H-loop/switch region; other site 441768000022 DNA gyrase subunit B; Validated; Region: gyrB; PRK05644 441768000023 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 441768000024 ATP binding site [chemical binding]; other site 441768000025 Mg2+ binding site [ion binding]; other site 441768000026 G-X-G motif; other site 441768000027 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 441768000028 anchoring element; other site 441768000029 dimer interface [polypeptide binding]; other site 441768000030 ATP binding site [chemical binding]; other site 441768000031 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 441768000032 active site 441768000033 putative metal-binding site [ion binding]; other site 441768000034 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 441768000035 DNA gyrase subunit A; Validated; Region: PRK05560 441768000036 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 441768000037 CAP-like domain; other site 441768000038 active site 441768000039 primary dimer interface [polypeptide binding]; other site 441768000040 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 441768000041 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 441768000042 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 441768000043 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 441768000044 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 441768000045 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 441768000046 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 441768000047 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 441768000048 Walker A/P-loop; other site 441768000049 ATP binding site [chemical binding]; other site 441768000050 Q-loop/lid; other site 441768000051 ABC transporter signature motif; other site 441768000052 Walker B; other site 441768000053 D-loop; other site 441768000054 H-loop/switch region; other site 441768000055 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 441768000056 FtsX-like permease family; Region: FtsX; pfam02687 441768000057 seryl-tRNA synthetase; Provisional; Region: PRK05431 441768000058 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 441768000059 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 441768000060 dimer interface [polypeptide binding]; other site 441768000061 active site 441768000062 motif 1; other site 441768000063 motif 2; other site 441768000064 motif 3; other site 441768000065 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 441768000066 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 441768000067 active site 441768000068 phosphorylation site [posttranslational modification] 441768000069 intermolecular recognition site; other site 441768000070 dimerization interface [polypeptide binding]; other site 441768000071 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 441768000072 DNA binding site [nucleotide binding] 441768000073 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 441768000074 HAMP domain; Region: HAMP; pfam00672 441768000075 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 441768000076 dimer interface [polypeptide binding]; other site 441768000077 phosphorylation site [posttranslational modification] 441768000078 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 441768000079 ATP binding site [chemical binding]; other site 441768000080 Mg2+ binding site [ion binding]; other site 441768000081 G-X-G motif; other site 441768000082 HINT (histidine triad nucleotide-binding protein) subgroup: Members of this CD belong to the superfamily of histidine triad hydrolases that act on alpha-phosphate of ribonucleotides. This subgroup includes members from all three forms of cellular life; Region: HINT_subgroup; cd01277 441768000083 HIT family signature motif; other site 441768000084 catalytic residue [active] 441768000085 propanediol utilization phosphotransacylase; Provisional; Region: PRK15070 441768000086 Propanediol utilisation protein PduL; Region: PduL; pfam06130 441768000087 Propanediol utilisation protein PduL; Region: PduL; pfam06130 441768000088 HD superfamily phosphohydrolases [General function prediction only]; Region: COG1078 441768000089 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 441768000090 Zn2+ binding site [ion binding]; other site 441768000091 Mg2+ binding site [ion binding]; other site 441768000092 Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from...; Region: TOPRIM; cl00718 441768000093 ribonuclease M5; Region: 5S_RNA_mat_M5; TIGR00334 441768000094 active site 441768000095 metal binding site [ion binding]; metal-binding site 441768000096 Domain of unknown function (DUF4093); Region: DUF4093; pfam13331 441768000097 Dimethyladenosine transferase (rRNA methylation) [Translation, ribosomal structure and biogenesis]; Region: KsgA; COG0030 441768000098 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 441768000099 regulatory protein SpoVG; Reviewed; Region: PRK13259 441768000100 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 441768000101 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 441768000102 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 441768000103 active site 441768000104 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 441768000105 putative active site [active] 441768000106 catalytic residue [active] 441768000107 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 441768000108 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 441768000109 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 441768000110 ATP binding site [chemical binding]; other site 441768000111 putative Mg++ binding site [ion binding]; other site 441768000112 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 441768000113 nucleotide binding region [chemical binding]; other site 441768000114 ATP-binding site [chemical binding]; other site 441768000115 TRCF domain; Region: TRCF; cl04088 441768000116 F420-0:Gamma-glutamyl ligase; Region: F420_ligase; pfam01996 441768000117 F420-0:Gamma-glutamyl ligase; Region: F420_ligase; pfam01996 441768000118 Aminotransferase class I and II; Region: Aminotran_1_2; pfam00155 441768000119 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 441768000120 pyridoxal 5'-phosphate binding site [chemical binding]; other site 441768000121 homodimer interface [polypeptide binding]; other site 441768000122 catalytic residue [active] 441768000123 maltose O-acetyltransferase; Provisional; Region: PRK10092 441768000124 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 441768000125 active site 441768000126 substrate binding site [chemical binding]; other site 441768000127 trimer interface [polypeptide binding]; other site 441768000128 CoA binding site [chemical binding]; other site 441768000129 cardiolipin synthetase; Reviewed; Region: cls; PRK01642 441768000130 Phospholipase_D-nuclease N-terminal; Region: PLDc_N; pfam13396 441768000131 Putative catalytic domain, repeat 1, of Streptococcus mutans uncharacterized protein SMU_988 and similar proteins; Region: PLDc_SMU_988_like_1; cd09154 441768000132 putative active site [active] 441768000133 catalytic site [active] 441768000134 Putative catalytic domain, repeat 2, of Streptococcus mutans uncharacterized protein SMU_988 and similar proteins; Region: PLDc_SMU_988_like_2; cd09160 441768000135 putative active site [active] 441768000136 catalytic site [active] 441768000137 AAA domain; Region: AAA_33; pfam13671 441768000138 AAA domain; Region: AAA_17; pfam13207 441768000139 formate acetyltransferase 1; Region: pyr_form_ly_1; TIGR01255 441768000140 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 441768000141 pyruvate formate-lyase 1-activating enzyme; Region: PFLA; TIGR02493 441768000142 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 441768000143 FeS/SAM binding site; other site 441768000144 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 441768000145 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 441768000146 ligand binding site [chemical binding]; other site 441768000147 flexible hinge region; other site 441768000148 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 441768000149 putative switch regulator; other site 441768000150 non-specific DNA interactions [nucleotide binding]; other site 441768000151 DNA binding site [nucleotide binding] 441768000152 sequence specific DNA binding site [nucleotide binding]; other site 441768000153 putative cAMP binding site [chemical binding]; other site 441768000154 Protein of unknown function (DUF328); Region: DUF328; cl01143 441768000155 formate--tetrahydrofolate ligase; Provisional; Region: PRK13505 441768000156 Formyltetrahydrofolate synthetase (FTHFS) catalyzes the ATP-dependent activation of formate ion via its addition to the N10 position of tetrahydrofolate. FTHFS is a highly expressed key enzyme in both the Wood-Ljungdahl pathway of autotrophic CO2...; Region: FTHFS; cd00477 441768000157 Potassium binding sites [ion binding]; other site 441768000158 Cesium cation binding sites [ion binding]; other site 441768000159 5,10-methylene-tetrahydrofolate dehydrogenase/Methenyl tetrahydrofolate cyclohydrolase [Coenzyme metabolism]; Region: FolD; COG0190 441768000160 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 441768000161 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 441768000162 homodimer interface [polypeptide binding]; other site 441768000163 NADP binding site [chemical binding]; other site 441768000164 substrate binding site [chemical binding]; other site 441768000165 Transcriptional regulators [Transcription]; Region: PurR; COG1609 441768000166 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 441768000167 DNA binding site [nucleotide binding] 441768000168 domain linker motif; other site 441768000169 Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily; Region: PBP1_LacI_sugar_binding_like; cd06267 441768000170 dimerization interface [polypeptide binding]; other site 441768000171 ligand binding site [chemical binding]; other site 441768000172 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 441768000173 ABC-type sugar transport systems, permease components [Carbohydrate transport and metabolism]; Region: UgpA; COG1175 441768000174 dimer interface [polypeptide binding]; other site 441768000175 conserved gate region; other site 441768000176 putative PBP binding loops; other site 441768000177 ABC-ATPase subunit interface; other site 441768000178 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 441768000179 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 441768000180 dimer interface [polypeptide binding]; other site 441768000181 conserved gate region; other site 441768000182 putative PBP binding loops; other site 441768000183 ABC-ATPase subunit interface; other site 441768000184 Cellobiose phosphorylase [Carbohydrate transport and metabolism]; Region: COG3459 441768000185 N-terminal domain of cellobiose phosphorylase (CBP) and similar proteins; Region: GH94N_CBP_like; cd11754 441768000186 catalytic domain interface [polypeptide binding]; other site 441768000187 homodimer interface [polypeptide binding]; other site 441768000188 putative active site [active] 441768000189 OsmC-like protein; Region: OsmC; cl00767 441768000190 Listeria-Bacteroides repeat domain (List_Bact_rpt); Region: Flg_new; pfam09479 441768000191 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; cl02712 441768000192 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; cl02712 441768000193 amidase catalytic site [active] 441768000194 Zn binding residues [ion binding]; other site 441768000195 Bacterial Ig-like domain 2; Region: BID_2; smart00635 441768000196 Listeria-Bacteroides repeat domain (List_Bact_rpt); Region: Flg_new; pfam09479 441768000197 Listeria-Bacteroides repeat domain (List_Bact_rpt); Region: Flg_new; pfam09479 441768000198 Listeria-Bacteroides repeat domain (List_Bact_rpt); Region: Flg_new; cl09714 441768000199 Bacterial surface proteins containing Ig-like domains [Cell motility and secretion]; Region: COG5492 441768000200 Bacterial Ig-like domain (group 2); Region: Big_2; pfam02368 441768000201 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; cl02712 441768000202 substrate binding site [chemical binding]; other site 441768000203 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; cl02712 441768000204 amidase catalytic site [active] 441768000205 Zn binding residues [ion binding]; other site 441768000206 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 441768000207 dimer interface [polypeptide binding]; other site 441768000208 substrate binding site [chemical binding]; other site 441768000209 metal binding sites [ion binding]; metal-binding site 441768000210 hypothetical protein; Provisional; Region: PRK12378 441768000211 transcriptional repressor DicA; Reviewed; Region: PRK09706 441768000212 HipA N-terminal domain; Region: Couple_hipA; cl11853 441768000213 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 441768000214 Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of hydroxymethyl...; Region: SHMT; cd00378 441768000215 dimer interface [polypeptide binding]; other site 441768000216 active site 441768000217 glycine-pyridoxal phosphate binding site [chemical binding]; other site 441768000218 folate binding site [chemical binding]; other site 441768000219 electron transport complex, RnfABCDGE type, C subunit; Region: rnfC; TIGR01945 441768000220 SLBB domain; Region: SLBB; pfam10531 441768000221 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 441768000222 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; cl00779 441768000223 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 441768000224 Membrane-associated lipoprotein involved in thiamine biosynthesis [Coenzyme metabolism]; Region: ApbE; COG1477 441768000225 ApbE family; Region: ApbE; pfam02424 441768000226 N-Utilization Substance G (NusG) N terminal (NGN) insert and Lin0431 are part of DUF1312; Region: DUF1312; cl02206 441768000227 Heptaprenyl diphosphate synthase component I; Region: Hpre_diP_synt_I; pfam07456 441768000228 50S ribosomal protein L31 type B; Reviewed; Region: rpmE2; PRK01678 441768000229 thymidine kinase; Provisional; Region: PRK04296 441768000230 Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn dependent and catalyze the deamination of nucleosides. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a...; Region: nucleoside_deaminase; cd01285 441768000231 nucleoside/Zn binding site; other site 441768000232 dimer interface [polypeptide binding]; other site 441768000233 catalytic motif [active] 441768000234 Transketolase [Carbohydrate transport and metabolism]; Region: TktA; COG0021 441768000235 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 441768000236 TPP-binding site [chemical binding]; other site 441768000237 dimer interface [polypeptide binding]; other site 441768000238 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 441768000239 PYR/PP interface [polypeptide binding]; other site 441768000240 dimer interface [polypeptide binding]; other site 441768000241 TPP binding site [chemical binding]; other site 441768000242 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 441768000243 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 441768000244 tRNA:m(5)U-54 methyltransferase; Region: gid_trmFO; TIGR00137 441768000245 tRNA (uracil-5-)-methyltransferase Gid; Reviewed; Region: PRK05335 441768000246 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 441768000247 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 441768000248 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 441768000249 Bacterial protein of unknown function (DUF951); Region: DUF951; cl01864 441768000250 hypothetical protein; Provisional; Region: PRK11770 441768000251 Domain of unknown function (DUF307); Region: DUF307; pfam03733 441768000252 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 441768000253 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 441768000254 EDD domain protein, DegV family; Region: DegV; TIGR00762 441768000255 Uncharacterized protein, DegV family COG1307; Region: DegV; pfam02645 441768000256 Transcriptional regulators [Transcription]; Region: MarR; COG1846 441768000257 MarR family; Region: MarR; pfam01047 441768000258 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 441768000259 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 441768000260 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 441768000261 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 441768000262 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 441768000263 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 441768000264 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 441768000265 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 441768000266 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 441768000267 putative translocon binding site; other site 441768000268 protein-rRNA interface [nucleotide binding]; other site 441768000269 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 441768000270 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 441768000271 G-X-X-G motif; other site 441768000272 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 441768000273 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 441768000274 23S rRNA interface [nucleotide binding]; other site 441768000275 5S rRNA interface [nucleotide binding]; other site 441768000276 putative antibiotic binding site [chemical binding]; other site 441768000277 L25 interface [polypeptide binding]; other site 441768000278 L27 interface [polypeptide binding]; other site 441768000279 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 441768000280 23S rRNA interface [nucleotide binding]; other site 441768000281 putative translocon interaction site; other site 441768000282 signal recognition particle (SRP54) interaction site; other site 441768000283 L23 interface [polypeptide binding]; other site 441768000284 trigger factor interaction site; other site 441768000285 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 441768000286 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 441768000287 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 441768000288 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 441768000289 RNA binding site [nucleotide binding]; other site 441768000290 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 441768000291 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 441768000292 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 441768000293 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 441768000294 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 441768000295 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 441768000296 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 441768000297 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 441768000298 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 441768000299 23S rRNA interface [nucleotide binding]; other site 441768000300 L21e interface [polypeptide binding]; other site 441768000301 5S rRNA interface [nucleotide binding]; other site 441768000302 L27 interface [polypeptide binding]; other site 441768000303 L5 interface [polypeptide binding]; other site 441768000304 ribosomal protein S5, bacterial/organelle type; Region: rpsE_bact; TIGR01021 441768000305 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 441768000306 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 441768000307 Ribosomal protein L30, which is found in eukaryotes and prokaryotes but not in archaea, is one of the smallest ribosomal proteins with a molecular mass of about 7kDa. L30 binds the 23SrRNA as well as the 5S rRNA and is one of five ribosomal proteins that...; Region: Ribosomal_L30; cd01658 441768000308 23S rRNA binding site [nucleotide binding]; other site 441768000309 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 441768000310 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 441768000311 SecY translocase; Region: SecY; pfam00344 441768000312 adenylate kinase; Reviewed; Region: adk; PRK00279 441768000313 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 441768000314 AMP-binding site [chemical binding]; other site 441768000315 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 441768000316 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 441768000317 active site 441768000318 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 441768000319 rRNA binding site [nucleotide binding]; other site 441768000320 predicted 30S ribosome binding site; other site 441768000321 Ribosomal protein L36; Region: Ribosomal_L36; pfam00444 441768000322 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 441768000323 30S ribosomal protein S13; Region: bact_S13; TIGR03631 441768000324 30S ribosomal protein S11; Validated; Region: PRK05309 441768000325 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 441768000326 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 441768000327 alphaNTD homodimer interface [polypeptide binding]; other site 441768000328 alphaNTD - beta interaction site [polypeptide binding]; other site 441768000329 alphaNTD - beta' interaction site [polypeptide binding]; other site 441768000330 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 441768000331 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 441768000332 Listeria-Bacteroides repeat domain (List_Bact_rpt); Region: Flg_new; pfam09479 441768000333 Endonuclease I; Region: Endonuclease_1; cl01003 441768000334 Methyladenine glycosylase; Region: Adenine_glyco; pfam03352 441768000335 Peptidase family M3B Oligopeptidase F (PepF); Region: M3B_PepF_1; cd09606 441768000336 oligoendopeptidase, M3 family; Region: M3_not_pepF; TIGR02289 441768000337 active site 441768000338 Zn binding site [ion binding]; other site 441768000339 Domain of unknown function (DU1801); Region: DUF1801; pfam08818 441768000340 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 441768000341 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 441768000342 catalytic residues [active] 441768000343 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 441768000344 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 441768000345 Walker A/P-loop; other site 441768000346 ATP binding site [chemical binding]; other site 441768000347 Q-loop/lid; other site 441768000348 ABC transporter signature motif; other site 441768000349 Walker B; other site 441768000350 D-loop; other site 441768000351 H-loop/switch region; other site 441768000352 cobalt transporter ATP-binding subunit; Provisional; Region: cbiO; PRK13634 441768000353 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 441768000354 Walker A/P-loop; other site 441768000355 ATP binding site [chemical binding]; other site 441768000356 Q-loop/lid; other site 441768000357 ABC transporter signature motif; other site 441768000358 Walker B; other site 441768000359 D-loop; other site 441768000360 H-loop/switch region; other site 441768000361 Cobalt transport protein; Region: CbiQ; cl00463 441768000362 Cobalt transport protein; Region: CbiQ; pfam02361 441768000363 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 441768000364 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 441768000365 dimerization interface 3.5A [polypeptide binding]; other site 441768000366 active site 441768000367 thymidylate kinase; Validated; Region: tmk; PRK00698 441768000368 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 441768000369 TMP-binding site; other site 441768000370 ATP-binding site [chemical binding]; other site 441768000371 DNA polymerase III subunit delta'; Validated; Region: PRK08058 441768000372 DNA polymerase III subunit delta'; Validated; Region: PRK08485 441768000373 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 441768000374 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 441768000375 S-adenosylmethionine binding site [chemical binding]; other site 441768000376 Predicted methyltransferases [General function prediction only]; Region: COG0313 441768000377 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 441768000378 putative SAM binding site [chemical binding]; other site 441768000379 putative homodimer interface [polypeptide binding]; other site 441768000380 methionyl-tRNA synthetase; Reviewed; Region: PRK11893 441768000381 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 441768000382 HIGH motif; other site 441768000383 active site 441768000384 KMSKS motif; other site 441768000385 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 441768000386 tRNA binding surface [nucleotide binding]; other site 441768000387 anticodon binding site; other site 441768000388 Uncharacterized conserved protein [Function unknown]; Region: COG1284 441768000389 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 441768000390 Uncharacterized protein conserved in bacteria (DUF2179); Region: DUF2179; pfam10035 441768000391 Uncharacterized conserved protein [Function unknown]; Region: COG0393 441768000392 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 441768000393 PAS domain; Region: PAS_9; pfam13426 441768000394 putative active site [active] 441768000395 heme pocket [chemical binding]; other site 441768000396 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 441768000397 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 441768000398 metal binding site [ion binding]; metal-binding site 441768000399 active site 441768000400 I-site; other site 441768000401 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 441768000402 23S rRNA interface [nucleotide binding]; other site 441768000403 L3 interface [polypeptide binding]; other site 441768000404 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 441768000405 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 441768000406 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 441768000407 active site 441768000408 HIGH motif; other site 441768000409 KMSKS motif; other site 441768000410 Na+/H+ antiporter NhaD and related arsenite permeases [Inorganic ion transport and metabolism]; Region: ArsB; COG1055 441768000411 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 441768000412 transmembrane helices; other site 441768000413 Domain of unknown function(DUF2779); Region: DUF2779; pfam11074 441768000414 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 441768000415 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 441768000416 active site 441768000417 HIGH motif; other site 441768000418 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 441768000419 KMSKS motif; other site 441768000420 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 441768000421 anticodon binding site; other site 441768000422 tRNA binding surface [nucleotide binding]; other site 441768000423 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; cl00258 441768000424 active site 441768000425 metal binding site [ion binding]; metal-binding site 441768000426 dimerization interface [polypeptide binding]; other site 441768000427 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 441768000428 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 441768000429 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 441768000430 motif II; other site 441768000431 rRNA methylase, putative, group 3; Region: rRNA_methyl_3; TIGR00186 441768000432 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; pfam08032 441768000433 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 441768000434 RNA polymerase sigma factor, sigma-70 family; Region: sigma70-ECF; TIGR02937 441768000435 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 441768000436 Sigma-70, region 4; Region: Sigma70_r4_2; pfam08281 441768000437 Short C-terminal domain; Region: SHOCT; pfam09851 441768000438 50S ribosomal protein L33; Validated; Region: rpmG; PRK00504 441768000439 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; pfam00584 441768000440 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 441768000441 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 441768000442 putative homodimer interface [polypeptide binding]; other site 441768000443 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 441768000444 heterodimer interface [polypeptide binding]; other site 441768000445 homodimer interface [polypeptide binding]; other site 441768000446 SynChlorMet cassette protein ScmC; Region: SCM_chp_ScmC; TIGR04249 441768000447 Endonuclease I; Region: Endonuclease_1; cl01003 441768000448 Endonuclease I; Region: Endonuclease_1; pfam04231 441768000449 Listeria-Bacteroides repeat domain (List_Bact_rpt); Region: Flg_new; pfam09479 441768000450 Listeria-Bacteroides repeat domain (List_Bact_rpt); Region: Flg_new; pfam09479 441768000451 Endonuclease I; Region: Endonuclease_1; pfam04231 441768000452 SPFH domain / Band 7 family; Region: Band_7; pfam01145 441768000453 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_12; cd07255 441768000454 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 441768000455 putative metal binding site [ion binding]; other site 441768000456 This domain superfamily is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins; Region: Glo_EDI_BRP_like; cl14632 441768000457 active site 441768000458 Protein of unknown function (DUF3267); Region: DUF3267; pfam11667 441768000459 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 441768000460 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 441768000461 putative thiostrepton binding site; other site 441768000462 23S rRNA interface [nucleotide binding]; other site 441768000463 L7/L12 interface [polypeptide binding]; other site 441768000464 L25 interface [polypeptide binding]; other site 441768000465 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 441768000466 mRNA/rRNA interface [nucleotide binding]; other site 441768000467 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 441768000468 23S rRNA interface [nucleotide binding]; other site 441768000469 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 441768000470 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 441768000471 core dimer interface [polypeptide binding]; other site 441768000472 peripheral dimer interface [polypeptide binding]; other site 441768000473 L10 interface [polypeptide binding]; other site 441768000474 L11 interface [polypeptide binding]; other site 441768000475 putative EF-Tu interaction site [polypeptide binding]; other site 441768000476 putative EF-G interaction site [polypeptide binding]; other site 441768000477 16S RNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]; Region: RsmC; COG2813 441768000478 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 441768000479 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl17585 441768000480 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 441768000481 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 441768000482 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 441768000483 RPB10 interaction site [polypeptide binding]; other site 441768000484 RPB1 interaction site [polypeptide binding]; other site 441768000485 RPB11 interaction site [polypeptide binding]; other site 441768000486 RPB3 interaction site [polypeptide binding]; other site 441768000487 RPB12 interaction site [polypeptide binding]; other site 441768000488 DNA-directed RNA polymerase subunit beta'; Provisional; Region: PRK00566 441768000489 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 441768000490 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 441768000491 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 441768000492 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 441768000493 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 441768000494 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 441768000495 DNA binding site [nucleotide binding] 441768000496 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 441768000497 Predicted acetyltransferase [General function prediction only]; Region: COG2388 441768000498 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 441768000499 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 441768000500 metal binding site [ion binding]; metal-binding site 441768000501 active site 441768000502 I-site; other site 441768000503 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the...; Region: Peptidase_S24_S26; cl10465 441768000504 Catalytic site [active] 441768000505 bifunctional acetaldehyde-CoA/alcohol dehydrogenase; Provisional; Region: PRK13805 441768000506 Coenzyme A acylating aldehyde dehydrogenase (ACDH), ALDH family 20-like; Region: ALDH_F20_ACDH; cd07122 441768000507 putative catalytic cysteine [active] 441768000508 C-terminal alcohol dehydrogenase domain of the acetaldehyde dehydrogenase-alcohol dehydrogenase bifunctional two-domain protein (AAD); Region: AAD_C; cd08178 441768000509 putative active site [active] 441768000510 metal binding site [ion binding]; metal-binding site 441768000511 SynChlorMet cassette protein ScmC; Region: SCM_chp_ScmC; TIGR04249 441768000512 Uncharacterized BCR, COG1649; Region: DUF187; pfam02638 441768000513 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1649 441768000514 Uncharacterized BCR, COG1649; Region: DUF187; pfam02638 441768000515 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 441768000516 S17 interaction site [polypeptide binding]; other site 441768000517 S8 interaction site; other site 441768000518 16S rRNA interaction site [nucleotide binding]; other site 441768000519 streptomycin interaction site [chemical binding]; other site 441768000520 23S rRNA interaction site [nucleotide binding]; other site 441768000521 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 441768000522 30S ribosomal protein S7; Validated; Region: PRK05302 441768000523 elongation factor G; Reviewed; Region: PRK00007 441768000524 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 441768000525 G1 box; other site 441768000526 putative GEF interaction site [polypeptide binding]; other site 441768000527 GTP/Mg2+ binding site [chemical binding]; other site 441768000528 Switch I region; other site 441768000529 G2 box; other site 441768000530 G3 box; other site 441768000531 Switch II region; other site 441768000532 G4 box; other site 441768000533 G5 box; other site 441768000534 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 441768000535 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 441768000536 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 441768000537 elongation factor Tu; Reviewed; Region: PRK00049 441768000538 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 441768000539 G1 box; other site 441768000540 GEF interaction site [polypeptide binding]; other site 441768000541 GTP/Mg2+ binding site [chemical binding]; other site 441768000542 Switch I region; other site 441768000543 G2 box; other site 441768000544 G3 box; other site 441768000545 Switch II region; other site 441768000546 G4 box; other site 441768000547 G5 box; other site 441768000548 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 441768000549 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 441768000550 Antibiotic Binding Site [chemical binding]; other site 441768000551 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 441768000552 active site 441768000553 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 441768000554 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 441768000555 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 441768000556 Competence-damaged protein; Region: CinA; pfam02464 441768000557 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 441768000558 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 441768000559 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 441768000560 dimer interface [polypeptide binding]; other site 441768000561 ssDNA binding site [nucleotide binding]; other site 441768000562 tetramer (dimer of dimers) interface [polypeptide binding]; other site 441768000563 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 441768000564 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional; Region: PRK14538 441768000565 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 441768000566 DHH family; Region: DHH; pfam01368 441768000567 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 441768000568 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 441768000569 replicative DNA helicase; Region: DnaB; TIGR00665 441768000570 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 441768000571 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 441768000572 Walker A motif; other site 441768000573 ATP binding site [chemical binding]; other site 441768000574 Walker B motif; other site 441768000575 DNA binding loops [nucleotide binding] 441768000576 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 441768000577 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 441768000578 dimerization interface [polypeptide binding]; other site 441768000579 DPS ferroxidase diiron center [ion binding]; other site 441768000580 ion pore; other site 441768000581 Chromate transporter; Region: Chromate_transp; pfam02417 441768000582 Chromate transporter; Region: Chromate_transp; pfam02417 441768000583 peptide chain release factor 1; Validated; Region: prfA; PRK00591 441768000584 PCRF domain; Region: PCRF; pfam03462 441768000585 RF-1 domain; Region: RF-1; pfam00472 441768000586 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional; Region: PRK09328 441768000587 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 441768000588 S-adenosylmethionine binding site [chemical binding]; other site 441768000589 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 441768000590 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 441768000591 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 441768000592 G1 box; other site 441768000593 putative GEF interaction site [polypeptide binding]; other site 441768000594 GTP/Mg2+ binding site [chemical binding]; other site 441768000595 Switch I region; other site 441768000596 G2 box; other site 441768000597 G3 box; other site 441768000598 Switch II region; other site 441768000599 G4 box; other site 441768000600 G5 box; other site 441768000601 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 441768000602 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 441768000603 ribose-5-phosphate isomerase B; Provisional; Region: PRK05571 441768000604 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 441768000605 active site 441768000606 Uncharacterized conserved protein [Function unknown]; Region: COG1739 441768000607 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 441768000608 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 441768000609 tRNA CCA-pyrophosphorylase; Provisional; Region: PRK13299 441768000610 active site 441768000611 NTP binding site [chemical binding]; other site 441768000612 metal binding triad [ion binding]; metal-binding site 441768000613 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 441768000614 tRNA nucleotidyltransferase domain 2 putative; Region: tRNA_NucTran2_2; pfam13735 441768000615 3'-5' exoribonuclease YhaM; Provisional; Region: PRK13480 441768000616 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 441768000617 Zn2+ binding site [ion binding]; other site 441768000618 Mg2+ binding site [ion binding]; other site 441768000619 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 441768000620 rRNA large subunit methyltransferase; Provisional; Region: PRK00103 441768000621 Large-conductance mechanosensitive channel, MscL; Region: MscL; cl00860 441768000622 large-conductance mechanosensitive channel; Reviewed; Region: mscL; PRK00567 441768000623 EDD domain protein, DegV family; Region: DegV; TIGR00762 441768000624 Uncharacterized protein, DegV family COG1307; Region: DegV; pfam02645 441768000625 3-deoxy-7-phosphoheptulonate synthase; Reviewed; Region: PRK08673 441768000626 phospho-2-dehydro-3-deoxyheptonate aldolase; Region: DAHP_synth_Bsub; TIGR01361 441768000627 Prephenate dehydrogenase [Amino acid transport and metabolism]; Region: TyrA; COG0287 441768000628 prephenate dehydrogenase; Validated; Region: PRK08507 441768000629 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 441768000630 active site 441768000631 dimer interface [polypeptide binding]; other site 441768000632 metal binding site [ion binding]; metal-binding site 441768000633 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 441768000634 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 441768000635 hinge; other site 441768000636 active site 441768000637 Chorismate mutase type II; Region: CM_2; smart00830 441768000638 shikimate 5-dehydrogenase; Reviewed; Region: aroE; PRK00258 441768000639 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 441768000640 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 441768000641 shikimate binding site; other site 441768000642 NAD(P) binding site [chemical binding]; other site 441768000643 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 441768000644 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 441768000645 Tetramer interface [polypeptide binding]; other site 441768000646 active site 441768000647 FMN-binding site [chemical binding]; other site 441768000648 Predicted membrane protein [Function unknown]; Region: COG4129 441768000649 Bacterial protein of unknown function (DUF939); Region: DUF939; pfam06081 441768000650 DUF939 C-terminal domain; Region: DUF939_C; pfam11728 441768000651 Class II hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase (HMGR); Region: HMG-CoA_reductase_classII; cd00644 441768000652 homodimer interface [polypeptide binding]; other site 441768000653 catalytic residues [active] 441768000654 NAD binding site [chemical binding]; other site 441768000655 substrate binding pocket [chemical binding]; other site 441768000656 flexible flap; other site 441768000657 "initiating" condensing enzymes are a subclass of decarboxylating condensing enzymes, including beta-ketoacyl [ACP] synthase, type III and polyketide synthases, type III, which include chalcone synthase and related enzymes. They are...; Region: init_cond_enzymes; cd00827 441768000658 3-hydroxy-3-methylglutaryl CoA synthase, prokaryotic clade; Region: HMG-CoA-S_prok; TIGR01835 441768000659 dimer interface [polypeptide binding]; other site 441768000660 active site 441768000661 ATP-dependent DNA helicase RecG; Provisional; Region: PRK10917 441768000662 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 441768000663 ATP binding site [chemical binding]; other site 441768000664 putative Mg++ binding site [ion binding]; other site 441768000665 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 441768000666 nucleotide binding region [chemical binding]; other site 441768000667 ATP-binding site [chemical binding]; other site 441768000668 putative phosphate acyltransferase; Provisional; Region: PRK05331 441768000669 ribonuclease III; Reviewed; Region: rnc; PRK00102 441768000670 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 441768000671 dimerization interface [polypeptide binding]; other site 441768000672 active site 441768000673 metal binding site [ion binding]; metal-binding site 441768000674 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 441768000675 dsRNA binding site [nucleotide binding]; other site 441768000676 Putative primosome component and related proteins [DNA replication, recombination, and repair]; Region: DnaD; COG3935 441768000677 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 441768000678 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 441768000679 minor groove reading motif; other site 441768000680 helix-hairpin-helix signature motif; other site 441768000681 substrate binding pocket [chemical binding]; other site 441768000682 active site 441768000683 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 441768000684 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 441768000685 non-specific DNA binding site [nucleotide binding]; other site 441768000686 salt bridge; other site 441768000687 sequence-specific DNA binding site [nucleotide binding]; other site 441768000688 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 441768000689 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 441768000690 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 441768000691 Walker A/P-loop; other site 441768000692 ATP binding site [chemical binding]; other site 441768000693 Q-loop/lid; other site 441768000694 ABC transporter signature motif; other site 441768000695 Walker B; other site 441768000696 D-loop; other site 441768000697 H-loop/switch region; other site 441768000698 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 441768000699 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 441768000700 ATP-binding cassette domain of glucan transporter and related proteins, subfamily C; Region: ABCC_Glucan_exporter_like; cd03254 441768000701 Walker A/P-loop; other site 441768000702 ATP binding site [chemical binding]; other site 441768000703 Q-loop/lid; other site 441768000704 ABC transporter signature motif; other site 441768000705 Walker B; other site 441768000706 D-loop; other site 441768000707 H-loop/switch region; other site 441768000708 Uncharacterized flavoproteins [Energy production and conversion]; Region: FpaA; COG0426 441768000709 Flavodoxin-like fold; Region: Flavodoxin_2; cl00438 441768000710 DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]; Region: DnaE; COG0587 441768000711 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III; Region: PHP_PolIIIA; cd07431 441768000712 active site 441768000713 PHP Thumb interface [polypeptide binding]; other site 441768000714 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 441768000715 generic binding surface II; other site 441768000716 generic binding surface I; other site 441768000717 Leucyl aminopeptidase (aminopeptidase T) [Amino acid transport and metabolism]; Region: AmpS; COG2309 441768000718 Thermophilic metalloprotease (M29); Region: Peptidase_M29; pfam02073 441768000719 Predicted flavoprotein [General function prediction only]; Region: COG0431 441768000720 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 441768000721 Domain of unknown function (DU1801); Region: DUF1801; pfam08818 441768000722 Lactonase, 7-bladed beta-propeller; Region: Lactonase; pfam10282 441768000723 acyl carrier protein; Provisional; Region: acpP; PRK00982 441768000724 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 441768000725 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 441768000726 HIGH motif; other site 441768000727 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 441768000728 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 441768000729 active site 441768000730 KMSKS motif; other site 441768000731 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 441768000732 tRNA binding surface [nucleotide binding]; other site 441768000733 Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP_PGM_like; cd07067 441768000734 catalytic core [active] 441768000735 Methyltransferase domain; Region: Methyltransf_31; pfam13847 441768000736 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 441768000737 S-adenosylmethionine binding site [chemical binding]; other site 441768000738 Predicted Fe-S oxidoreductase [General function prediction only]; Region: COG1242 441768000739 DNA polymerase III PolC; Validated; Region: polC; PRK00448 441768000740 DNA polymerase III polC-type N-terminus; Region: DNA_pol3_alph_N; pfam11490 441768000741 polC_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold nucleic acid binding domain of Bacillus subtilis type C replicative DNA polymerase III alpha subunit (polC). Replication in B. subtilis and Staphylococcus aureus requires two...; Region: polC_OBF; cd04484 441768000742 generic binding surface I; other site 441768000743 generic binding surface II; other site 441768000744 Polymerase and Histidinol Phosphatase domain; Region: PHP; cl17102 441768000745 active site 441768000746 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 441768000747 active site 441768000748 catalytic site [active] 441768000749 substrate binding site [chemical binding]; other site 441768000750 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at PolC gene; Region: PHP_PolIIIA_POLC; cd07435 441768000751 Bax inhibitor 1 like; Region: BaxI_1; cl17691 441768000752 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 441768000753 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 441768000754 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 441768000755 dimer interface [polypeptide binding]; other site 441768000756 motif 1; other site 441768000757 active site 441768000758 motif 2; other site 441768000759 motif 3; other site 441768000760 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 441768000761 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 441768000762 putative tRNA-binding site [nucleotide binding]; other site 441768000763 B3/4 domain; Region: B3_4; pfam03483 441768000764 tRNA synthetase B5 domain; Region: B5; smart00874 441768000765 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 441768000766 dimer interface [polypeptide binding]; other site 441768000767 motif 1; other site 441768000768 motif 3; other site 441768000769 motif 2; other site 441768000770 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 441768000771 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK14455 441768000772 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 441768000773 FeS/SAM binding site; other site 441768000774 GTPase RsgA; Reviewed; Region: PRK00098 441768000775 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 441768000776 RNA binding site [nucleotide binding]; other site 441768000777 Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases; Region: YjeQ_EngC; cd01854 441768000778 GTPase/Zn-binding domain interface [polypeptide binding]; other site 441768000779 GTP/Mg2+ binding site [chemical binding]; other site 441768000780 G4 box; other site 441768000781 G5 box; other site 441768000782 G1 box; other site 441768000783 Switch I region; other site 441768000784 G2 box; other site 441768000785 G3 box; other site 441768000786 Switch II region; other site 441768000787 Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]; Region: Rpe; COG0036 441768000788 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 441768000789 substrate binding site [chemical binding]; other site 441768000790 hexamer interface [polypeptide binding]; other site 441768000791 metal binding site [ion binding]; metal-binding site 441768000792 thiamine pyrophosphokinase; Region: thi_PPkinase; TIGR01378 441768000793 Thiamine pyrophosphokinase; Region: TPK; cd07995 441768000794 active site 441768000795 dimerization interface [polypeptide binding]; other site 441768000796 thiamine binding site [chemical binding]; other site 441768000797 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 441768000798 DAK2 domain fusion protein YloV; Region: YloV; TIGR03599 441768000799 DAK2 domain; Region: Dak2; pfam02734 441768000800 Uncharacterized protein conserved in bacteria (DUF2130); Region: DUF2130; pfam09903 441768000801 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 441768000802 Predicted periplasmic protein (DUF2233); Region: DUF2233; pfam09992 441768000803 Transcriptional regulators [Transcription]; Region: RpiR; COG1737 441768000804 Helix-turn-helix domain, rpiR family; Region: HTH_6; pfam01418 441768000805 RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate...; Region: SIS_RpiR; cd05013 441768000806 putative active site [active] 441768000807 anhydro-N-acetylmuramic acid kinase; Reviewed; Region: anmK; PRK09585 441768000808 Alpha-galactosidases/6-phospho-beta-glucosidases, family 4 of glycosyl hydrolases [Carbohydrate transport and metabolism]; Region: CelF; COG1486 441768000809 Glycoside Hydrolases Family 4; Phospho-beta-glucosidase; Region: GH4_P_beta_glucosidase; cd05296 441768000810 NAD binding site [chemical binding]; other site 441768000811 sugar binding site [chemical binding]; other site 441768000812 divalent metal binding site [ion binding]; other site 441768000813 tetramer (dimer of dimers) interface [polypeptide binding]; other site 441768000814 dimer interface [polypeptide binding]; other site 441768000815 Uncharacterized BCR, COG1649; Region: DUF187; pfam02638 441768000816 Uncharacterized BCR, COG1649; Region: DUF187; pfam02638 441768000817 Chitobiase/beta-hexosaminidase C-terminal domain; Region: CHB_HEX_C; pfam03174 441768000818 Chitobiase/beta-hexosaminidase C-terminal domain; Region: CHB_HEX_C; pfam03174 441768000819 Uncharacterized BCR, COG1649; Region: DUF187; pfam02638 441768000820 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 441768000821 Beta-lactamase; Region: Beta-lactamase; pfam00144 441768000822 Bacterial surface proteins containing Ig-like domains [Cell motility and secretion]; Region: COG5492 441768000823 Bacterial Ig-like domain (group 2); Region: Big_2; pfam02368 441768000824 Bacterial Ig-like domain (group 2); Region: Big_2; cl02708 441768000825 Bacterial Ig-like domain (group 2); Region: Big_2; pfam02368 441768000826 Right handed beta helix region; Region: Beta_helix; pfam13229 441768000827 Bacterial Ig-like domain (group 2); Region: Big_2; cl02708 441768000828 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 441768000829 amidase catalytic site [active] 441768000830 Zn binding residues [ion binding]; other site 441768000831 substrate binding site [chemical binding]; other site 441768000832 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 441768000833 Carbohydrate Binding Module 6 (CBM6) and CBM35_like superfamily; Region: CBM6-CBM35-CBM36_like; cl14880 441768000834 Carbohydrate Binding Module 6 (CBM6); appended to several carbohydrate binding enzymes, including several glycoside hydrolase (GH) family 26 mannanase domains; Region: CBM6_mannanase-like; cd04086 441768000835 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 441768000836 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 441768000837 ABC-type polysaccharide transport system, permease component [Carbohydrate transport and metabolism]; Region: LplB; COG4209 441768000838 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 441768000839 dimer interface [polypeptide binding]; other site 441768000840 conserved gate region; other site 441768000841 putative PBP binding loops; other site 441768000842 ABC-ATPase subunit interface; other site 441768000843 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 441768000844 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 441768000845 dimer interface [polypeptide binding]; other site 441768000846 conserved gate region; other site 441768000847 putative PBP binding loops; other site 441768000848 ABC-ATPase subunit interface; other site 441768000849 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 441768000850 dimer interface [polypeptide binding]; other site 441768000851 conserved gate region; other site 441768000852 putative PBP binding loops; other site 441768000853 ABC-ATPase subunit interface; other site 441768000854 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 441768000855 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 441768000856 dimer interface [polypeptide binding]; other site 441768000857 conserved gate region; other site 441768000858 putative PBP binding loops; other site 441768000859 ABC-ATPase subunit interface; other site 441768000860 Protein of unknown function, DUF624; Region: DUF624; pfam04854 441768000861 Protein of unknown function (DUF1343); Region: DUF1343; pfam07075 441768000862 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 441768000863 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; pfam00933 441768000864 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 441768000865 nucleotide binding site [chemical binding]; other site 441768000866 N-acetylmuramic acid-6-phosphate etherase; Reviewed; Region: murQ; PRK05441 441768000867 N-acetylmuramic acid 6-phosphate etherase. Members of this family contain the SIS (Sugar ISomerase) domain. The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. The bacterial cell wall sugar N-acetylmuramic acid...; Region: SIS_Etherase; cd05007 441768000868 putative active site [active] 441768000869 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 441768000870 Coenzyme A binding pocket [chemical binding]; other site 441768000871 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 441768000872 GlcN6P_deaminase: Glucosamine-6-phosphate (GlcN6P) deaminase subfamily; GlcN6P deaminase catalyzes the reversible conversion of GlcN6P to D-fructose-6-phosphate (Fru6P) and ammonium. The reaction is an aldo-keto isomerization coupled with an amination or...; Region: GlcN6P_deaminase; cd01399 441768000873 active site 441768000874 trimer interface [polypeptide binding]; other site 441768000875 allosteric site; other site 441768000876 active site lid [active] 441768000877 hexamer (dimer of trimers) interface [polypeptide binding]; other site 441768000878 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 441768000879 GlcNAc-PI de-N-acetylase; Region: PIG-L; pfam02585 441768000880 hypothetical protein; Provisional; Region: PRK13662 441768000881 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 441768000882 tetramer interfaces [polypeptide binding]; other site 441768000883 binuclear metal-binding site [ion binding]; other site 441768000884 NAD-dependent deacetylase; Provisional; Region: PRK00481 441768000885 SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+; Region: SIR2; cl00195 441768000886 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic...; Region: S2P-M50; cd05709 441768000887 active site 441768000888 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 441768000889 S-adenosylmethionine binding site [chemical binding]; other site 441768000890 Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box...; Region: CSP_CDS; cd04458 441768000891 DNA-binding site [nucleotide binding]; DNA binding site 441768000892 RNA-binding motif; other site 441768000893 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]; Region: COG2996 441768000894 S1 domain; Region: S1_2; pfam13509 441768000895 prolyl-tRNA synthetase; Provisional; Region: PRK08661 441768000896 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_arch_euk; cd00778 441768000897 dimer interface [polypeptide binding]; other site 441768000898 motif 1; other site 441768000899 active site 441768000900 motif 2; other site 441768000901 motif 3; other site 441768000902 ProRS Prolyl-anticodon binding domain, long version found predominantly in eukaryotes and archaea. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in...; Region: ProRS_anticodon_zinc; cd00862 441768000903 anticodon binding site; other site 441768000904 zinc-binding site [ion binding]; other site 441768000905 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2819 441768000906 Putative esterase; Region: Esterase; pfam00756 441768000907 Elongation factor G (EF-G) family; Region: EF-G_bact; cd04170 441768000908 elongation factor G; Reviewed; Region: PRK12740 441768000909 G1 box; other site 441768000910 putative GEF interaction site [polypeptide binding]; other site 441768000911 GTP/Mg2+ binding site [chemical binding]; other site 441768000912 Switch I region; other site 441768000913 G2 box; other site 441768000914 G3 box; other site 441768000915 Switch II region; other site 441768000916 G4 box; other site 441768000917 G5 box; other site 441768000918 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 441768000919 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 441768000920 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 441768000921 RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal...; Region: RaiA; cd00552 441768000922 30S subunit binding site; other site 441768000923 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 441768000924 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 441768000925 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 441768000926 Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]; Region: COG1293 441768000927 Domain of unknown function (DUF814); Region: DUF814; pfam05670 441768000928 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 441768000929 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 441768000930 catalytic site [active] 441768000931 G-X2-G-X-G-K; other site 441768000932 DNA-directed RNA polymerase subunit omega; Reviewed; Region: rpoZ; PRK00392 441768000933 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 441768000934 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 441768000935 GIY-YIG motif/motif A; other site 441768000936 active site 441768000937 catalytic site [active] 441768000938 putative DNA binding site [nucleotide binding]; other site 441768000939 metal binding site [ion binding]; metal-binding site 441768000940 UvrB/uvrC motif; Region: UVR; pfam02151 441768000941 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 441768000942 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 441768000943 active site 441768000944 catalytic site [active] 441768000945 substrate binding site [chemical binding]; other site 441768000946 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 441768000947 H+ Antiporter protein; Region: 2A0121; TIGR00900 441768000948 putative substrate translocation pore; other site 441768000949 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 441768000950 Metallo-beta-lactamase superfamily; Region: Lactamase_B; pfam00753 441768000951 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 441768000952 Predicted hydrolases of the HAD superfamily [General function prediction only]; Region: Cof; COG0561 441768000953 haloacid dehalogenase-like hydrolase; Region: HAD; pfam12710 441768000954 aldose 1-epimerase superfamily; Region: Aldose_epim; cl14648 441768000955 active site 441768000956 catalytic residues [active] 441768000957 Zn-dependent dipeptidase, microsomal dipeptidase homolog [Amino acid transport and metabolism]; Region: COG2355 441768000958 renal dipeptidase (rDP), best studied in mammals and also called membrane or microsomal dipeptidase, is a membrane-bound glycoprotein hydrolyzing dipeptides and is involved in hydrolytic metabolism of penem and carbapenem beta-lactam antibiotics; Region: rDP_like; cd01301 441768000959 active site 441768000960 dimer interface [polypeptide binding]; other site 441768000961 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 441768000962 Predicted glutamine amidotransferases [General function prediction only]; Region: COG2071 441768000963 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 441768000964 catalytic triad [active] 441768000965 phosphopantetheine adenylyltransferase; Provisional; Region: coaD; PRK00168 441768000966 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 441768000967 active site 441768000968 (T/H)XGH motif; other site 441768000969 Sm and related proteins; Region: Sm_like; cl00259 441768000970 transcription elongation factor NusA; Provisional; Region: nusA; PRK12327 441768000971 NusA N-terminal domain; Region: NusA_N; pfam08529 441768000972 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 441768000973 RNA binding site [nucleotide binding]; other site 441768000974 homodimer interface [polypeptide binding]; other site 441768000975 NusA-like KH domain; Region: KH_5; pfam13184 441768000976 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 441768000977 G-X-X-G motif; other site 441768000978 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; cd00279 441768000979 putative RNA binding cleft [nucleotide binding]; other site 441768000980 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; Region: Ribosomal_L7Ae; cl00600 441768000981 translation initiation factor IF-2; Region: IF-2; TIGR00487 441768000982 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 441768000983 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 441768000984 G1 box; other site 441768000985 putative GEF interaction site [polypeptide binding]; other site 441768000986 GTP/Mg2+ binding site [chemical binding]; other site 441768000987 Switch I region; other site 441768000988 G2 box; other site 441768000989 G3 box; other site 441768000990 Switch II region; other site 441768000991 G4 box; other site 441768000992 G5 box; other site 441768000993 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 441768000994 Translation-initiation factor 2; Region: IF-2; pfam11987 441768000995 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 441768000996 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 441768000997 Beta propeller domain; Region: Beta_propel; pfam09826 441768000998 LytTr DNA-binding domain; Region: LytTR; pfam04397 441768000999 Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]; Region: PriA; COG1198 441768001000 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 441768001001 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 441768001002 putative active site [active] 441768001003 substrate binding site [chemical binding]; other site 441768001004 putative cosubstrate binding site; other site 441768001005 catalytic site [active] 441768001006 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 441768001007 substrate binding site [chemical binding]; other site 441768001008 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 441768001009 tetramer interfaces [polypeptide binding]; other site 441768001010 binuclear metal-binding site [ion binding]; other site 441768001011 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 441768001012 Zn2+ binding site [ion binding]; other site 441768001013 Mg2+ binding site [ion binding]; other site 441768001014 S-adenosylmethionine synthetase; Validated; Region: PRK05250 441768001015 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 441768001016 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 441768001017 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 441768001018 LemA family; Region: LemA; cl00742 441768001019 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 441768001020 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 441768001021 ATP binding site [chemical binding]; other site 441768001022 putative Mg++ binding site [ion binding]; other site 441768001023 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 441768001024 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; cl17351 441768001025 nucleotide binding region [chemical binding]; other site 441768001026 ATP-binding site [chemical binding]; other site 441768001027 peptide chain release factor 2; Validated; Region: prfB; PRK00578 441768001028 This domain is found in peptide chain release factors; Region: PCRF; smart00937 441768001029 RF-1 domain; Region: RF-1; pfam00472 441768001030 Uncharacterized conserved protein [Function unknown]; Region: COG1284 441768001031 Uncharacterized BCR, YitT family COG1284; Region: DUF161; pfam02588 441768001032 Uncharacterized protein conserved in bacteria (DUF2179); Region: DUF2179; pfam10035 441768001033 RecX family; Region: RecX; cl00936 441768001034 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 441768001035 haloacid dehalogenase-like hydrolase; Region: Hydrolase_3; pfam08282 441768001036 active site 441768001037 motif I; other site 441768001038 motif II; other site 441768001039 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 441768001040 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 441768001041 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 441768001042 This domain directs oriented DNA translocation and forms a winged helix structure; Region: Ftsk_gamma; smart00843 441768001043 ribosome biogenesis GTP-binding protein YlqF; Region: GTPase_YlqF; TIGR03596 441768001044 Circularly permuted YlqF GTPase; Region: YlqF; cd01856 441768001045 GTP/Mg2+ binding site [chemical binding]; other site 441768001046 G4 box; other site 441768001047 G5 box; other site 441768001048 G1 box; other site 441768001049 Switch I region; other site 441768001050 G2 box; other site 441768001051 G3 box; other site 441768001052 Switch II region; other site 441768001053 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 441768001054 RNA/DNA hybrid binding site [nucleotide binding]; other site 441768001055 active site 441768001056 DNA topoisomerase I; Validated; Region: PRK05582 441768001057 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 441768001058 active site 441768001059 interdomain interaction site; other site 441768001060 putative metal-binding site [ion binding]; other site 441768001061 nucleotide binding site [chemical binding]; other site 441768001062 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 441768001063 domain I; other site 441768001064 DNA binding groove [nucleotide binding] 441768001065 phosphate binding site [ion binding]; other site 441768001066 domain II; other site 441768001067 domain III; other site 441768001068 nucleotide binding site [chemical binding]; other site 441768001069 catalytic site [active] 441768001070 domain IV; other site 441768001071 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 441768001072 Listeria-Bacteroides repeat domain (List_Bact_rpt); Region: Flg_new; pfam09479 441768001073 Listeria-Bacteroides repeat domain (List_Bact_rpt); Region: Flg_new; pfam09479 441768001074 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 441768001075 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 441768001076 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 441768001077 Walker A/P-loop; other site 441768001078 ATP binding site [chemical binding]; other site 441768001079 Q-loop/lid; other site 441768001080 ABC transporter signature motif; other site 441768001081 Walker B; other site 441768001082 D-loop; other site 441768001083 H-loop/switch region; other site 441768001084 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 441768001085 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 441768001086 Walker A/P-loop; other site 441768001087 ATP binding site [chemical binding]; other site 441768001088 Q-loop/lid; other site 441768001089 ABC transporter signature motif; other site 441768001090 Walker B; other site 441768001091 D-loop; other site 441768001092 H-loop/switch region; other site 441768001093 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 441768001094 FtsX-like permease family; Region: FtsX; pfam02687 441768001095 Peptidase family U32; Region: Peptidase_U32; cl03113 441768001096 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 441768001097 Peptidase family U32; Region: Peptidase_U32; pfam01136 441768001098 Peroxiredoxin (PRX) family, Atypical 2-cys PRX subfamily; composed of PRXs containing peroxidatic and resolving cysteines, similar to the homodimeric thiol specific antioxidant (TSA) protein also known as TRX-dependent thiol peroxidase (Tpx). Tpx is a...; Region: PRX_Atyp2cys; cd03014 441768001099 dimer interface [polypeptide binding]; other site 441768001100 catalytic triad [active] 441768001101 peroxidatic and resolving cysteines [active] 441768001102 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 441768001103 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 441768001104 The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes. SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The...; Region: SRP; cd03115 441768001105 GTP binding site [chemical binding]; other site 441768001106 putative DNA-binding protein; Validated; Region: PRK00118 441768001107 signal recognition particle protein; Provisional; Region: PRK10867 441768001108 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 441768001109 The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes. SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The...; Region: SRP; cd03115 441768001110 P loop; other site 441768001111 GTP binding site [chemical binding]; other site 441768001112 Signal peptide binding domain; Region: SRP_SPB; pfam02978 441768001113 DNA polymerase I; Provisional; Region: PRK05755 441768001114 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 441768001115 active site 441768001116 metal binding site 1 [ion binding]; metal-binding site 441768001117 putative 5' ssDNA interaction site; other site 441768001118 metal binding site 3; metal-binding site 441768001119 metal binding site 2 [ion binding]; metal-binding site 441768001120 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 441768001121 putative DNA binding site [nucleotide binding]; other site 441768001122 putative metal binding site [ion binding]; other site 441768001123 inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and similar family-A DNA polymerases; Region: DNA_polA_I_Bacillus_like_exo; cd06140 441768001124 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 441768001125 active site 441768001126 DNA binding site [nucleotide binding] 441768001127 catalytic site [active] 441768001128 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 441768001129 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 441768001130 DNA binding site [nucleotide binding] 441768001131 catalytic residue [active] 441768001132 H2TH interface [polypeptide binding]; other site 441768001133 putative catalytic residues [active] 441768001134 turnover-facilitating residue; other site 441768001135 intercalation triad [nucleotide binding]; other site 441768001136 8OG recognition residue [nucleotide binding]; other site 441768001137 putative reading head residues; other site 441768001138 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 441768001139 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 441768001140 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 441768001141 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 441768001142 CoA-binding site [chemical binding]; other site 441768001143 ATP-binding [chemical binding]; other site 441768001144 Replication initiation/membrane attachment protein [DNA replication, recombination, and repair]; Region: DnaB; COG3611 441768001145 primosomal protein DnaI; Reviewed; Region: PRK08939 441768001146 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 441768001147 Walker A motif; other site 441768001148 ATP binding site [chemical binding]; other site 441768001149 Walker B motif; other site 441768001150 arginine finger; other site 441768001151 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 441768001152 TGS _ThrRS_N: ThrRS (threonyl-tRNA Synthetase) is a class II tRNA synthetase that couples threonine to its cognate tRNA. In addition to its catalytic and anticodon-binding domains, ThrRS has an N-terminal TGS domain, named after the ThrRS, GTPase, and...; Region: TGS_ThrRS_N; cd01667 441768001153 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 441768001154 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 441768001155 active site 441768001156 dimer interface [polypeptide binding]; other site 441768001157 motif 1; other site 441768001158 motif 2; other site 441768001159 motif 3; other site 441768001160 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 441768001161 anticodon binding site; other site 441768001162 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: COG4152 441768001163 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 441768001164 Walker A/P-loop; other site 441768001165 ATP binding site [chemical binding]; other site 441768001166 Q-loop/lid; other site 441768001167 ABC transporter signature motif; other site 441768001168 Walker B; other site 441768001169 D-loop; other site 441768001170 H-loop/switch region; other site 441768001171 Domain of unknown function (DUF4162); Region: DUF4162; pfam13732 441768001172 ABC-type Na+ efflux pump, permease component [Energy production and conversion / Inorganic ion transport and metabolism]; Region: NatB; COG1668 441768001173 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Mrp; COG0489 441768001174 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 441768001175 Uncharacterized protein containing a NRPS condensation (elongation) domain [General function prediction only]; Region: COG4908 441768001176 HupE / UreJ protein; Region: HupE_UreJ; cl01011 441768001177 hypothetical protein; Reviewed; Region: PRK00024 441768001178 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 441768001179 MPN+ (JAMM) motif; other site 441768001180 Zinc-binding site [ion binding]; other site 441768001181 Domain of unknown function (DUF697); Region: DUF697; pfam05128 441768001182 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 441768001183 hypothetical protein; Provisional; Region: PRK14553 441768001184 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 441768001185 GTPase CgtA; Reviewed; Region: obgE; PRK12297 441768001186 GTP1/OBG; Region: GTP1_OBG; pfam01018 441768001187 Obg GTPase; Region: Obg; cd01898 441768001188 G1 box; other site 441768001189 GTP/Mg2+ binding site [chemical binding]; other site 441768001190 Switch I region; other site 441768001191 G2 box; other site 441768001192 G3 box; other site 441768001193 Switch II region; other site 441768001194 G4 box; other site 441768001195 G5 box; other site 441768001196 Domain of unknown function (DUF1967); Region: DUF1967; pfam09269 441768001197 putative lipoprotein; Provisional; Region: PRK10533 441768001198 Holliday junction DNA helicase RuvA; Provisional; Region: ruvA; PRK14600 441768001199 RuvA N terminal domain; Region: RuvA_N; pfam01330 441768001200 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 441768001201 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 441768001202 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 441768001203 Walker A motif; other site 441768001204 ATP binding site [chemical binding]; other site 441768001205 Walker B motif; other site 441768001206 arginine finger; other site 441768001207 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 441768001208 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 441768001209 Bacitracin resistance protein BacA; Region: BacA; pfam02673 441768001210 PTS_IIB, PTS system, glucose/sucrose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family...; Region: PTS_IIB_glc; cl00164 441768001211 active site turn [active] 441768001212 Histidine-containing phosphocarrier protein (HPr)-like proteins. HPr is a central component of the bacterial phosphoenolpyruvate sugar phosphotransferase system (PTS). The PTS catalyses the phosphorylation of sugar substrates during their translocation...; Region: PTS-HPr_like; cd00367 441768001213 dimerization domain swap beta strand [polypeptide binding]; other site 441768001214 regulatory protein interface [polypeptide binding]; other site 441768001215 active site 441768001216 regulatory phosphorylation site [posttranslational modification]; other site 441768001217 Domain of unknown function (DUF368); Region: DUF368; cl00893 441768001218 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 441768001219 S-adenosylmethionine binding site [chemical binding]; other site 441768001220 Cellulase M and related proteins [Carbohydrate transport and metabolism]; Region: FrvX; COG1363 441768001221 M42 Peptidase, Endoglucanases; Region: M42_Frv; cd05656 441768001222 oligomer interface [polypeptide binding]; other site 441768001223 active site 441768001224 metal binding site [ion binding]; metal-binding site 441768001225 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 441768001226 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 441768001227 active site 441768001228 catalytic tetrad [active] 441768001229 DNA gyrase subunit B; Validated; Region: gyrB; PRK05644 441768001230 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 441768001231 ATP binding site [chemical binding]; other site 441768001232 Mg2+ binding site [ion binding]; other site 441768001233 G-X-G motif; other site 441768001234 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 441768001235 anchoring element; other site 441768001236 dimer interface [polypeptide binding]; other site 441768001237 ATP binding site [chemical binding]; other site 441768001238 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 441768001239 active site 441768001240 putative metal-binding site [ion binding]; other site 441768001241 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 441768001242 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 441768001243 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 441768001244 CAP-like domain; other site 441768001245 active site 441768001246 primary dimer interface [polypeptide binding]; other site 441768001247 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 441768001248 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 441768001249 Uridine kinase [Nucleotide transport and metabolism]; Region: Udk; COG0572 441768001250 Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK); Region: UMPK_like; cd02028 441768001251 active site 441768001252 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cl17326 441768001253 putative DNA binding helix; other site 441768001254 EDD domain protein, DegV family; Region: DegV; TIGR00762 441768001255 Uncharacterized protein, DegV family COG1307; Region: DegV; pfam02645 441768001256 Uncharacterized ABC-type transport system, periplasmic component/surface lipoprotein [General function prediction only]; Region: Med; COG1744 441768001257 Periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea; Region: PBP1_BmpA_PnrA_like; cd06354 441768001258 ligand binding site [chemical binding]; other site 441768001259 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 441768001260 Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette; Region: TM_PBP1_transp_TpRbsC_like; cd06580 441768001261 TM-ABC transporter signature motif; other site 441768001262 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 441768001263 Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette; Region: TM_PBP1_transp_TpRbsC_like; cd06580 441768001264 TM-ABC transporter signature motif; other site 441768001265 Deoxyribonucleoside kinase (dNK) catalyzes the phosphorylation of deoxyribonucleosides to yield corresponding monophosphates (dNMPs). This family consists of various deoxynucleoside kinases including deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC 2.7.1; Region: dNK; cd01673 441768001266 Substrate-binding site [chemical binding]; other site 441768001267 Substrate specificity [chemical binding]; other site 441768001268 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 441768001269 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 441768001270 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 441768001271 DNA binding residues [nucleotide binding] 441768001272 Glycine cleavage system P-protein, alpha- and beta-subunits. This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2.1; Region: GDC-P; cd00613 441768001273 tetramer interface [polypeptide binding]; other site 441768001274 pyridoxal 5'-phosphate binding site [chemical binding]; other site 441768001275 catalytic residue [active] 441768001276 Glycine cleavage system protein P (pyridoxal-binding), N-terminal domain [Amino acid transport and metabolism]; Region: GcvP; COG0403 441768001277 Glycine cleavage system P-protein, alpha- and beta-subunits. This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2.1; Region: GDC-P; cd00613 441768001278 tetramer interface [polypeptide binding]; other site 441768001279 pyridoxal 5'-phosphate binding site [chemical binding]; other site 441768001280 catalytic residue [active] 441768001281 Glycine cleavage H-protein. Glycine cleavage H-proteins are part of the glycine cleavage system (GCS) found in bacteria, archea and the mitochondria of eukaryotes. GCS is a multienzyme complex consisting of 4 different components (P-, H-, T- and...; Region: GCS_H; cd06848 441768001282 lipoyl attachment site [posttranslational modification]; other site 441768001283 glycine cleavage system aminomethyltransferase T; Reviewed; Region: gcvT; PRK00389 441768001284 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 441768001285 phosphoprotein phosphatases of the metallophosphatase superfamily, metallophosphatase domain; Region: MPP_PPP_family; cd00144 441768001286 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 441768001287 active site 441768001288 metal binding site [ion binding]; metal-binding site 441768001289 Phosphoglyceromutase [Carbohydrate transport and metabolism]; Region: GpmI; COG0696 441768001290 phosphoglyceromutase; Provisional; Region: PRK05434 441768001291 Predicted membrane protein [Function unknown]; Region: COG3601 441768001292 Protein of unknown function (DUF3816); Region: DUF3816; pfam12822 441768001293 enolase; Provisional; Region: eno; PRK00077 441768001294 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 441768001295 dimer interface [polypeptide binding]; other site 441768001296 metal binding site [ion binding]; metal-binding site 441768001297 substrate binding pocket [chemical binding]; other site 441768001298 Methylglyoxal synthase catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The first part of the catalytic mechanism is believed to be similar to TIM (triosephosphate isomerase) in that both enzymes utilize DHAP to...; Region: MGS; cd01422 441768001299 active site 441768001300 dimer interfaces [polypeptide binding]; other site 441768001301 catalytic residues [active] 441768001302 Exoribonuclease R [Transcription]; Region: VacB; COG0557 441768001303 RNB domain; Region: RNB; pfam00773 441768001304 S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase...; Region: S1_RNase_R; cd04471 441768001305 RNA binding site [nucleotide binding]; other site 441768001306 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 441768001307 SmpB-tmRNA interface; other site 441768001308 Hypothetical patatin similar to Z1214 protein of Escherichia coli; Region: Pat_hypo_Ecoli_Z1214_like; cd07209 441768001309 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 441768001310 nucleophile elbow; other site 441768001311 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 441768001312 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 441768001313 active site 441768001314 Autoinducer synthetase; Region: Autoind_synth; cl17404 441768001315 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 441768001316 Coenzyme A binding pocket [chemical binding]; other site 441768001317 Restriction endonuclease; Region: Mrr_cat; pfam04471 441768001318 HRDC domain; Region: HRDC; pfam00570 441768001319 HRDC domain; Region: HRDC; cl02578 441768001320 2'-5' RNA ligase superfamily; Region: 2_5_RNA_ligase2; pfam13563 441768001321 Domain of unknown function (DUF4288); Region: DUF4288; pfam14119 441768001322 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 441768001323 Fructokinases (FRKs) mainly from bacteria and plants are enzymes with high specificity for fructose, as are all FRKs, but they catalyzes the conversion of fructose to fructose-6-phosphate, which is an entry point into glycolysis via conversion into...; Region: bac_FRK; cd01167 441768001324 putative substrate binding site [chemical binding]; other site 441768001325 putative ATP binding site [chemical binding]; other site 441768001326 DNA polymerase IV; Reviewed; Region: PRK03103 441768001327 umuC subunit of DNA Polymerase V; Region: PolY_Pol_V_umuC; cd01700 441768001328 active site 441768001329 DNA binding site [nucleotide binding] 441768001330 Domain of unknown function (DUF4113); Region: DUF4113; pfam13438 441768001331 Transcriptional regulators [Transcription]; Region: MarR; COG1846 441768001332 MarR family; Region: MarR_2; pfam12802 441768001333 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 441768001334 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 441768001335 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 441768001336 Walker A/P-loop; other site 441768001337 ATP binding site [chemical binding]; other site 441768001338 Q-loop/lid; other site 441768001339 ABC transporter signature motif; other site 441768001340 Walker B; other site 441768001341 D-loop; other site 441768001342 H-loop/switch region; other site 441768001343 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 441768001344 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 441768001345 ATP-binding cassette domain of glucan transporter and related proteins, subfamily C; Region: ABCC_Glucan_exporter_like; cd03254 441768001346 Walker A/P-loop; other site 441768001347 ATP binding site [chemical binding]; other site 441768001348 Q-loop/lid; other site 441768001349 ABC transporter signature motif; other site 441768001350 Walker B; other site 441768001351 D-loop; other site 441768001352 H-loop/switch region; other site 441768001353 Uncharacterized conserved protein [Function unknown]; Region: COG0398 441768001354 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 441768001355 trans-2-enoyl-CoA reductase; Provisional; Region: PRK13656 441768001356 NAD(P)H binding domain of trans-2-enoyl-CoA reductase; Region: Eno-Rase_NADH_b; pfam12242 441768001357 Trans-2-enoyl-CoA reductase catalytic region; Region: Enoyl_reductase; pfam12241 441768001358 Enoyl reductase FAD binding domain; Region: Eno-Rase_FAD_bd; pfam07055 441768001359 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 441768001360 Group of bacterial proteins containing an alpha crystallin domain (ACD) similar to Lactobacillus plantarum (Lp) small heat shock proteins (sHsp) HSP 18.5, HSP 18.55 and HSP 19.3. sHsps are molecular chaperones that suppress protein aggregation and...; Region: ACD_LpsHSP_like; cd06471 441768001361 putative dimer interface [polypeptide binding]; other site 441768001362 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 441768001363 FAD binding domain; Region: FAD_binding_4; pfam01565 441768001364 Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]; Region: PhnA; COG2824 441768001365 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; pfam08274 441768001366 PhnA protein; Region: PhnA; pfam03831 441768001367 DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]; Region: RpoE; COG1595 441768001368 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 441768001369 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 441768001370 DNA binding residues [nucleotide binding] 441768001371 iron-sulfur cluster repair di-iron protein; Region: FeS_repair_RIC; TIGR03652 441768001372 heavy metal translocating P-type ATPase; Region: ATPase-IB_hvy; TIGR01525 441768001373 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 441768001374 Soluble P-type ATPase [General function prediction only]; Region: COG4087 441768001375 Copper chaperone [Inorganic ion transport and metabolism]; Region: CopZ; COG2608 441768001376 metal-binding site [ion binding] 441768001377 PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This...; Region: PTS_IIA_fru; cd00211 441768001378 active site 441768001379 phosphorylation site [posttranslational modification] 441768001380 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 441768001381 DEAD-like helicases superfamily; Region: DEXDc; smart00487 441768001382 ATP binding site [chemical binding]; other site 441768001383 Mg++ binding site [ion binding]; other site 441768001384 motif III; other site 441768001385 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 441768001386 nucleotide binding region [chemical binding]; other site 441768001387 ATP-binding site [chemical binding]; other site 441768001388 RNA recognition motif in the DbpA subfamily of prokaryotic DEAD-box rRNA helicases; Region: RRM_DbpA; cd12252 441768001389 RNA binding site [nucleotide binding]; other site 441768001390 Domain of unknown function (DUF4194); Region: DUF4194; pfam13835 441768001391 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4913 441768001392 P-loop containing region of AAA domain; Region: AAA_29; pfam13555 441768001393 Putative exonuclease SbcCD, C subunit; Region: SbcCD_C; pfam13558 441768001394 Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]; Region: PtsA; COG1080 441768001395 PEP-utilising enzyme, N-terminal; Region: PEP-utilisers_N; pfam05524 441768001396 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 441768001397 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 441768001398 Fic family protein [Function unknown]; Region: COG3177 441768001399 Fic/DOC family; Region: Fic; pfam02661 441768001400 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 441768001401 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 441768001402 S-adenosylmethionine binding site [chemical binding]; other site 441768001403 Chloride channel protein EriC [Inorganic ion transport and metabolism]; Region: EriC; COG0038 441768001404 ClC chloride channel EriC. This domain is found in the EriC chloride transporters that mediate the extreme acid resistance response in eubacteria and archaea. This response allows bacteria to survive in the acidic environments by decarboxylation-linked...; Region: EriC; cd01031 441768001405 Cl- selectivity filter; other site 441768001406 Cl- binding residues [ion binding]; other site 441768001407 pore gating glutamate residue; other site 441768001408 dimer interface [polypeptide binding]; other site 441768001409 H+/Cl- coupling transport residue; other site 441768001410 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 441768001411 non-specific DNA binding site [nucleotide binding]; other site 441768001412 salt bridge; other site 441768001413 sequence-specific DNA binding site [nucleotide binding]; other site 441768001414 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 441768001415 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 441768001416 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 441768001417 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 441768001418 metal binding site [ion binding]; metal-binding site 441768001419 active site 441768001420 I-site; other site 441768001421 Alpha amylase catalytic domain found in cyclomaltodextrinases and related proteins; Region: AmyAc_CMD; cd11338 441768001422 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 441768001423 active site 441768001424 homodimer interface [polypeptide binding]; other site 441768001425 catalytic site [active] 441768001426 von Willebrand factor; Region: vWF_A; pfam12450 441768001427 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]; Region: COG2304 441768001428 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 441768001429 metal ion-dependent adhesion site (MIDAS); other site 441768001430 Domain of unknown function (DUF3520); Region: DUF3520; pfam12034 441768001431 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 441768001432 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 441768001433 metal binding site [ion binding]; metal-binding site 441768001434 active site 441768001435 I-site; other site 441768001436 heavy metal translocating P-type ATPase; Region: ATPase-IB_hvy; TIGR01525 441768001437 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 441768001438 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 441768001439 motif II; other site 441768001440 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated; Region: PRK06302 441768001441 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 441768001442 carboxyltransferase (CT) interaction site; other site 441768001443 biotinylation site [posttranslational modification]; other site 441768001444 acetyl-CoA carboxylase biotin carboxylase subunit; Validated; Region: PRK08591 441768001445 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 441768001446 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 441768001447 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 441768001448 acetyl-CoA carboxylase, carboxyl transferase, beta subunit; Region: accD; TIGR00515 441768001449 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 441768001450 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated; Region: PRK05724 441768001451 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 441768001452 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 441768001453 dimer interface [polypeptide binding]; other site 441768001454 active site 441768001455 CoA binding pocket [chemical binding]; other site 441768001456 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 441768001457 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 441768001458 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05557 441768001459 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 441768001460 NAD(P) binding site [chemical binding]; other site 441768001461 homotetramer interface [polypeptide binding]; other site 441768001462 homodimer interface [polypeptide binding]; other site 441768001463 active site 441768001464 beta-ketoacyl-acyl-carrier-protein synthase II; Region: fabF; TIGR03150 441768001465 Beta-ketoacyl-acyl carrier protein (ACP) synthase (KAS), type I and II. KASs are responsible for the elongation steps in fatty acid biosynthesis. KASIII catalyses the initial condensation and KAS I and II catalyze further elongation steps by Claisen...; Region: KAS_I_II; cd00834 441768001466 dimer interface [polypeptide binding]; other site 441768001467 active site 441768001468 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 441768001469 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 441768001470 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 441768001471 Uncharacterized conserved protein [General function prediction only]; Region: BioY; COG1268 441768001472 Protein of unknown function (DUF3816); Region: DUF3816; pfam12822 441768001473 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 441768001474 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 441768001475 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 441768001476 Predicted transcriptional regulators [Transcription]; Region: COG1695 441768001477 Transcriptional regulator PadR-like family; Region: PadR; pfam03551 441768001478 Protein of unknown function (DUF1700); Region: DUF1700; pfam08006 441768001479 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 441768001480 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 441768001481 Walker A/P-loop; other site 441768001482 ATP binding site [chemical binding]; other site 441768001483 Q-loop/lid; other site 441768001484 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 441768001485 ABC transporter signature motif; other site 441768001486 Walker B; other site 441768001487 D-loop; other site 441768001488 H-loop/switch region; other site 441768001489 TOBE domain; Region: TOBE_2; pfam08402 441768001490 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 441768001491 dimer interface [polypeptide binding]; other site 441768001492 conserved gate region; other site 441768001493 putative PBP binding loops; other site 441768001494 ABC-ATPase subunit interface; other site 441768001495 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 441768001496 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 441768001497 dimer interface [polypeptide binding]; other site 441768001498 conserved gate region; other site 441768001499 putative PBP binding loops; other site 441768001500 ABC-ATPase subunit interface; other site 441768001501 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 441768001502 Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; Region: PotD; COG0687 441768001503 transcription antitermination factor NusB; Region: nusB; TIGR01951 441768001504 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 441768001505 ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a...; Region: ExoVII_LU_OBF; cd04489 441768001506 generic binding surface II; other site 441768001507 generic binding surface I; other site 441768001508 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK00977 441768001509 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 441768001510 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 441768001511 RNA binding surface [nucleotide binding]; other site 441768001512 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 441768001513 S-adenosylmethionine binding site [chemical binding]; other site 441768001514 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 441768001515 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 441768001516 Walker A/P-loop; other site 441768001517 ATP binding site [chemical binding]; other site 441768001518 Q-loop/lid; other site 441768001519 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 441768001520 ABC transporter signature motif; other site 441768001521 Walker B; other site 441768001522 D-loop; other site 441768001523 H-loop/switch region; other site 441768001524 Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]; Region: DinP; COG0389 441768001525 DNA Polymerase IV/Kappa; Region: PolY_Pol_IV_kappa; cd03586 441768001526 active site 441768001527 DNA binding site [nucleotide binding] 441768001528 DEAD-like helicases superfamily; Region: DEXDc; smart00487 441768001529 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 441768001530 ATP binding site [chemical binding]; other site 441768001531 putative Mg++ binding site [ion binding]; other site 441768001532 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 441768001533 nucleotide binding region [chemical binding]; other site 441768001534 ATP-binding site [chemical binding]; other site 441768001535 endonuclease IV; Provisional; Region: PRK01060 441768001536 AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites; the alignment also contains hexulose-6-phosphate isomerases, enzymes that catalyze the epimerization of...; Region: AP2Ec; cd00019 441768001537 AP (apurinic/apyrimidinic) site pocket; other site 441768001538 DNA interaction; other site 441768001539 Metal-binding active site; metal-binding site 441768001540 Uncharacterized family 2; belongs to a superfamily containing transcriptional regulators CsoR (copper-sensitive operon repressor), RcnR, and FrmR, and related domains; this family was previously known as part of DUF156; Region: CsoR-like_DUF156_2; cd10159 441768001541 putative homodimer interface [polypeptide binding]; other site 441768001542 putative homotetramer interface [polypeptide binding]; other site 441768001543 putative allosteric switch controlling residues; other site 441768001544 putative metal binding site [ion binding]; other site 441768001545 putative homodimer-homodimer interface [polypeptide binding]; other site 441768001546 arginyl-tRNA synthetase; Reviewed; Region: PRK12451 441768001547 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 441768001548 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 441768001549 active site 441768001550 HIGH motif; other site 441768001551 KMSK motif region; other site 441768001552 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 441768001553 tRNA binding surface [nucleotide binding]; other site 441768001554 anticodon binding site; other site 441768001555 Uncharacterized protein family (UPF0104); Region: UPF0104; pfam03706 441768001556 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 441768001557 This family is most closely related to the GT1 family of glycosyltransferases. UDP-glucose-diacylglycerol glucosyltransferase (UGDG; also known as 1,2-diacylglycerol 3-glucosyltransferase) catalyzes the transfer of glucose from UDP-glucose to 1; Region: GT1_UGDG_like; cd03817 441768001558 putative ADP-binding pocket [chemical binding]; other site 441768001559 Protein-tyrosine-phosphatase [Signal transduction mechanisms]; Region: Wzb; COG0394 441768001560 Low molecular weight phosphatase family; Region: LMWPc; cd00115 441768001561 active site 441768001562 Predicted membrane protein, putative toxin regulator [General function prediction only]; Region: PfoR; COG3641 441768001563 Phosphotransferase system, EIIC; Region: PTS_EIIC_2; pfam13303 441768001564 nicotinate phosphoribosyltransferase; Validated; Region: PRK09243 441768001565 Nicotinate phosphoribosyltransferase (NAPRTase), subgroup A. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting, reaction...; Region: NAPRTase_A; cd01570 441768001566 active site 441768001567 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Bacillus subtilis yoeA; Region: MATE_yoeA_like; cd13138 441768001568 putative efflux protein, MATE family; Region: matE; TIGR00797 441768001569 Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]; Region: CspR; COG0219 441768001570 Haemolysin-III related; Region: HlyIII; cl03831 441768001571 channel protein, hemolysin III family; Region: hlyIII; TIGR01065 441768001572 acetate kinase A/propionate kinase 2; Reviewed; Region: PRK00180 441768001573 propionate/acetate kinase; Provisional; Region: PRK12379 441768001574 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 441768001575 Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivH_like; cd06582 441768001576 TM-ABC transporter signature motif; other site 441768001577 ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]; Region: LivM; COG4177 441768001578 Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of...; Region: TM_PBP1_LivM_like; cd06581 441768001579 TM-ABC transporter signature motif; other site 441768001580 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivG; COG0411 441768001581 ATP-binding cassette component of branched chain amino acids transport system; Region: ABC_Mj1267_LivG_branched; cd03219 441768001582 Walker A/P-loop; other site 441768001583 ATP binding site [chemical binding]; other site 441768001584 Q-loop/lid; other site 441768001585 ABC transporter signature motif; other site 441768001586 Walker B; other site 441768001587 D-loop; other site 441768001588 H-loop/switch region; other site 441768001589 ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]; Region: LivF; COG0410 441768001590 ATP-binding cassette domain of branched-chain amino acid transporter; Region: ABC_TM1139_LivF_branched; cd03224 441768001591 Walker A/P-loop; other site 441768001592 ATP binding site [chemical binding]; other site 441768001593 Q-loop/lid; other site 441768001594 ABC transporter signature motif; other site 441768001595 Walker B; other site 441768001596 D-loop; other site 441768001597 H-loop/switch region; other site 441768001598 Bacterial Ig-like domain (group 3); Region: Big_3; pfam07523 441768001599 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 441768001600 Periplasmic binding protein; Region: Peripla_BP_6; pfam13458 441768001601 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 441768001602 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 441768001603 putative acyltransferase; Provisional; Region: PRK05790 441768001604 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 441768001605 dimer interface [polypeptide binding]; other site 441768001606 active site 441768001607 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 441768001608 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 441768001609 NAD(P) binding site [chemical binding]; other site 441768001610 homotetramer interface [polypeptide binding]; other site 441768001611 homodimer interface [polypeptide binding]; other site 441768001612 active site 441768001613 hypothetical protein; Validated; Region: PRK06840 441768001614 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 441768001615 active site 441768001616 Acetyl-CoA hydrolase/transferase N-terminal domain; Region: AcetylCoA_hydro; pfam02550 441768001617 butyryl-CoA:acetate CoA-transferase; Region: butyr_acet_CoA; TIGR03948 441768001618 Acetyl-CoA hydrolase/transferase C-terminal domain; Region: AcetylCoA_hyd_C; pfam13336 441768001619 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 441768001620 Alpha/beta hydrolase of unknown function (DUF1057); Region: DUF1057; pfam06342 441768001621 TAP-like protein; Region: Abhydrolase_4; pfam08386 441768001622 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 441768001623 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 441768001624 homoserine O-acetyltransferase; Provisional; Region: metX; cl17114 441768001625 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 441768001626 TRAM domain; Region: TRAM; pfam01938 441768001627 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 441768001628 S-adenosylmethionine binding site [chemical binding]; other site 441768001629 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 441768001630 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 441768001631 ATP binding site [chemical binding]; other site 441768001632 Mg++ binding site [ion binding]; other site 441768001633 motif III; other site 441768001634 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 441768001635 nucleotide binding region [chemical binding]; other site 441768001636 ATP-binding site [chemical binding]; other site 441768001637 SAM-dependent methyltransferases related to tRNA (uracil-5-)-methyltransferase [Translation, ribosomal structure and biogenesis]; Region: TrmA; COG2265 441768001638 TRAM domain; Region: TRAM; pfam01938 441768001639 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 441768001640 S-adenosylmethionine binding site [chemical binding]; other site 441768001641 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional; Region: PRK10841 441768001642 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 441768001643 oxalate/formate antiporter family transporter; Region: 2A0111; TIGR00890 441768001644 putative substrate translocation pore; other site 441768001645 glycogen synthase; Provisional; Region: glgA; PRK00654 441768001646 This family is most closely related to the GT1 family of glycosyltransferases. Glycogen synthase catalyzes the formation and elongation of the alpha-1,4-glucose backbone using ADP-glucose, the second and key step of glycogen biosynthesis. This family...; Region: GT1_Glycogen_synthase_DULL1_like; cd03791 441768001647 ADP-binding pocket [chemical binding]; other site 441768001648 homodimer interface [polypeptide binding]; other site 441768001649 glucose-1-phosphate adenylyltransferase; Provisional; Region: glgC; PRK05293 441768001650 ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch; Region: ADP_Glucose_PP; cd02508 441768001651 ligand binding site; other site 441768001652 oligomer interface; other site 441768001653 Glucose-1-phosphate adenylyltransferase, C-terminal Left-handed parallel beta helix (LbH) domain: Glucose-1-phosphate adenylyltransferase is also known as ADP-glucose synthase or ADP-glucose pyrophosphorylase. It catalyzes the first committed and...; Region: LbH_G1P_AT_C; cd04651 441768001654 dimer interface [polypeptide binding]; other site 441768001655 N-terminal domain interface [polypeptide binding]; other site 441768001656 sulfate 1 binding site; other site 441768001657 Bacterial surface proteins containing Ig-like domains [Cell motility and secretion]; Region: COG5492 441768001658 Bacterial Ig-like domain (group 2); Region: Big_2; pfam02368 441768001659 Bacterial Ig-like domain (group 2); Region: Big_2; pfam02368 441768001660 Bacterial surface proteins containing Ig-like domains [Cell motility and secretion]; Region: COG5492 441768001661 Bacterial Ig-like domain (group 2); Region: Big_2; pfam02368 441768001662 Bacterial Ig-like domain (group 2); Region: Big_2; cl02708 441768001663 Bacterial surface proteins containing Ig-like domains [Cell motility and secretion]; Region: COG5492 441768001664 Bacterial Ig-like domain (group 2); Region: Big_2; cl02708 441768001665 N-acetylmuramoyl-L-alanine amidase; Region: Amidase_2; pfam01510 441768001666 substrate binding site [chemical binding]; other site 441768001667 HRDC domain; Region: HRDC; pfam00570 441768001668 Protein of unknown function (DUF4011); Region: DUF4011; pfam13195 441768001669 Part of AAA domain; Region: AAA_19; pfam13245 441768001670 Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair]; Region: COG1112 441768001671 AAA domain; Region: AAA_12; pfam13087 441768001672 Protein of unknown function (DUF1294); Region: DUF1294; pfam06961 441768001673 Uncharacterized protein conserved in bacteria (DUF2188); Region: DUF2188; pfam09954 441768001674 Uncharacterized ACR, COG2135; Region: DUF159; pfam02586 441768001675 probable oxidoreductase, LLM family; Region: LLM_2I7G; TIGR03858 441768001676 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases [Energy production and conversion]; Region: COG2141 441768001677 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 441768001678 glycogen/starch/alpha-glucan phosphorylases; Region: P_ylase; TIGR02093 441768001679 glycogen branching enzyme; Provisional; Region: PRK12313 441768001680 N-terminal Early set domain associated with the catalytic domain of prokaryotic glycogen branching enzyme; Region: E_set_GBE_prok_N; cd02855 441768001681 Alpha amylase catalytic domain found in the Glycogen branching enzyme (also called 1,4-alpha-glucan branching enzyme); Region: AmyAc_Glg_BE; cd11322 441768001682 active site 441768001683 catalytic site [active] 441768001684 Alpha amylase, C-terminal all-beta domain; Region: Alpha-amylase_C; pfam02806 441768001685 Transcriptional regulators [Transcription]; Region: PurR; COG1609 441768001686 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 441768001687 DNA binding site [nucleotide binding] 441768001688 domain linker motif; other site 441768001689 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 441768001690 pullulanase, type I; Region: pulA_typeI; TIGR02104 441768001691 Early set domain associated with the catalytic domain of pullulanase (also called dextrinase and alpha-dextrin endo-1,6-alpha glucosidase); Region: E_set_Pullulanase; cd02860 441768001692 Alpha amylase catalytic domain found in Pullulanase (also called dextrinase; alpha-dextrin endo-1,6-alpha glucosidase), limit dextrinase, and related proteins; Region: AmyAc_Pullulanase_LD-like; cd11341 441768001693 Ca binding site [ion binding]; other site 441768001694 active site 441768001695 catalytic site [active] 441768001696 D-allose kinase; Provisional; Region: PRK09698 441768001697 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 441768001698 nucleotide binding site [chemical binding]; other site 441768001699 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 441768001700 This family is most closely related to the GT1 family of glycosyltransferases and named after YqgM in Bacillus licheniformis about which little is known. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to...; Region: GT1_YqgM_like; cd03801 441768001701 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 441768001702 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 441768001703 active site 441768001704 catalytic tetrad [active] 441768001705 trigger factor; Provisional; Region: tig; PRK01490 441768001706 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 441768001707 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 441768001708 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 441768001709 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 441768001710 Walker A motif; other site 441768001711 ATP binding site [chemical binding]; other site 441768001712 Walker B motif; other site 441768001713 arginine finger; other site 441768001714 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 441768001715 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 441768001716 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 441768001717 G1 box; other site 441768001718 GTP/Mg2+ binding site [chemical binding]; other site 441768001719 Switch I region; other site 441768001720 G2 box; other site 441768001721 G3 box; other site 441768001722 Switch II region; other site 441768001723 G4 box; other site 441768001724 G5 box; other site 441768001725 EDD domain protein, DegV family; Region: DegV; TIGR00762 441768001726 Uncharacterized protein, DegV family COG1307; Region: DegV; pfam02645 441768001727 biliverdin IX beta reductase (BVR-B, aka flavin reductase)-like proteins; atypical (a) SDRs; Region: BVR-B_like_SDR_a; cd05244 441768001728 NADH(P)-binding; Region: NAD_binding_10; pfam13460 441768001729 NAD binding site [chemical binding]; other site 441768001730 substrate binding site [chemical binding]; other site 441768001731 putative active site [active] 441768001732 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 441768001733 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 441768001734 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 441768001735 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 441768001736 active site 441768001737 HIGH motif; other site 441768001738 nucleotide binding site [chemical binding]; other site 441768001739 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 441768001740 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 441768001741 active site 441768001742 KMSKS motif; other site 441768001743 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 441768001744 tRNA binding surface [nucleotide binding]; other site 441768001745 anticodon binding site; other site 441768001746 Valyl tRNA synthetase tRNA binding arm; Region: Val_tRNA-synt_C; pfam10458 441768001747 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 441768001748 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 441768001749 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 441768001750 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 441768001751 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 441768001752 Major Facilitator Superfamily; Region: MFS_1; pfam07690 441768001753 Transcriptional regulator PadR-like family; Region: PadR; cl17335 441768001754 Predicted transcriptional regulators [Transcription]; Region: COG1695 441768001755 Glycerol-3-phosphate acyltransferase; Region: G3P_acyltransf; cl00410 441768001756 heat-inducible transcription repressor; Provisional; Region: hrcA; PRK00082 441768001757 Winged helix-turn-helix transcription repressor, HrcA DNA-binding; Region: HrcA_DNA-bdg; pfam03444 441768001758 GrpE; Region: GrpE; pfam01025 441768001759 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 441768001760 dimer interface [polypeptide binding]; other site 441768001761 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 441768001762 Nucleotide-binding domain of human HSPA9 and similar proteins; Region: HSPA9-Ssq1-like_NBD; cd10234 441768001763 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 441768001764 nucleotide binding site [chemical binding]; other site 441768001765 NEF interaction site [polypeptide binding]; other site 441768001766 SBD interface [polypeptide binding]; other site 441768001767 chaperone protein DnaJ; Region: DnaJ_bact; TIGR02349 441768001768 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 441768001769 HSP70 interaction site [polypeptide binding]; other site 441768001770 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 441768001771 Zn binding sites [ion binding]; other site 441768001772 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 441768001773 dimer interface [polypeptide binding]; other site 441768001774 Lipoate-protein ligase A [Coenzyme metabolism]; Region: LplA; COG0095 441768001775 lipoyltransferase and lipoate-protein ligase; Region: lipoyltrans; TIGR00545 441768001776 Bacterial lipoate protein ligase C-terminus; Region: Lip_prot_lig_C; pfam10437 441768001777 Uncharacterized ACR, COG1399; Region: DUF177; pfam02620 441768001778 50S ribosomal protein L32; Reviewed; Region: rpmF; PRK12286 441768001779 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 441768001780 MraW methylase family; Region: Methyltransf_5; cl17771 441768001781 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 441768001782 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 441768001783 putative acyl-acceptor binding pocket; other site 441768001784 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cl17326 441768001785 metal binding site 2 [ion binding]; metal-binding site 441768001786 putative DNA binding helix; other site 441768001787 metal binding site 1 [ion binding]; metal-binding site 441768001788 dimer interface [polypeptide binding]; other site 441768001789 structural Zn2+ binding site [ion binding]; other site 441768001790 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 441768001791 nicotinate (nicotinamide) nucleotide adenylyltransferase; Region: TIGR00482 441768001792 active site 441768001793 (T/H)XGH motif; other site 441768001794 NAD synthetase; Reviewed; Region: nadE; PRK02628 441768001795 Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases); Region: GAT_Gln-NAD-synth; cd07570 441768001796 multimer interface [polypeptide binding]; other site 441768001797 active site 441768001798 catalytic triad [active] 441768001799 protein interface 1 [polypeptide binding]; other site 441768001800 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 441768001801 homodimer interface [polypeptide binding]; other site 441768001802 NAD binding pocket [chemical binding]; other site 441768001803 ATP binding pocket [chemical binding]; other site 441768001804 Mg binding site [ion binding]; other site 441768001805 active-site loop [active] 441768001806 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 441768001807 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 441768001808 Ligand Binding Site [chemical binding]; other site 441768001809 helicase, putative, RecD/TraA family; Region: recD_rel; TIGR01448 441768001810 AAA domain; Region: AAA_30; pfam13604 441768001811 Family description; Region: UvrD_C_2; pfam13538 441768001812 Predicted peptidase [General function prediction only]; Region: COG4099 441768001813 Prephenate dehydratase [Amino acid transport and metabolism]; Region: PheA; COG0077 441768001814 Prephenate dehydratase; Region: PDT; pfam00800 441768001815 ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Region: ACT; cl09141 441768001816 N-terminal domain of Sphingobium chlorophenolicum 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and similar proteins; Region: PcpA_N_like; cd08346 441768001817 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 441768001818 Zn binding site [ion binding]; other site 441768001819 C-terminal domain of Sphingobium chlorophenolicum 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and similar proteins; Region: PcpA_C_like; cd08347 441768001820 Zn binding site [ion binding]; other site 441768001821 Bacterial protein of unknown function (DUF896); Region: DUF896; pfam05979 441768001822 N-terminal domain of Sphingobium chlorophenolicum 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and similar proteins; Region: PcpA_N_like; cd08346 441768001823 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 441768001824 Zn binding site [ion binding]; other site 441768001825 C-terminal domain of Sphingobium chlorophenolicum 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and similar proteins; Region: PcpA_C_like; cd08347 441768001826 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 441768001827 Zn binding site [ion binding]; other site 441768001828 helix_turn_helix multiple antibiotic resistance protein; Region: HTH_MARR; smart00347 441768001829 MarR family; Region: MarR_2; pfam12802 441768001830 MarR family; Region: MarR_2; cl17246 441768001831 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 441768001832 Diadenosine hexaphosphate (Ap6A) hydrolase is a member of the Nudix hydrolase superfamily. Ap6A hydrolase specifically hydrolyzes diadenosine polyphosphates, but not ATP or diadenosine triphosphate, and it generates ATP as the product. Ap6A, the most...; Region: Ap6A_hydrolase; cd03673 441768001833 active site 441768001834 Ap6A binding site [chemical binding]; other site 441768001835 nudix motif; other site 441768001836 metal binding site [ion binding]; metal-binding site 441768001837 23S rRNA (uracil-5-)-methyltransferase RumB; Region: meth_trns_rumB; TIGR02085 441768001838 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 441768001839 S-adenosylmethionine binding site [chemical binding]; other site 441768001840 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 441768001841 AAA domain; Region: AAA_13; pfam13166 441768001842 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 441768001843 ABC transporter signature motif; other site 441768001844 Walker B; other site 441768001845 D-loop; other site 441768001846 H-loop/switch region; other site 441768001847 Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]; Region: CyaA; COG2114 441768001848 cyclase homology domain; Region: CHD; cd07302 441768001849 nucleotidyl binding site; other site 441768001850 metal binding site [ion binding]; metal-binding site 441768001851 dimer interface [polypeptide binding]; other site 441768001852 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 441768001853 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; cd00338 441768001854 catalytic residues [active] 441768001855 catalytic nucleophile [active] 441768001856 Recombinase; Region: Recombinase; pfam07508 441768001857 Recombinase zinc beta ribbon domain; Region: Zn_ribbon_recom; pfam13408 441768001858 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 441768001859 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 441768001860 non-specific DNA binding site [nucleotide binding]; other site 441768001861 salt bridge; other site 441768001862 sequence-specific DNA binding site [nucleotide binding]; other site 441768001863 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 441768001864 non-specific DNA binding site [nucleotide binding]; other site 441768001865 salt bridge; other site 441768001866 sequence-specific DNA binding site [nucleotide binding]; other site 441768001867 Site-specific recombinase XerC [DNA replication, recombination, and repair]; Region: XerC; COG4973 441768001868 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 441768001869 active site 441768001870 DNA binding site [nucleotide binding] 441768001871 Int/Topo IB signature motif; other site 441768001872 BRO family, N-terminal domain; Region: Bro-N; cl10591 441768001873 Phage antirepressor protein KilAC domain; Region: ANT; pfam03374 441768001874 Helix-turn-helix domain; Region: HTH_17; pfam12728 441768001875 Domain of unknown function (DUF4373); Region: DUF4373; pfam14297 441768001876 HsdM N-terminal domain; Region: HsdM_N; pfam12161 441768001877 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 441768001878 Methyltransferase domain; Region: Methyltransf_26; pfam13659 441768001879 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 441768001880 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 441768001881 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 441768001882 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 441768001883 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 441768001884 ATP binding site [chemical binding]; other site 441768001885 putative Mg++ binding site [ion binding]; other site 441768001886 Domain of unknown function (DUF3387); Region: DUF3387; pfam11867 441768001887 Predicted nuclease of the RecB family [DNA replication, recombination, and repair]; Region: COG1637 441768001888 ParB-like nuclease domain; Region: ParBc; pfam02195 441768001889 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 441768001890 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 441768001891 DNA methylase; Region: N6_N4_Mtase; pfam01555 441768001892 S-adenosylmethionine synthetase; Validated; Region: PRK05250 441768001893 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 441768001894 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 441768001895 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 441768001896 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 441768001897 active site 441768001898 Domain of unknown function (DUF4297); Region: DUF4297; pfam14130 441768001899 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 441768001900 SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+; Region: SIR2; cl00195 441768001901 Protein of unknown function (DUF2971); Region: DUF2971; pfam11185 441768001902 Phage terminase-like protein, large subunit [General function prediction only]; Region: COG4626 441768001903 Phage-related protein [Function unknown]; Region: COG4695; cl01923 441768001904 Phage portal protein; Region: Phage_portal; pfam04860 441768001905 Caudovirus prohead protease; Region: Peptidase_U35; pfam04586 441768001906 phage major capsid protein, HK97 family; Region: major_cap_HK97; TIGR01554 441768001907 Phage capsid family; Region: Phage_capsid; pfam05065 441768001908 Bacteriophage protein of unknown function (DUF646); Region: DUF646; pfam04883 441768001909 phage major tail protein, phi13 family; Region: maj_tail_phi13; TIGR01603 441768001910 Phage-related minor tail protein [Function unknown]; Region: COG5280 441768001911 DNA polymerase III PolC; Validated; Region: polC; PRK00448 441768001912 Holin family; Region: Phage_holin_4; pfam05105 441768001913 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 441768001914 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 441768001915 Domain of unknown function (DUF3578); Region: DUF3578; pfam12102 441768001916 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 441768001917 McrBC 5-methylcytosine restriction system component; Region: McrBC; pfam10117 441768001918 ribonuclease III, bacterial; Region: RNaseIII; TIGR02191 441768001919 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 441768001920 dimerization interface [polypeptide binding]; other site 441768001921 active site 441768001922 metal binding site [ion binding]; metal-binding site 441768001923 haloacid dehalogenase-like hydrolase; Region: Hydrolase_3; pfam08282 441768001924 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 441768001925 active site 441768001926 motif I; other site 441768001927 motif II; other site 441768001928 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 441768001929 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 441768001930 putative acyl-acceptor binding pocket; other site 441768001931 Na+/glutamate symporter [Amino acid transport and metabolism]; Region: GltS; COG0786 441768001932 Transcriptional regulators [Transcription]; Region: MarR; COG1846 441768001933 MarR family; Region: MarR_2; pfam12802 441768001934 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 441768001935 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 441768001936 Walker A/P-loop; other site 441768001937 ATP binding site [chemical binding]; other site 441768001938 Q-loop/lid; other site 441768001939 ABC transporter signature motif; other site 441768001940 Walker B; other site 441768001941 D-loop; other site 441768001942 H-loop/switch region; other site 441768001943 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 441768001944 FtsX-like permease family; Region: FtsX; pfam02687 441768001945 alpha/beta hydrolase fold; Region: Abhydrolase_3; pfam07859 441768001946 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 441768001947 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 441768001948 active site 441768001949 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 441768001950 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 441768001951 RNA binding surface [nucleotide binding]; other site 441768001952 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 441768001953 active site 441768001954 GPR1/FUN34/yaaH family; Region: Grp1_Fun34_YaaH; cl00685 441768001955 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 441768001956 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 441768001957 substrate binding pocket [chemical binding]; other site 441768001958 membrane-bound complex binding site; other site 441768001959 hinge residues; other site 441768001960 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 441768001961 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 441768001962 dimer interface [polypeptide binding]; other site 441768001963 conserved gate region; other site 441768001964 putative PBP binding loops; other site 441768001965 ABC-ATPase subunit interface; other site 441768001966 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 441768001967 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 441768001968 Walker A/P-loop; other site 441768001969 ATP binding site [chemical binding]; other site 441768001970 Q-loop/lid; other site 441768001971 ABC transporter signature motif; other site 441768001972 Walker B; other site 441768001973 D-loop; other site 441768001974 H-loop/switch region; other site 441768001975 Formate/nitrite transporter; Region: Form_Nir_trans; cl00927 441768001976 short chain dehydrogenase; Validated; Region: PRK06182 441768001977 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 441768001978 NADP binding site [chemical binding]; other site 441768001979 active site 441768001980 steroid binding site; other site 441768001981 methionine sulfoxide reductase B; Provisional; Region: PRK00222 441768001982 SelR domain; Region: SelR; pfam01641 441768001983 4-alpha-glucanotransferase; Provisional; Region: PRK14508 441768001984 alpha,alpha-phosphotrehalase; Region: trehalose_treC; TIGR02403 441768001985 Alpha amylase catalytic domain found in Sucrose isomerases, oligo-1,6-glucosidase (also called isomaltase; sucrase-isomaltase; alpha-limit dextrinase), dextran glucosidase (also called glucan 1,6-alpha-glucosidase), and related proteins; Region: AmyAc_SI_OligoGlu_DGase; cd11333 441768001986 Ca binding site [ion binding]; other site 441768001987 active site 441768001988 catalytic site [active] 441768001989 N-terminal Early set domain associated with the catalytic domain of cyclomaltodextrinase and pullulan-degrading enzymes; Region: E_set_CDase_PDE_N; cd02857 441768001990 homodimer interface [polypeptide binding]; other site 441768001991 Alpha amylase catalytic domain found in cyclomaltodextrinases and related proteins; Region: AmyAc_CMD; cd11338 441768001992 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 441768001993 active site 441768001994 homodimer interface [polypeptide binding]; other site 441768001995 catalytic site [active] 441768001996 Alpha amylase catalytic domain found in archaeal and bacterial Alpha-amylases (also called 1,4-alpha-D-glucan-4-glucanohydrolase); Region: AmyAc_arch_bac_AmyA; cd11313 441768001997 Glycosidases [Carbohydrate transport and metabolism]; Region: AmyA; COG0366 441768001998 active site 441768001999 catalytic site [active] 441768002000 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 441768002001 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 441768002002 dimer interface [polypeptide binding]; other site 441768002003 conserved gate region; other site 441768002004 putative PBP binding loops; other site 441768002005 ABC-ATPase subunit interface; other site 441768002006 ABC-type polysaccharide transport system, permease component [Carbohydrate transport and metabolism]; Region: LplB; COG4209 441768002007 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 441768002008 dimer interface [polypeptide binding]; other site 441768002009 conserved gate region; other site 441768002010 putative PBP binding loops; other site 441768002011 ABC-ATPase subunit interface; other site 441768002012 Maltose-binding periplasmic proteins/domains [Carbohydrate transport and metabolism]; Region: MalE; COG2182 441768002013 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 441768002014 Family 41 Carbohydrate-Binding Module from pullulanase-like enzymes; Region: CBM41_pullulanase; cl04227 441768002015 carbohydrate binding site [chemical binding]; other site 441768002016 Predicted integral membrane protein [Function unknown]; Region: COG5521 441768002017 RDD family; Region: RDD; pfam06271 441768002018 Family 41 Carbohydrate-Binding Module from pullulanase-like enzymes; Region: CBM41_pullulanase; cd10315 441768002019 carbohydrate binding site [chemical binding]; other site 441768002020 pullulanase, type I; Region: pulA_typeI; TIGR02104 441768002021 Early set domain associated with the catalytic domain of pullulanase (also called dextrinase and alpha-dextrin endo-1,6-alpha glucosidase); Region: E_set_Pullulanase; cd02860 441768002022 Alpha amylase catalytic domain found in Pullulanase (also called dextrinase; alpha-dextrin endo-1,6-alpha glucosidase), limit dextrinase, and related proteins; Region: AmyAc_Pullulanase_LD-like; cd11341 441768002023 Ca binding site [ion binding]; other site 441768002024 active site 441768002025 catalytic site [active] 441768002026 alpha,alpha-phosphotrehalase; Region: trehalose_treC; TIGR02403 441768002027 Alpha amylase catalytic domain found in bacterial Alpha-amylases (also called 1,4-alpha-D-glucan-4-glucanohydrolase); Region: AmyAc_bac2_AmyA; cd11316 441768002028 Ca binding site [ion binding]; other site 441768002029 active site 441768002030 catalytic site [active] 441768002031 glycerol-3-phosphate transporter ATP-binding subunit; Provisional; Region: ugpC; PRK11650 441768002032 The N-terminal ATPase domain of the maltose transporter, MalK; Region: ABC_MalK_N; cd03301 441768002033 Walker A/P-loop; other site 441768002034 ATP binding site [chemical binding]; other site 441768002035 Q-loop/lid; other site 441768002036 ABC transporter signature motif; other site 441768002037 Walker B; other site 441768002038 D-loop; other site 441768002039 H-loop/switch region; other site 441768002040 Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue per...; Region: GSH_Peroxidase; cd00340 441768002041 catalytic residues [active] 441768002042 dimer interface [polypeptide binding]; other site 441768002043 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 441768002044 Domain of unknown function DUF21; Region: DUF21; pfam01595 441768002045 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 441768002046 Transporter associated domain; Region: CorC_HlyC; pfam03471 441768002047 Protein of unknown function (DUF1307); Region: DUF1307; cl01981 441768002048 5TMR of 5TMR-LYT; Region: 5TM-5TMR_LYT; pfam07694 441768002049 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 441768002050 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 441768002051 metal binding site [ion binding]; metal-binding site 441768002052 active site 441768002053 I-site; other site 441768002054 c-di-GMP phosphodiesterase class II (HD-GYP domain) [Signal transduction mechanisms]; Region: COG2206 441768002055 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 441768002056 Zn2+ binding site [ion binding]; other site 441768002057 Mg2+ binding site [ion binding]; other site 441768002058 LemA family; Region: LemA; cl00742 441768002059 GTP-binding protein LepA; Provisional; Region: PRK05433 441768002060 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 441768002061 G1 box; other site 441768002062 putative GEF interaction site [polypeptide binding]; other site 441768002063 GTP/Mg2+ binding site [chemical binding]; other site 441768002064 Switch I region; other site 441768002065 G2 box; other site 441768002066 G3 box; other site 441768002067 Switch II region; other site 441768002068 G4 box; other site 441768002069 G5 box; other site 441768002070 lepA_II: This subfamily represents the domain II of LepA, a GTP-binding protein localized in the cytoplasmic membrane. The N-terminal domain of LepA shares regions of homology to translation factors. In terms of interaction with the ribosome, EF-G, EF-Tu...; Region: lepA_II; cd03699 441768002071 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 441768002072 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 441768002073 coproporphyrinogen III oxidase; Provisional; Region: PRK08599 441768002074 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 441768002075 FeS/SAM binding site; other site 441768002076 HemN C-terminal domain; Region: HemN_C; pfam06969 441768002077 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 441768002078 XerD and XerC integrases, DNA breaking-rejoining enzymes, N- and C-terminal domains. XerD-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination...; Region: INT_XerDC; cd00798 441768002079 active site 441768002080 Int/Topo IB signature motif; other site 441768002081 phosphopentomutase; Provisional; Region: PRK05362 441768002082 Metalloenzyme superfamily; Region: Metalloenzyme; pfam01676 441768002083 Uncharacterized protein family (UPF0154); Region: UPF0154; cl01536 441768002084 Conserved hypothetical protein 95; Region: Cons_hypoth95; pfam03602 441768002085 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 441768002086 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 441768002087 pyrimidine-nucleoside phosphorylase; Region: Y_phosphoryl; TIGR02644 441768002088 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 441768002089 Pyrimidine nucleoside phosphorylase C-terminal domain; Region: PYNP_C; smart00941 441768002090 Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction; Region: HP_PGM_like; cd07067 441768002091 catalytic core [active] 441768002092 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 441768002093 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 441768002094 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 441768002095 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 441768002096 putative acyl-acceptor binding pocket; other site 441768002097 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 441768002098 Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5; Region: DHFR; cd00209 441768002099 folate binding site [chemical binding]; other site 441768002100 NADP+ binding site [chemical binding]; other site 441768002101 thymidylate synthase; Reviewed; Region: thyA; PRK01827 441768002102 Thymidylate synthase and pyrimidine hydroxymethylase: Thymidylate synthase (TS) and deoxycytidylate hydroxymethylase (dCMP-HMase) are homologs that catalyze analogous alkylation of C5 of pyrimidine nucleotides. Both enzymes are involved in the...; Region: TS_Pyrimidine_HMase; cd00351 441768002103 dimerization interface [polypeptide binding]; other site 441768002104 active site 441768002105 dipeptidase PepV; Reviewed; Region: PRK07318 441768002106 M20 Peptidase Xaa-His dipeptidase (PepV) degrades hydrophobic dipeptides; Region: M20_PepV; cd03888 441768002107 active site 441768002108 metal binding site [ion binding]; metal-binding site 441768002109 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 441768002110 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 441768002111 dimer interface [polypeptide binding]; other site 441768002112 ssDNA binding site [nucleotide binding]; other site 441768002113 tetramer (dimer of dimers) interface [polypeptide binding]; other site 441768002114 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 441768002115 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 441768002116 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 441768002117 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 441768002118 Uridine phosphorylase [Nucleotide transport and metabolism]; Region: Udp; COG2820 441768002119 2-deoxyribose-5-phosphate aldolase (DERA) of the DeoC family; Region: DeoC; cd00959 441768002120 intersubunit interface [polypeptide binding]; other site 441768002121 active site 441768002122 catalytic residue [active] 441768002123 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 441768002124 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 441768002125 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 441768002126 active site 441768002127 HIGH motif; other site 441768002128 nucleotide binding site [chemical binding]; other site 441768002129 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 441768002130 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 441768002131 active site 441768002132 KMSKS motif; other site 441768002133 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 441768002134 tRNA binding surface [nucleotide binding]; other site 441768002135 anticodon binding site; other site 441768002136 Protein of unknown function (DUF552); Region: DUF552; pfam04472 441768002137 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 441768002138 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 441768002139 catalytic residue [active] 441768002140 GTP-binding protein YchF; Reviewed; Region: PRK09601 441768002141 YchF GTPase; Region: YchF; cd01900 441768002142 G1 box; other site 441768002143 GTP/Mg2+ binding site [chemical binding]; other site 441768002144 Switch I region; other site 441768002145 G2 box; other site 441768002146 Switch II region; other site 441768002147 G3 box; other site 441768002148 G4 box; other site 441768002149 G5 box; other site 441768002150 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 441768002151 cell division protein FtsZ; Validated; Region: PRK09330 441768002152 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 441768002153 nucleotide binding site [chemical binding]; other site 441768002154 SulA interaction site; other site 441768002155 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 441768002156 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 441768002157 QueT transporter; Region: QueT; pfam06177 441768002158 A/G-specific DNA glycosylase [DNA replication, recombination, and repair]; Region: MutY; COG1194 441768002159 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 441768002160 minor groove reading motif; other site 441768002161 helix-hairpin-helix signature motif; other site 441768002162 active site 441768002163 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 441768002164 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 441768002165 DNA binding and oxoG recognition site [nucleotide binding] 441768002166 Nitroreductase-like family 1. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and...; Region: Nitroreductase_1; cd02137 441768002167 dimer interface [polypeptide binding]; other site 441768002168 FMN binding site [chemical binding]; other site 441768002169 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 441768002170 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 441768002171 Walker A/P-loop; other site 441768002172 ATP binding site [chemical binding]; other site 441768002173 Q-loop/lid; other site 441768002174 ABC transporter signature motif; other site 441768002175 Walker B; other site 441768002176 D-loop; other site 441768002177 H-loop/switch region; other site 441768002178 FtsX-like permease family; Region: FtsX; pfam02687 441768002179 ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]; Region: SalY; COG0577 441768002180 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 441768002181 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 441768002182 Walker A/P-loop; other site 441768002183 ATP binding site [chemical binding]; other site 441768002184 Q-loop/lid; other site 441768002185 ABC transporter signature motif; other site 441768002186 Walker B; other site 441768002187 D-loop; other site 441768002188 H-loop/switch region; other site 441768002189 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 441768002190 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 441768002191 motif II; other site 441768002192 Transcriptional regulators [Transcription]; Region: PurR; COG1609 441768002193 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 441768002194 DNA binding site [nucleotide binding] 441768002195 domain linker motif; other site 441768002196 Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily; Region: PBP1_LacI_sugar_binding_like; cd06267 441768002197 dimerization interface [polypeptide binding]; other site 441768002198 ligand binding site [chemical binding]; other site 441768002199 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; pfam00933 441768002200 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 441768002201 Glycosyl hydrolase family 3 C-terminal domain; Region: Glyco_hydro_3_C; pfam01915 441768002202 Laminarinase, member of the glycosyl hydrolase family 16; Region: GH16_laminarinase_like; cd08023 441768002203 active site 441768002204 catalytic residues [active] 441768002205 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 441768002206 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 441768002207 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 441768002208 ABC-ATPase subunit interface; other site 441768002209 putative PBP binding loops; other site 441768002210 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 441768002211 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 441768002212 ABC-ATPase subunit interface; other site 441768002213 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 441768002214 binding surface 441768002215 TPR repeat; Region: TPR_11; pfam13414 441768002216 TPR motif; other site 441768002217 Yip1 domain; Region: Yip1; cl17815 441768002218 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 441768002219 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 441768002220 dimer interface [polypeptide binding]; other site 441768002221 conserved gate region; other site 441768002222 ABC-ATPase subunit interface; other site 441768002223 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 441768002224 dimer interface [polypeptide binding]; other site 441768002225 conserved gate region; other site 441768002226 ABC-ATPase subunit interface; other site 441768002227 Carbohydrate Binding Module 6 (CBM6); appended to several carbohydrate binding enzymes, including several glycoside hydrolase (GH) family 26 mannanase domains; Region: CBM6_mannanase-like; cd04086 441768002228 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 441768002229 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 441768002230 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 441768002231 O-Glycosyl hydrolase [Cell envelope biogenesis, outer membrane]; Region: COG5520 441768002232 O-Glycosyl hydrolase family 30; Region: Glyco_hydro_30; pfam02055 441768002233 Laminarinase, member of the glycosyl hydrolase family 16; Region: GH16_laminarinase_like; cd08023 441768002234 active site 441768002235 catalytic residues [active] 441768002236 Cellobiose phosphorylase [Carbohydrate transport and metabolism]; Region: COG3459 441768002237 N-terminal domain of glycoside hydrolase family 94 and related domains; Region: GH94N_like; cl17067 441768002238 Glycosyl hydrolase family 3 C-terminal domain; Region: Glyco_hydro_3_C; pfam01915 441768002239 Fibronectin type III-like domain; Region: Fn3-like; pfam14310 441768002240 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; pfam00933 441768002241 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 441768002242 Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FrnE; COG2761 441768002243 DsbA family, FrnE subfamily; FrnE is a DsbA-like protein containing a CXXC motif. It is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the aromatic antibiotics frenolicin and nanaomycins; Region: DsbA_FrnE; cd03024 441768002244 catalytic residues [active] 441768002245 oligoendopeptidase F; Region: pepF; TIGR00181 441768002246 Peptidase family M3B Oligopeptidase F (PepF); Region: M3B_PepF_4; cd09609 441768002247 active site 441768002248 Zn binding site [ion binding]; other site 441768002249 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 441768002250 non-specific DNA binding site [nucleotide binding]; other site 441768002251 salt bridge; other site 441768002252 sequence-specific DNA binding site [nucleotide binding]; other site 441768002253 EDD domain protein, DegV family; Region: DegV; TIGR00762 441768002254 Uncharacterized protein, DegV family COG1307; Region: DegV; pfam02645 441768002255 Uncharacterized conserved protein [Function unknown]; Region: LemA; COG1704 441768002256 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 441768002257 cation diffusion facilitator family transporter; Region: CDF; TIGR01297 441768002258 putative enoyl-[acyl-carrier-protein] reductase II; Region: enACPred_II; TIGR03151 441768002259 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 441768002260 FMN binding site [chemical binding]; other site 441768002261 substrate binding site [chemical binding]; other site 441768002262 putative catalytic residue [active] 441768002263 (R)-hydratase [(R)-specific enoyl-CoA hydratase] catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. (R)-hydratase contains a hot-dog fold similar to those of thioesterase...; Region: R_hydratase; cd03449 441768002264 dimer interaction site [polypeptide binding]; other site 441768002265 substrate-binding tunnel; other site 441768002266 active site 441768002267 catalytic site [active] 441768002268 substrate binding site [chemical binding]; other site 441768002269 Predicted divalent heavy-metal cations transporter [Inorganic ion transport and metabolism]; Region: COG0428 441768002270 Iron dependent repressor, N-terminal DNA binding domain; Region: Fe_dep_repress; pfam01325 441768002271 Helix-turn-helix diphteria tox regulatory element; Region: HTH_DTXR; smart00529 441768002272 Iron dependent repressor, metal binding and dimerisation domain; Region: Fe_dep_repr_C; pfam02742 441768002273 FeoA domain; Region: FeoA; pfam04023 441768002274 Putative hydrophobic ligand-binding SRPBCC domain of Micromonospora echinospora CalC, human Aha1, and related proteins; Region: SRPBCC_CalC_Aha1-like; cd07814 441768002275 putative hydrophobic ligand binding site [chemical binding]; other site 441768002276 SdpI/YhfL protein family; Region: SdpI; pfam13630 441768002277 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 441768002278 active site 441768002279 Sugar-specific transcriptional regulator TrmB; Region: TrmB; pfam01978 441768002280 Middle phospholipase D-like domain of the transcriptional regulator TrmB and similar proteins; Region: PLDc_like_TrmB_middle; cd09124 441768002281 C-terminal domain interface [polypeptide binding]; other site 441768002282 sugar binding site [chemical binding]; other site 441768002283 Uncharacterized protein YrkD from Bacillus subtilis and related domains; this domain superfamily was previously known as part of DUF156; Region: BsYrkD-like_DUF156; cd10155 441768002284 putative homodimer interface [polypeptide binding]; other site 441768002285 putative homotetramer interface [polypeptide binding]; other site 441768002286 putative metal binding site [ion binding]; other site 441768002287 putative homodimer-homodimer interface [polypeptide binding]; other site 441768002288 putative allosteric switch controlling residues; other site 441768002289 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 441768002290 active site residue [active] 441768002291 CoA-disulfide reductase; Region: CoA_CoA_reduc; TIGR03385 441768002292 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 441768002293 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 441768002294 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 441768002295 Member of the Rhodanese Homology Domain superfamily. Included in this CD are the Lactococcus lactis NADH oxidase, Bacillus cereus NADH dehydrogenase, and Bacteroides thetaiotaomicron pyridine nucleotide-disulphide oxidoreductase, and similar...; Region: RHOD_Pyr_redox; cd01524 441768002296 active site residue [active] 441768002297 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 441768002298 active site residue [active] 441768002299 Thioredoxin domain; Region: Thioredoxin_3; pfam13192 441768002300 Predicted permeases [General function prediction only]; Region: COG0701 441768002301 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 441768002302 dimerization interface [polypeptide binding]; other site 441768002303 putative DNA binding site [nucleotide binding]; other site 441768002304 putative Zn2+ binding site [ion binding]; other site 441768002305 ABC-2 family transporter protein; Region: ABC2_membrane_2; pfam12679 441768002306 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 441768002307 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 441768002308 Walker A/P-loop; other site 441768002309 ATP binding site [chemical binding]; other site 441768002310 Q-loop/lid; other site 441768002311 ABC transporter signature motif; other site 441768002312 Walker B; other site 441768002313 D-loop; other site 441768002314 H-loop/switch region; other site 441768002315 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 441768002316 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 441768002317 diaminopimelate dehydrogenase; Region: DAP-DH; TIGR01921 441768002318 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; pfam03807 441768002319 CotH protein; Region: CotH; pfam08757 441768002320 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 441768002321 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 441768002322 active site 441768002323 catalytic tetrad [active] 441768002324 Helix-turn-helix domain of transposase family ISL3; Region: HTH_Tnp_ISL3; pfam13542 441768002325 Cellulase M and related proteins [Carbohydrate transport and metabolism]; Region: FrvX; COG1363 441768002326 M42 Peptidase, Endoglucanase-like subfamily; Region: M42_glucanase_like; cd05657 441768002327 putative oligomer interface [polypeptide binding]; other site 441768002328 putative active site [active] 441768002329 metal binding site [ion binding]; metal-binding site 441768002330 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins; Region: MATE_like_8; cd13134 441768002331 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 441768002332 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 441768002333 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 441768002334 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 441768002335 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 441768002336 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 441768002337 Walker A/P-loop; other site 441768002338 ATP binding site [chemical binding]; other site 441768002339 Q-loop/lid; other site 441768002340 ABC transporter signature motif; other site 441768002341 Walker B; other site 441768002342 D-loop; other site 441768002343 H-loop/switch region; other site 441768002344 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 441768002345 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 441768002346 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 441768002347 pyridoxal 5'-phosphate binding site [chemical binding]; other site 441768002348 catalytic residue [active] 441768002349 Transposase domain (DUF772); Region: DUF772; pfam05598 441768002350 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 441768002351 metal-binding site [ion binding] 441768002352 mercuric reductase; Region: MerA; TIGR02053 441768002353 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 441768002354 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 441768002355 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 441768002356 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 441768002357 metal-binding site [ion binding] 441768002358 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG2963 441768002359 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: Tra5; COG2801 441768002360 Integrase core domain; Region: rve; pfam00665 441768002361 Integrase core domain; Region: rve_2; pfam13333 441768002362 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 441768002363 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 441768002364 Coenzyme A binding pocket [chemical binding]; other site 441768002365 dihydrodipicolinate reductase; Provisional; Region: PRK00048 441768002366 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 441768002367 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 441768002368 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 441768002369 dihydrodipicolinate synthase; Region: dapA; TIGR00674 441768002370 dimer interface [polypeptide binding]; other site 441768002371 active site 441768002372 catalytic residue [active] 441768002373 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 441768002374 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 441768002375 aspartate kinase; Reviewed; Region: PRK06635 441768002376 AAK_AKii-LysC-BS: Amino Acid Kinase Superfamily (AAK), AKii; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis 168, and the lysine plus threonine-sensitive...; Region: AAK_AKii-LysC-BS; cd04261 441768002377 putative nucleotide binding site [chemical binding]; other site 441768002378 putative catalytic residues [active] 441768002379 putative Mg ion binding site [ion binding]; other site 441768002380 putative aspartate binding site [chemical binding]; other site 441768002381 ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII and related proteins; Region: ACT_AK-LysC-DapG-like_1; cd04891 441768002382 ACT domains of the lysine-sensitive, aspartokinase (AK) isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related domains; Region: ACT_AKii-LysC-BS-like_2; cd04936 441768002383 diaminopimelate decarboxylase; Region: lysA; TIGR01048 441768002384 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 441768002385 active site 441768002386 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 441768002387 substrate binding site [chemical binding]; other site 441768002388 catalytic residues [active] 441768002389 dimer interface [polypeptide binding]; other site 441768002390 Escherichia coli UshA-like family, N-terminal metallophosphatase domain; Region: MPP_UshA_N_like; cd00845 441768002391 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 441768002392 active site 441768002393 metal binding site [ion binding]; metal-binding site 441768002394 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 441768002395 PAS domain S-box; Region: sensory_box; TIGR00229 441768002396 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 441768002397 putative active site [active] 441768002398 heme pocket [chemical binding]; other site 441768002399 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 441768002400 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 441768002401 metal binding site [ion binding]; metal-binding site 441768002402 active site 441768002403 I-site; other site 441768002404 guanosine 5'-monophosphate oxidoreductase; Provisional; Region: PRK05458 441768002405 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 441768002406 active site 441768002407 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 441768002408 active site 2 [active] 441768002409 active site 1 [active] 441768002410 isopentenyl pyrophosphate isomerase; Provisional; Region: PRK05437 441768002411 Isopentenyl-diphosphate:dimethylallyl diphosphate isomerase type 2 (IDI-2) FMN-binding domain. Two types of IDIs have been characterized at present. The long known IDI-1 is only dependent on divalent metals for activity, whereas IDI-2 requires a metal; Region: IDI-2_FMN; cd02811 441768002412 homotetramer interface [polypeptide binding]; other site 441768002413 FMN binding site [chemical binding]; other site 441768002414 homodimer contacts [polypeptide binding]; other site 441768002415 putative active site [active] 441768002416 putative substrate binding site [chemical binding]; other site 441768002417 phosphomevalonate kinase, ERG8-type, Gram-positive branch; Region: Pmev_kin_Gr_pos; TIGR01220 441768002418 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 441768002419 GHMP kinases C terminal; Region: GHMP_kinases_C; pfam08544 441768002420 Mevalonate pyrophosphate decarboxylase [Lipid metabolism]; Region: MVD1; COG3407 441768002421 diphosphomevalonate decarboxylase; Region: PLN02407 441768002422 mevalonate kinase; Region: mevalon_kin; TIGR00549 441768002423 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 441768002424 active site 441768002425 Indigoidine synthase A like protein; Region: Indigoidine_A; pfam04227 441768002426 yybP-ykoY element 441768002427 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; pfam00690 441768002428 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: MgtA; COG0474 441768002429 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 441768002430 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 441768002431 Soluble P-type ATPase [General function prediction only]; Region: COG4087 441768002432 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 441768002433 Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily; Region: PI-PLCc_GDPD_SF; cl14615 441768002434 active site 441768002435 catalytic site [active] 441768002436 Glycerophosphodiester phosphodiesterase domain as found in prokaryota and eukaryota, and similar proteins; Region: GDPD; cd08556 441768002437 active site 441768002438 Domain of unknown function (DUF4191); Region: DUF4191; pfam13829 441768002439 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 441768002440 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 441768002441 RNase E interface [polypeptide binding]; other site 441768002442 trimer interface [polypeptide binding]; other site 441768002443 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 441768002444 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 441768002445 RNase E interface [polypeptide binding]; other site 441768002446 trimer interface [polypeptide binding]; other site 441768002447 active site 441768002448 Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to...; Region: PNPase_KH; cd02393 441768002449 putative nucleic acid binding region [nucleotide binding]; other site 441768002450 G-X-X-G motif; other site 441768002451 S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA; Region: S1_PNPase; cd04472 441768002452 RNA binding site [nucleotide binding]; other site 441768002453 domain interface; other site 441768002454 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 441768002455 16S/18S rRNA binding site [nucleotide binding]; other site 441768002456 S13e-L30e interaction site [polypeptide binding]; other site 441768002457 25S rRNA binding site [nucleotide binding]; other site 441768002458 Protein of unknown function (DUF970); Region: DUF970; cl17525 441768002459 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed; Region: PRK05627 441768002460 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 441768002461 active site 441768002462 Riboflavin kinase; Region: Flavokinase; smart00904 441768002463 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK01550 441768002464 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 441768002465 RNA binding site [nucleotide binding]; other site 441768002466 active site 441768002467 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 441768002468 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 441768002469 catalytic residues [active] 441768002470 recombination and DNA strand exchange inhibitor protein; Reviewed; Region: PRK00409 441768002471 MutS domain III; Region: MutS_III; pfam05192 441768002472 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 441768002473 Walker A/P-loop; other site 441768002474 ATP binding site [chemical binding]; other site 441768002475 Q-loop/lid; other site 441768002476 ABC transporter signature motif; other site 441768002477 Walker B; other site 441768002478 D-loop; other site 441768002479 H-loop/switch region; other site 441768002480 Smr domain; Region: Smr; pfam01713 441768002481 ribonuclease HIII; Provisional; Region: PRK00996 441768002482 Domain of unknown function (DUF3378); Region: DUF3378; pfam11858 441768002483 bacterial Ribonuclease HIII-like; Region: RNase_HII_bacteria_HIII_like; cd06590 441768002484 RNA/DNA hybrid binding site [nucleotide binding]; other site 441768002485 active site 441768002486 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 441768002487 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 441768002488 RNA binding surface [nucleotide binding]; other site 441768002489 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 441768002490 active site 441768002491 Signal peptidase (SPase) II; Region: Peptidase_A8; pfam01252 441768002492 Predicted secreted protein containing a PDZ domain [Signal transduction mechanisms]; Region: SdrC; COG3480 441768002493 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 441768002494 Deoxycytidylate deaminase domain. Deoxycytidylate deaminase catalyzes the deamination of dCMP to dUMP, providing the nucleotide substrate for thymidylate synthase. The enzyme binds Zn++, which is required for catalytic activity. The activity of the...; Region: deoxycytidylate_deaminase; cd01286 441768002495 catalytic motif [active] 441768002496 Zn binding site [ion binding]; other site 441768002497 methionine sulfoxide reductase A; Provisional; Region: PRK14054 441768002498 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 441768002499 EcAspRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli aspartyl-tRNA synthetase (AspRS), the human mitochondrial (mt) AspRS-2, the discriminating (D) Thermus thermophilus AspRS-1, and the nondiscriminating (ND)...; Region: EcAspRS_like_N; cd04317 441768002500 dimer interface [polypeptide binding]; other site 441768002501 anticodon binding site; other site 441768002502 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 441768002503 motif 1; other site 441768002504 dimer interface [polypeptide binding]; other site 441768002505 active site 441768002506 motif 2; other site 441768002507 GAD domain; Region: GAD; pfam02938 441768002508 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 441768002509 active site 441768002510 motif 3; other site 441768002511 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 441768002512 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 441768002513 dimer interface [polypeptide binding]; other site 441768002514 motif 1; other site 441768002515 active site 441768002516 motif 2; other site 441768002517 motif 3; other site 441768002518 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 441768002519 anticodon binding site; other site 441768002520 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 441768002521 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 441768002522 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 441768002523 Domain of unknown function DUF20; Region: UPF0118; pfam01594 441768002524 D-tyrosyl-tRNA(Tyr) deacylase; Provisional; Region: PRK05273 441768002525 putative active site [active] 441768002526 dimerization interface [polypeptide binding]; other site 441768002527 putative tRNAtyr binding site [nucleotide binding]; other site 441768002528 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 441768002529 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 441768002530 Zn2+ binding site [ion binding]; other site 441768002531 Mg2+ binding site [ion binding]; other site 441768002532 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 441768002533 synthetase active site [active] 441768002534 NTP binding site [chemical binding]; other site 441768002535 metal binding site [ion binding]; metal-binding site 441768002536 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 441768002537 ACT domain found C-terminal of the RelA/SpoT domains; Region: ACT_RelA-SpoT; cd04876 441768002538 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 441768002539 active site 441768002540 recombination factor protein RarA; Reviewed; Region: PRK13342 441768002541 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 441768002542 Walker A motif; other site 441768002543 ATP binding site [chemical binding]; other site 441768002544 Walker B motif; other site 441768002545 arginine finger; other site 441768002546 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 441768002547 intracellular protease, PfpI family; Region: PfpI; TIGR01382 441768002548 A type 1 glutamine amidotransferase (GATase1)-like domain found in PfpI from Pyrococcus furiosus; Region: GATase1_PfpI_like; cd03134 441768002549 proposed catalytic triad [active] 441768002550 conserved cys residue [active] 441768002551 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 441768002552 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 441768002553 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 441768002554 Holliday junction-specific endonuclease; Reviewed; Region: recU; PRK02234 441768002555 Thiamine transporter protein (Thia_YuaJ); Region: Thia_YuaJ; cl17491 441768002556 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: COG1585 441768002557 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 441768002558 Band_7_stomatin_like: A subgroup of the band 7 domain of flotillin (reggie) like proteins similar to stomatin and podicin (two lipid raft-associated integral membrane proteins). Individual proteins of this band 7 domain family may cluster to form...; Region: Band_7_stomatin_like; cd03403 441768002559 Cellulase M and related proteins [Carbohydrate transport and metabolism]; Region: FrvX; COG1363 441768002560 M42 Peptidase, Endoglucanases; Region: M42_Frv; cd05656 441768002561 oligomer interface [polypeptide binding]; other site 441768002562 active site 441768002563 metal binding site [ion binding]; metal-binding site 441768002564 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 441768002565 active site 441768002566 tetramer interface; other site 441768002567 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 441768002568 23S rRNA binding site [nucleotide binding]; other site 441768002569 L21 binding site [polypeptide binding]; other site 441768002570 L13 binding site [polypeptide binding]; other site 441768002571 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 441768002572 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 441768002573 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 441768002574 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 441768002575 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 441768002576 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 441768002577 ATP-binding cassette domain of glucan transporter and related proteins, subfamily C; Region: ABCC_Glucan_exporter_like; cd03254 441768002578 Walker A/P-loop; other site 441768002579 ATP binding site [chemical binding]; other site 441768002580 Q-loop/lid; other site 441768002581 ABC transporter signature motif; other site 441768002582 Walker B; other site 441768002583 D-loop; other site 441768002584 H-loop/switch region; other site 441768002585 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 441768002586 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 441768002587 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 441768002588 Walker A/P-loop; other site 441768002589 ATP binding site [chemical binding]; other site 441768002590 Q-loop/lid; other site 441768002591 ABC transporter signature motif; other site 441768002592 Walker B; other site 441768002593 D-loop; other site 441768002594 H-loop/switch region; other site 441768002595 proline aminopeptidase P II; Provisional; Region: PRK10879 441768002596 Aminopeptidase P, N-terminal domain; Region: AMP_N; smart01011 441768002597 Prolidase. E.C. 3.4.13.9. Also known as Xaa-Pro dipeptidase, X-Pro dipeptidase, proline dipeptidase., imidodipeptidase, peptidase D, gamma-peptidase. Catalyses hydrolysis of Xaa-Pro dipeptides; also acts on aminoacyl-hydroxyproline analogs. No action on...; Region: Prolidase; cd01087 441768002598 active site 441768002599 This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1). The mammalian PGM2 is thought to be a phosphopentomutase that catalyzes the conversion of the nucleoside breakdown products, ribose-1-phosphate and...; Region: PGM2; cd05799 441768002600 active site 441768002601 substrate binding site [chemical binding]; other site 441768002602 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 441768002603 metal binding site [ion binding]; metal-binding site 441768002604 Type III pantothenate kinase; Region: Pan_kinase; cl17198 441768002605 Zn-dependent hydrolases, including glyoxylases [General function prediction only]; Region: GloB; COG0491 441768002606 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 441768002607 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 441768002608 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 441768002609 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 441768002610 ABC transporter; Region: ABC_tran_2; pfam12848 441768002611 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 441768002612 MutT homolog-1 (MTH1) is a member of the Nudix hydrolase superfamily. MTH1, the mammalian counterpart of MutT, hydrolyzes oxidized purine nucleoside triphosphates, such as 8-oxo-dGTP and 2-hydroxy-ATP, to monophosphates, thereby preventing the...; Region: MTH1; cd03427 441768002613 putative active site [active] 441768002614 nucleotide binding site [chemical binding]; other site 441768002615 nudix motif; other site 441768002616 putative metal binding site [ion binding]; other site 441768002617 Bacterial Ig-like domain (group 3); Region: Big_3_3; pfam13750 441768002618 Type 1 glutamine amidotransferase (GATase1)-like domain found in peptidase E_like proteins; Region: GAT1_Peptidase_E_like; cd03129 441768002619 catalytic triad [active] 441768002620 active site nucleophile [active] 441768002621 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cl00290 441768002622 Phosphotransferase enzyme family; Region: APH; pfam01636 441768002623 Choline Kinase (ChoK). The ChoK subfamily is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and...; Region: ChoK; cd05151 441768002624 active site 441768002625 ATP binding site [chemical binding]; other site 441768002626 substrate binding site [chemical binding]; other site 441768002627 dimer interface [polypeptide binding]; other site 441768002628 Predicted phosphoesterases, related to the Icc protein [General function prediction only]; Region: COG2129 441768002629 Escherichia coli YfcE and related proteins, metallophosphatase domain; Region: MPP_YfcE; cd00841 441768002630 active site 441768002631 metal binding site [ion binding]; metal-binding site 441768002632 homotetramer interface [polypeptide binding]; other site 441768002633 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 441768002634 active site 441768002635 dimerization interface [polypeptide binding]; other site 441768002636 CAAX protease self-immunity; Region: Abi; pfam02517 441768002637 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 441768002638 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 441768002639 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 441768002640 ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other...; Region: ANK; cd00204 441768002641 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 441768002642 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 441768002643 IHF dimer interface [polypeptide binding]; other site 441768002644 IHF - DNA interface [nucleotide binding]; other site 441768002645 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 441768002646 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 441768002647 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 441768002648 GTP-binding protein Der; Reviewed; Region: PRK00093 441768002649 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 441768002650 G1 box; other site 441768002651 GTP/Mg2+ binding site [chemical binding]; other site 441768002652 Switch I region; other site 441768002653 G2 box; other site 441768002654 Switch II region; other site 441768002655 G3 box; other site 441768002656 G4 box; other site 441768002657 G5 box; other site 441768002658 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 441768002659 G1 box; other site 441768002660 GTP/Mg2+ binding site [chemical binding]; other site 441768002661 Switch I region; other site 441768002662 G2 box; other site 441768002663 G3 box; other site 441768002664 Switch II region; other site 441768002665 G4 box; other site 441768002666 G5 box; other site 441768002667 Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Region: RpsA; COG0539 441768002668 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 441768002669 RNA binding site [nucleotide binding]; other site 441768002670 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 441768002671 RNA binding site [nucleotide binding]; other site 441768002672 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 441768002673 RNA binding site [nucleotide binding]; other site 441768002674 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cd00164 441768002675 RNA binding site [nucleotide binding]; other site 441768002676 Ribosomal protein S1-like RNA-binding domain; Region: S1; smart00316 441768002677 RNA binding site [nucleotide binding]; other site 441768002678 cytidylate kinase; Provisional; Region: cmk; PRK00023 441768002679 Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor; Region: CMPK; cd02020 441768002680 CMP-binding site; other site 441768002681 The sites determining sugar specificity; other site 441768002682 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 441768002683 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 441768002684 RNA binding surface [nucleotide binding]; other site 441768002685 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 441768002686 active site 441768002687 elongation factor P; Validated; Region: PRK00529 441768002688 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 441768002689 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 441768002690 RNA binding site [nucleotide binding]; other site 441768002691 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 441768002692 RNA binding site [nucleotide binding]; other site 441768002693 Dehydroquinase class II; Region: DHquinase_II; pfam01220 441768002694 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 441768002695 trimer interface [polypeptide binding]; other site 441768002696 active site 441768002697 dimer interface [polypeptide binding]; other site 441768002698 Shikimate kinase [Amino acid transport and metabolism]; Region: AroK; COG0703 441768002699 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 441768002700 ADP binding site [chemical binding]; other site 441768002701 magnesium binding site [ion binding]; other site 441768002702 putative shikimate binding site; other site 441768002703 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 441768002704 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 441768002705 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 441768002706 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 441768002707 ATP binding site [chemical binding]; other site 441768002708 Mg2+ binding site [ion binding]; other site 441768002709 G-X-G motif; other site 441768002710 MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is...; Region: MutL_Trans; cd00782 441768002711 ATP binding site [chemical binding]; other site 441768002712 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 441768002713 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 441768002714 MutS domain I; Region: MutS_I; pfam01624 441768002715 MutS domain II; Region: MutS_II; pfam05188 441768002716 MutS domain III; Region: MutS_III; pfam05192 441768002717 MutS domain V; Region: MutS_V; pfam00488 441768002718 Walker A/P-loop; other site 441768002719 ATP binding site [chemical binding]; other site 441768002720 Q-loop/lid; other site 441768002721 ABC transporter signature motif; other site 441768002722 Walker B; other site 441768002723 D-loop; other site 441768002724 H-loop/switch region; other site 441768002725 Deinococcus radiodurans DR1281 and related proteins, metallophosphatase domain; Region: MPP_DR1281; cd07382 441768002726 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 441768002727 putative active site [active] 441768002728 metal binding site [ion binding]; metal-binding site 441768002729 homodimer binding site [polypeptide binding]; other site 441768002730 phosphodiesterase; Provisional; Region: PRK12704 441768002731 KH domain; Region: KH_1; pfam00013 441768002732 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 441768002733 Zn2+ binding site [ion binding]; other site 441768002734 Mg2+ binding site [ion binding]; other site 441768002735 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 441768002736 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 441768002737 ATP-binding cassette domain of glucan transporter and related proteins, subfamily C; Region: ABCC_Glucan_exporter_like; cd03254 441768002738 Walker A/P-loop; other site 441768002739 ATP binding site [chemical binding]; other site 441768002740 Q-loop/lid; other site 441768002741 ABC transporter signature motif; other site 441768002742 Walker B; other site 441768002743 D-loop; other site 441768002744 H-loop/switch region; other site 441768002745 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 441768002746 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 441768002747 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 441768002748 Walker A/P-loop; other site 441768002749 ATP binding site [chemical binding]; other site 441768002750 Q-loop/lid; other site 441768002751 ABC transporter signature motif; other site 441768002752 Walker B; other site 441768002753 D-loop; other site 441768002754 H-loop/switch region; other site 441768002755 recombinase A; Provisional; Region: recA; PRK09354 441768002756 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 441768002757 hexamer interface [polypeptide binding]; other site 441768002758 Walker A motif; other site 441768002759 ATP binding site [chemical binding]; other site 441768002760 Walker B motif; other site 441768002761 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 441768002762 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 441768002763 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 441768002764 active site 441768002765 catalytic site [active] 441768002766 substrate binding site [chemical binding]; other site 441768002767 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK05574 441768002768 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 441768002769 Competence protein; Region: Competence; cl00471 441768002770 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 441768002771 SLBB domain; Region: SLBB; pfam10531 441768002772 Helix-hairpin-helix motif; Region: HHH_3; pfam12836 441768002773 Oligomerisation domain; Region: Oligomerisation; cl00519 441768002774 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 441768002775 Zn2+ binding site [ion binding]; other site 441768002776 Mg2+ binding site [ion binding]; other site 441768002777 LIM is a small protein-protein interaction domain, containing two zinc fingers; Region: LIM; cl02475 441768002778 ribosome biogenesis GTPase YqeH; Region: GTPase_YqeH; TIGR03597 441768002779 Zn binding site [ion binding]; other site 441768002780 Circularly permuted YlqF-related GTPases; Region: YlqF_related_GTPase; cl17249 441768002781 GTP/Mg2+ binding site [chemical binding]; other site 441768002782 G4 box; other site 441768002783 G5 box; other site 441768002784 G1 box; other site 441768002785 Switch I region; other site 441768002786 G2 box; other site 441768002787 G3 box; other site 441768002788 Switch II region; other site 441768002789 Predicted hydrolase of the HAD superfamily [General function prediction only]; Region: COG2179 441768002790 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 441768002791 active site 441768002792 motif I; other site 441768002793 motif II; other site 441768002794 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 441768002795 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 441768002796 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 441768002797 Protein of unknown function DUF45; Region: DUF45; cl00636 441768002798 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 441768002799 S-adenosylmethionine binding site [chemical binding]; other site 441768002800 Protein of unknown function (DUF1292); Region: DUF1292; cl01608 441768002801 Holliday junction resolvase-like protein; Reviewed; Region: PRK00109 441768002802 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 441768002803 Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain. AlaRS is a homodimer. It is responsible for the attachment of alanine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: AlaRS_core; cd00673 441768002804 motif 1; other site 441768002805 active site 441768002806 motif 2; other site 441768002807 motif 3; other site 441768002808 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 441768002809 DHHA1 domain; Region: DHHA1; pfam02272 441768002810 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 441768002811 Domain of unknown function DUF21; Region: DUF21; pfam01595 441768002812 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 441768002813 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; cd02205 441768002814 Transporter associated domain; Region: CorC_HlyC; smart01091 441768002815 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl17215 441768002816 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 441768002817 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 441768002818 metal binding site [ion binding]; metal-binding site 441768002819 active site 441768002820 I-site; other site 441768002821 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 441768002822 NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]; Region: NhaP; COG0025 441768002823 Chromate transporter; Region: Chromate_transp; pfam02417 441768002824 chromate transporter, chromate ion transporter (CHR) family; Region: 2A51; TIGR00937 441768002825 Chromate transporter; Region: Chromate_transp; pfam02417 441768002826 Domain of unknown function (DUF1836); Region: DUF1836; pfam08876 441768002827 EDD domain protein, DegV family; Region: DegV; TIGR00762 441768002828 Uncharacterized protein, DegV family COG1307; Region: DegV; pfam02645 441768002829 MraW methylase family; Region: Methyltransf_5; cl17771 441768002830 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 441768002831 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 441768002832 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 441768002833 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity. They also contain a...; Region: Nudix_Hydrolase_1; cd03674 441768002834 nudix motif; other site 441768002835 Haloacid dehalogenase-like hydrolase; Region: HAD_2; pfam13419 441768002836 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 441768002837 motif II; other site 441768002838 proteins similar to Escherichia coli yceG; Region: yceG_like; cl17666 441768002839 The band 7 domain of flotillin (reggie) like proteins. This group contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. Many of these band 7 domain-containing proteins are lipid raft-associated. Individual proteins of this...; Region: Band_7; cl02525 441768002840 Domain of unknown function (DUF4339); Region: DUF4339; pfam14237 441768002841 zinc-ribbon domain; Region: zinc_ribbon_2; pfam13240 441768002842 Double zinc ribbon; Region: DZR; pfam12773 441768002843 Cro/C1-type HTH DNA-binding domain; Region: HTH_26; pfam13443 441768002844 Protein of unknown function (DUF1643); Region: DUF1643; cl01787 441768002845 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 441768002846 active site 441768002847 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 441768002848 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 441768002849 ATP-binding cassette domain of glucan transporter and related proteins, subfamily C; Region: ABCC_Glucan_exporter_like; cd03254 441768002850 Walker A/P-loop; other site 441768002851 ATP binding site [chemical binding]; other site 441768002852 Q-loop/lid; other site 441768002853 ABC transporter signature motif; other site 441768002854 Walker B; other site 441768002855 D-loop; other site 441768002856 H-loop/switch region; other site 441768002857 Predicted SAM-dependent methyltransferase [General function prediction only]; Region: COG2384 441768002858 Family of unknown function (DUF633); Region: DUF633; pfam04816 441768002859 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 441768002860 RNA polymerase sigma factor RpoD, C-terminal domain; Region: RpoD_Cterm; TIGR02393 441768002861 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 441768002862 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 441768002863 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 441768002864 DNA binding residues [nucleotide binding] 441768002865 CHC2 zinc finger; Region: zf-CHC2; pfam01807 441768002866 DNA primase; Validated; Region: dnaG; PRK05667 441768002867 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 441768002868 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 441768002869 active site 441768002870 metal binding site [ion binding]; metal-binding site 441768002871 interdomain interaction site; other site 441768002872 glycyl-tRNA synthetase; Provisional; Region: PRK04173 441768002873 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 441768002874 motif 1; other site 441768002875 Glycyl-tRNA synthetase (GlyRS)-like class II core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes. It is responsible for the attachment of glycine to the 3...; Region: GlyRS-like_core; cd00774 441768002876 active site 441768002877 motif 2; other site 441768002878 motif 3; other site 441768002879 GlyRS Glycyl-anticodon binding domain. GlyRS 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: GlyRS_anticodon; cd00858 441768002880 anticodon binding site; other site 441768002881 DNA repair protein RecO; Region: reco; TIGR00613 441768002882 Recombination protein O N terminal; Region: RecO_N; pfam11967 441768002883 Recombination protein O C terminal; Region: RecO_C; pfam02565 441768002884 GTPase Era; Reviewed; Region: era; PRK00089 441768002885 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 441768002886 G1 box; other site 441768002887 GTP/Mg2+ binding site [chemical binding]; other site 441768002888 Switch I region; other site 441768002889 G2 box; other site 441768002890 Switch II region; other site 441768002891 G3 box; other site 441768002892 G4 box; other site 441768002893 G5 box; other site 441768002894 KH domain; Region: KH_2; pfam07650 441768002895 Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on...; Region: cytidine_deaminase; cd01283 441768002896 active site 441768002897 catalytic motif [active] 441768002898 Zn binding site [ion binding]; other site 441768002899 metal-binding heat shock protein; Provisional; Region: PRK00016 441768002900 Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]; Region: PhoH; COG1702 441768002901 PhoH-like protein; Region: PhoH; pfam02562 441768002902 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 441768002903 16S ribosomal RNA methyltransferase RsmE; Provisional; Region: PRK11713 441768002904 RNA methyltransferase, RsmE family; Region: TIGR00046 441768002905 Preprotein translocase subunit SecG [Intracellular trafficking and secretion]; Region: SecG; COG1314 441768002906 Listeria-Bacteroides repeat domain (List_Bact_rpt); Region: Flg_new; pfam09479 441768002907 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between...; Region: TroA-like; cl00262 441768002908 Periplasmic binding protein; Region: Peripla_BP_2; pfam01497 441768002909 intersubunit interface [polypeptide binding]; other site 441768002910 ABC-type enterochelin transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CeuD; COG4604 441768002911 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 441768002912 Walker A/P-loop; other site 441768002913 ATP binding site [chemical binding]; other site 441768002914 Q-loop/lid; other site 441768002915 ABC transporter signature motif; other site 441768002916 Walker B; other site 441768002917 D-loop; other site 441768002918 H-loop/switch region; other site 441768002919 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 441768002920 ABC-ATPase subunit interface; other site 441768002921 dimer interface [polypeptide binding]; other site 441768002922 putative PBP binding regions; other site 441768002923 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 441768002924 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 441768002925 ABC-ATPase subunit interface; other site 441768002926 dimer interface [polypeptide binding]; other site 441768002927 putative PBP binding regions; other site 441768002928 Antibiotic biosynthesis monooxygenase; Region: ABM; cl10022 441768002929 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 441768002930 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]; Region: COG2317 441768002931 Peptidase family M32 includes thermostable carboxypeptidases TaqCP and PfuCP; Region: M32_Taq; cd06460 441768002932 active site 441768002933 Zn binding site [ion binding]; other site 441768002934 glucose-6-phosphate 1-dehydrogenase; Validated; Region: PRK05722 441768002935 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 441768002936 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 441768002937 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 441768002938 Predicted 6-phosphogluconate dehydrogenase [Carbohydrate transport and metabolism]; Region: Gnd; COG1023 441768002939 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 441768002940 MgtE intracellular N domain; Region: MgtE_N; pfam03448 441768002941 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain in the magnesium transporter, MgtE. MgtE and its homologs are found in eubacteria, archaebacteria, and eukaryota. Members of this family transport Mg2+ or other...; Region: CBS_pair_Mg_transporter; cd04606 441768002942 Divalent cation transporter; Region: MgtE; pfam01769 441768002943 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 441768002944 MgtE intracellular N domain; Region: MgtE_N; pfam03448 441768002945 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain in the magnesium transporter, MgtE. MgtE and its homologs are found in eubacteria, archaebacteria, and eukaryota. Members of this family transport Mg2+ or other...; Region: CBS_pair_Mg_transporter; cd04606 441768002946 Divalent cation transporter; Region: MgtE; pfam01769 441768002947 NQR2, RnfD, RnfE family; Region: NQR2_RnfD_RnfE; cl00779 441768002948 NADH:ubiquinone oxidoreductase, Na(+)-translocating, C subunit; Region: nqrC; TIGR01938 441768002949 FMN-binding domain; Region: FMN_bind; cl01081 441768002950 FMN-binding domain; Region: FMN_bind; pfam04205 441768002951 This conserved region includes the FMN-binding site of the NqrC protein as well as the NosR and NirI regulatory proteins; Region: FMN_bind; smart00900 441768002952 This conserved region includes the FMN-binding site of the NqrC protein as well as the NosR and NirI regulatory proteins; Region: FMN_bind; smart00900 441768002953 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 441768002954 Rnf-Nqr subunit, membrane protein; Region: Rnf-Nqr; cl00597 441768002955 Na(+)-translocating NADH-quinone reductase subunit F; Provisional; Region: PRK05464 441768002956 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 441768002957 catalytic loop [active] 441768002958 iron binding site [ion binding]; other site 441768002959 Phenol 2-monooxygenase (phenol hydroxylase) is a flavoprotein monooxygenase, able to use molecular oxygen as a substrate in the microbial degredation of phenol. This protein is encoded by a single gene and uses a tightly bound FAD cofactor in the NAD(P)H...; Region: phenol_2-monooxygenase_like; cd06211 441768002960 FAD binding pocket [chemical binding]; other site 441768002961 FAD binding motif [chemical binding]; other site 441768002962 phosphate binding motif [ion binding]; other site 441768002963 beta-alpha-beta structure motif; other site 441768002964 NAD binding pocket [chemical binding]; other site 441768002965 ATP synthase subunit D; Region: ATP-synt_D; cl00613 441768002966 V-type ATP synthase subunit B; Provisional; Region: PRK04196 441768002967 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 441768002968 V/A-type ATP synthase (non-catalytic) subunit B. These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi...; Region: V_A-ATPase_B; cd01135 441768002969 Walker A motif homologous position; other site 441768002970 Walker B motif; other site 441768002971 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 441768002972 V-type ATP synthase subunit A; Provisional; Region: PRK04192 441768002973 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 441768002974 V/A-type ATP synthase catalytic subunit A. These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi...; Region: V_A-ATPase_A; cd01134 441768002975 Walker A motif/ATP binding site; other site 441768002976 Walker B motif; other site 441768002977 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 441768002978 V-type ATP synthase subunit C; Provisional; Region: PRK01198; cl00660 441768002979 V-type ATP synthase subunit K; Validated; Region: PRK06558 441768002980 ATP synthase subunit C; Region: ATP-synt_C; cl00466 441768002981 ATP synthase subunit C; Region: ATP-synt_C; pfam00137 441768002982 V-type ATP synthase subunit I; Validated; Region: PRK05771 441768002983 F0F1-type ATP synthase, epsilon subunit (mitochondrial delta subunit) [Energy production and conversion]; Region: AtpC; COG0355 441768002984 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cl10033 441768002985 gamma subunit interface [polypeptide binding]; other site 441768002986 epsilon subunit interface [polypeptide binding]; other site 441768002987 LBP interface [polypeptide binding]; other site 441768002988 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 441768002989 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 441768002990 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 441768002991 alpha subunit interaction interface [polypeptide binding]; other site 441768002992 Walker A motif; other site 441768002993 ATP binding site [chemical binding]; other site 441768002994 Walker B motif; other site 441768002995 inhibitor binding site; inhibition site 441768002996 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 441768002997 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 441768002998 core domain interface [polypeptide binding]; other site 441768002999 delta subunit interface [polypeptide binding]; other site 441768003000 epsilon subunit interface [polypeptide binding]; other site 441768003001 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 441768003002 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 441768003003 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 441768003004 beta subunit interaction interface [polypeptide binding]; other site 441768003005 Walker A motif; other site 441768003006 ATP binding site [chemical binding]; other site 441768003007 Walker B motif; other site 441768003008 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 441768003009 F0F1-type ATP synthase, delta subunit (mitochondrial oligomycin sensitivity protein) [Energy production and conversion]; Region: AtpH; COG0712 441768003010 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 441768003011 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 441768003012 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl17192 441768003013 F0F1 ATP synthase subunit C; Provisional; Region: PRK13469 441768003014 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 441768003015 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; COG0312 441768003016 Predicted Zn-dependent proteases and their inactivated homologs [General function prediction only]; Region: TldD; COG0312 441768003017 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 441768003018 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 441768003019 ATP-binding cassette domain of glucan transporter and related proteins, subfamily C; Region: ABCC_Glucan_exporter_like; cd03254 441768003020 Walker A/P-loop; other site 441768003021 ATP binding site [chemical binding]; other site 441768003022 Q-loop/lid; other site 441768003023 ABC transporter signature motif; other site 441768003024 Walker B; other site 441768003025 D-loop; other site 441768003026 H-loop/switch region; other site 441768003027 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 441768003028 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 441768003029 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 441768003030 Walker A/P-loop; other site 441768003031 ATP binding site [chemical binding]; other site 441768003032 Q-loop/lid; other site 441768003033 ABC transporter signature motif; other site 441768003034 Walker B; other site 441768003035 D-loop; other site 441768003036 H-loop/switch region; other site 441768003037 Protein of unknown function (DUF2089); Region: DUF2089; pfam09862 441768003038 peptidase T; Region: peptidase-T; TIGR01882 441768003039 M20 Peptidase T specifically cleaves tripeptides; Region: M20_peptT; cd03892 441768003040 metal binding site [ion binding]; metal-binding site 441768003041 dimer interface [polypeptide binding]; other site 441768003042 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 441768003043 Aldo/keto reductase family; Region: Aldo_ket_red; pfam00248 441768003044 active site 441768003045 catalytic tetrad [active] 441768003046 AAA domain; Region: AAA_21; pfam13304 441768003047 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 441768003048 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 441768003049 Walker A/P-loop; other site 441768003050 ATP binding site [chemical binding]; other site 441768003051 Q-loop/lid; other site 441768003052 ABC transporter signature motif; other site 441768003053 Walker B; other site 441768003054 D-loop; other site 441768003055 H-loop/switch region; other site 441768003056 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cl00427 441768003057 NLPA lipoprotein; Region: Lipoprotein_9; cl17547 441768003058 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 441768003059 Mechanosensitive ion channel; Region: MS_channel; pfam00924 441768003060 Chitin/cellulose binding domains of chitinase and related enzymes; Region: ChtBD3; cl00046 441768003061 aromatic chitin/cellulose binding site residues [chemical binding]; other site 441768003062 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 441768003063 Catalytic site [active] 441768003064 GTPase subunit of restriction endonuclease [Defense mechanisms]; Region: McrB; COG1401 441768003065 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 441768003066 metal binding site [ion binding]; metal-binding site 441768003067 active site 441768003068 I-site; other site 441768003069 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 441768003070 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 441768003071 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 441768003072 Uncharacterized subfamily of N-terminal LabA-like domains; Region: LabA_like_N_1; cd11297 441768003073 putative metal binding site [ion binding]; other site 441768003074 C-terminal domain of LabA_like proteins; Region: LabA_like_C; cd10146 441768003075 EDD domain protein, DegV family; Region: DegV; TIGR00762 441768003076 Uncharacterized protein, DegV family COG1307; Region: DegV; pfam02645 441768003077 Capsular polysaccharide biosynthesis protein [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: CapC; COG4464 441768003078 exopolysaccharide/PEP-CTERM locus tyrosine autokinase; Region: pepcterm_TyrKin; TIGR03018 441768003079 Capsular polysaccharide biosynthesis protein [Cell envelope biogenesis, outer membrane]; Region: COG3944 441768003080 oligoendopeptidase, pepF/M3 family; Region: M3_fam_3; TIGR02290 441768003081 Peptidase family M3B Oligopeptidase F (PepF); Region: M3B_PepF_2; cd09607 441768003082 active site 441768003083 Zn binding site [ion binding]; other site 441768003084 excinuclease ABC subunit B; Provisional; Region: PRK05298 441768003085 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 441768003086 ATP binding site [chemical binding]; other site 441768003087 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 441768003088 nucleotide binding region [chemical binding]; other site 441768003089 ATP-binding site [chemical binding]; other site 441768003090 Ultra-violet resistance protein B; Region: UvrB; pfam12344 441768003091 UvrB/uvrC motif; Region: UVR; pfam02151 441768003092 flavoprotein, HI0933 family; Region: TIGR00275 441768003093 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 441768003094 K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]; Region: TrkA; COG0569 441768003095 TrkA-N domain; Region: TrkA_N; pfam02254 441768003096 TrkA-C domain; Region: TrkA_C; pfam02080 441768003097 potassium uptake protein, TrkH family; Region: 2a38; TIGR00933 441768003098 Trk-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: TrkG; COG0168 441768003099 Integral membrane protein (intg_mem_TP0381); Region: Intg_mem_TP0381; cl02331 441768003100 L-2-hydroxyisocapronate dehydrogenases and some bacterial L-lactate dehydrogenases; Region: HicDH_like; cd05291 441768003101 tetramer (dimer of dimers) interface [polypeptide binding]; other site 441768003102 L-lactate dehydrogenase; Region: L-LDH-NAD; TIGR01771 441768003103 NAD binding site [chemical binding]; other site 441768003104 dimer interface [polypeptide binding]; other site 441768003105 substrate binding site [chemical binding]; other site 441768003106 Helix-turn-helix domain; Region: HTH_19; pfam12844 441768003107 SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely...; Region: SGNH_hydrolase; cl01053 441768003108 active site 441768003109 catalytic triad [active] 441768003110 oxyanion hole [active] 441768003111 Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and...; Region: PEPCK_HprK; cl00270 441768003112 active site 441768003113 metal-binding site [ion binding] 441768003114 nucleotide-binding site [chemical binding]; other site 441768003115 coenzyme A disulfide reductase; Reviewed; Region: PRK09564 441768003116 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 441768003117 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 441768003118 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK14354 441768003119 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 441768003120 Substrate binding site; other site 441768003121 Mg++ binding site; other site 441768003122 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 441768003123 active site 441768003124 substrate binding site [chemical binding]; other site 441768003125 CoA binding site [chemical binding]; other site 441768003126 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 441768003127 phosphoglucosamine mutase; Provisional; Region: glmM; PRK14316 441768003128 active site 441768003129 substrate binding site [chemical binding]; other site 441768003130 metal binding site [ion binding]; metal-binding site 441768003131 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 441768003132 Bacterial members of the UDP-N-Acetylglucosamine (GlcNAc) 2-Epimerase family are known to catalyze the reversible interconversion of UDP-GlcNAc and UDP-N-acetylmannosamine (UDP-ManNAc). The enzyme serves to produce an activated form of ManNAc residues; Region: GT1_UDP-GlcNAc_2-Epimerase; cd03786 441768003133 active site 441768003134 homodimer interface [polypeptide binding]; other site 441768003135 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 441768003136 This family is most closely related to the GT1 family of glycosyltransferases. capH in Staphylococcus aureus has been shown to be required for the biosynthesis of the type 1 capsular polysaccharide (CP1); Region: GT1_CapH_like; cd03812 441768003137 putative ADP-binding pocket [chemical binding]; other site 441768003138 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 441768003139 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 441768003140 Bacterial members of the UDP-N-Acetylglucosamine (GlcNAc) 2-Epimerase family are known to catalyze the reversible interconversion of UDP-GlcNAc and UDP-N-acetylmannosamine (UDP-ManNAc). The enzyme serves to produce an activated form of ManNAc residues; Region: GT1_UDP-GlcNAc_2-Epimerase; cd03786 441768003141 active site 441768003142 homodimer interface [polypeptide binding]; other site 441768003143 capsular polysaccharide assembling protein (CAPF) like, extended (e) SDRs; Region: CAPF_like_SDR_e; cd05261 441768003144 NAD dependent epimerase/dehydratase family; Region: Epimerase; pfam01370 441768003145 putative NAD(P) binding site [chemical binding]; other site 441768003146 active site 441768003147 putative substrate binding site [chemical binding]; other site 441768003148 dTDP-4-dehydrorhamnose 3,5-epimerase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfbC; COG1898 441768003149 UDP-N-acetylglucosamine 4,6-dehydratase/5-epimerase; Region: FnlA; TIGR04130 441768003150 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 441768003151 NAD(P) binding site [chemical binding]; other site 441768003152 homodimer interface [polypeptide binding]; other site 441768003153 substrate binding site [chemical binding]; other site 441768003154 active site 441768003155 Polysaccharide biosynthesis protein C-terminal; Region: Polysacc_syn_2C; pfam08485 441768003156 This family is most closely related to the GT1 family of glycosyltransferases. wbuB in E. coli is involved in the biosynthesis of the O26 O-antigen. It has been proposed to function as an N-acetyl-L-fucosamine (L-FucNAc) transferase; Region: GT1_wbuB_like; cd03794 441768003157 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 441768003158 Predicted hydrolase (HAD superfamily) [General function prediction only]; Region: COG1011 441768003159 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 441768003160 motif II; other site 441768003161 carbamoyl phosphate synthase-like protein; Provisional; Region: PRK12767 441768003162 ATP-grasp domain; Region: ATP-grasp_4; pfam13535 441768003163 Bacterial sugar transferase; Region: Bac_transf; pfam02397 441768003164 aminotransferase, LLPSF_NHT_00031 family; Region: NHT_00031; TIGR04181 441768003165 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 441768003166 inhibitor-cofactor binding pocket; inhibition site 441768003167 pyridoxal 5'-phosphate binding site [chemical binding]; other site 441768003168 catalytic residue [active] 441768003169 Winged helix-turn-helix DNA-binding; Region: HTH_24; pfam13412 441768003170 UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]; Region: GalE; COG1087 441768003171 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 441768003172 NAD binding site [chemical binding]; other site 441768003173 homodimer interface [polypeptide binding]; other site 441768003174 active site 441768003175 substrate binding site [chemical binding]; other site 441768003176 KTSC domain; Region: KTSC; pfam13619 441768003177 Domain of unknown function DUF87; Region: DUF87; pfam01935 441768003178 AAA-like domain; Region: AAA_10; pfam12846 441768003179 SIR2-like domain; Region: SIR2_2; pfam13289 441768003180 Bacteriophage abortive infection AbiH; Region: AbiH; pfam14253 441768003181 Abi-like protein; Region: Abi_2; pfam07751 441768003182 Cellobiose phosphorylase [Carbohydrate transport and metabolism]; Region: COG3459 441768003183 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 441768003184 This PGM-like (phosphoglucomutase-like) protein of unknown function belongs to the alpha-D-phosphohexomutase superfamily and is found in both archaea and bacteria. The alpha-D-phosphohexomutases include several related enzymes that catalyze a reversible...; Region: PGM_like2; cd05800 441768003185 active site 441768003186 substrate binding site [chemical binding]; other site 441768003187 metal binding site [ion binding]; metal-binding site 441768003188 glycosyl hydrolase family 16; Region: Glyco_hydrolase_16; cd00413 441768003189 active site 441768003190 catalytic residues [active] 441768003191 glycosyl hydrolase family 16; Region: Glyco_hydrolase_16; cd00413 441768003192 active site 441768003193 catalytic residues [active] 441768003194 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 441768003195 putative DNA binding site [nucleotide binding]; other site 441768003196 putative Zn2+ binding site [ion binding]; other site 441768003197 Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; Region: NagC; COG1940 441768003198 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cd00012 441768003199 nucleotide binding site [chemical binding]; other site 441768003200 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 441768003201 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 441768003202 dimer interface [polypeptide binding]; other site 441768003203 conserved gate region; other site 441768003204 putative PBP binding loops; other site 441768003205 ABC-ATPase subunit interface; other site 441768003206 ABC-type polysaccharide transport system, permease component [Carbohydrate transport and metabolism]; Region: LplB; COG4209 441768003207 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 441768003208 dimer interface [polypeptide binding]; other site 441768003209 conserved gate region; other site 441768003210 putative PBP binding loops; other site 441768003211 ABC-ATPase subunit interface; other site 441768003212 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 441768003213 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 441768003214 Part of AAA domain; Region: AAA_19; pfam13245 441768003215 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 441768003216 non-specific DNA binding site [nucleotide binding]; other site 441768003217 salt bridge; other site 441768003218 sequence-specific DNA binding site [nucleotide binding]; other site 441768003219 Domain of unknown function (DUF955); Region: DUF955; cl01076 441768003220 Plasmid maintenance system killer protein; Region: Plasmid_killer; cl01422 441768003221 Band_7_flotillin: a subgroup of the band 7 domain of flotillin (reggie) like proteins. This subgroup contains proteins similar to stomatin, prohibitin, flotillin, HlfK/C and podicin. These two proteins are lipid raft-associated. Individual proteins of...; Region: Band_7_flotillin; cd03399 441768003222 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM)-like family; contains proteins similar to MCM, and the large subunit of Streptomyces coenzyme B12-dependent isobutyryl-CoA mutase (ICM). MCM catalyzes the isomerization of...; Region: MM_CoA_mutase; cl00817 441768003223 Predicted membrane protein [Function unknown]; Region: COG2261 441768003224 Short C-terminal domain; Region: SHOCT; pfam09851 441768003225 Listeria-Bacteroides repeat domain (List_Bact_rpt); Region: Flg_new; pfam09479 441768003226 Listeria-Bacteroides repeat domain (List_Bact_rpt); Region: Flg_new; cl09714 441768003227 Listeria-Bacteroides repeat domain (List_Bact_rpt); Region: Flg_new; pfam09479 441768003228 Dam-replacing family; Region: DRP; pfam06044 441768003229 T5orf172 domain; Region: T5orf172; pfam10544 441768003230 DpnII restriction endonuclease; Region: DpnII; pfam04556 441768003231 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 441768003232 DNA methylase; Region: N6_N4_Mtase; pfam01555 441768003233 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; cl17344 441768003234 multiple promoter invertase; Provisional; Region: mpi; PRK13413 441768003235 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 441768003236 catalytic residues [active] 441768003237 catalytic nucleophile [active] 441768003238 Presynaptic Site I dimer interface [polypeptide binding]; other site 441768003239 Synaptic Antiparallel dimer interface [polypeptide binding]; other site 441768003240 Synaptic Flat tetramer interface [polypeptide binding]; other site 441768003241 Synaptic Site I dimer interface [polypeptide binding]; other site 441768003242 DNA binding site [nucleotide binding] 441768003243 The MutT pyrophosphohydrolase is a prototypical Nudix hydrolase that catalyzes the hydrolysis of nucleoside and deoxynucleoside triphosphates (NTPs and dNTPs) by substitution at a beta-phosphorus to yield a nucleotide monophosphate (NMP) and inorganic...; Region: MutT_pyrophosphohydrolase; cd03425 441768003244 active site 441768003245 8-oxo-dGMP binding site [chemical binding]; other site 441768003246 nudix motif; other site 441768003247 metal binding site [ion binding]; metal-binding site 441768003248 N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain; Region: PLDc_N_DEXD_b2; cd09204 441768003249 PLD-like domain; Region: PLDc_2; pfam13091 441768003250 putative homodimer interface [polypeptide binding]; other site 441768003251 putative active site [active] 441768003252 catalytic site [active] 441768003253 DEAD-like helicases superfamily; Region: DEXDc; smart00487 441768003254 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 441768003255 ATP binding site [chemical binding]; other site 441768003256 putative Mg++ binding site [ion binding]; other site 441768003257 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 441768003258 nucleotide binding region [chemical binding]; other site 441768003259 ATP-binding site [chemical binding]; other site 441768003260 Domain of unknown function (DUF3427); Region: DUF3427; pfam11907 441768003261 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]; Region: COG1086 441768003262 Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes...; Region: LbetaH; cl00160 441768003263 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 441768003264 NAD(P) binding site [chemical binding]; other site 441768003265 homodimer interface [polypeptide binding]; other site 441768003266 substrate binding site [chemical binding]; other site 441768003267 active site 441768003268 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl17342 441768003269 pyruvate kinase; Provisional; Region: PRK05826 441768003270 domain interfaces; other site 441768003271 active site 441768003272 6-phosphofructokinase; Provisional; Region: PRK03202 441768003273 6-phosphofructokinase; Region: PFKA_ATP; TIGR02482 441768003274 active site 441768003275 ADP/pyrophosphate binding site [chemical binding]; other site 441768003276 dimerization interface [polypeptide binding]; other site 441768003277 allosteric effector site; other site 441768003278 fructose-1,6-bisphosphate binding site; other site 441768003279 6-phosphofructokinase; Provisional; Region: PRK14072 441768003280 6-phosphofructokinase; Region: PFKA_ATP; TIGR02482 441768003281 active site 441768003282 ADP/pyrophosphate binding site [chemical binding]; other site 441768003283 dimerization interface [polypeptide binding]; other site 441768003284 allosteric effector site; other site 441768003285 fructose-1,6-bisphosphate binding site; other site 441768003286 glutamate dehydrogenase; Provisional; Region: PRK09414 441768003287 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 441768003288 NAD(P) binding domain of amino acid dehydrogenase-like proteins; Region: NAD_bind_amino_acid_DH; cl17226 441768003289 NAD(P) binding pocket [chemical binding]; other site 441768003290 O-Antigen ligase; Region: Wzy_C; pfam04932 441768003291 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 441768003292 Alanine dehydrogenase NAD-binding and catalytic domains; Region: L-AlaDH; cd05305 441768003293 hexamer interface [polypeptide binding]; other site 441768003294 ligand binding site [chemical binding]; other site 441768003295 putative active site [active] 441768003296 NAD(P) binding site [chemical binding]; other site 441768003297 NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]; Region: NemA; COG1902 441768003298 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 441768003299 phosphate binding site [ion binding]; other site 441768003300 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 441768003301 metal binding site 2 [ion binding]; metal-binding site 441768003302 putative DNA binding helix; other site 441768003303 metal binding site 1 [ion binding]; metal-binding site 441768003304 dimer interface [polypeptide binding]; other site 441768003305 structural Zn2+ binding site [ion binding]; other site 441768003306 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 441768003307 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 441768003308 ABC-ATPase subunit interface; other site 441768003309 dimer interface [polypeptide binding]; other site 441768003310 putative PBP binding regions; other site 441768003311 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 441768003312 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 441768003313 Walker A/P-loop; other site 441768003314 ATP binding site [chemical binding]; other site 441768003315 Q-loop/lid; other site 441768003316 ABC transporter signature motif; other site 441768003317 Walker B; other site 441768003318 D-loop; other site 441768003319 H-loop/switch region; other site 441768003320 Periplasmic solute binding protein family; Region: SBP_bac_9; pfam01297 441768003321 Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between...; Region: TroA-like; cl00262 441768003322 intersubunit interface [polypeptide binding]; other site 441768003323 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 441768003324 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 441768003325 DNA binding site [nucleotide binding] 441768003326 active site 441768003327 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 441768003328 Coenzyme A binding pocket [chemical binding]; other site 441768003329 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 441768003330 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 441768003331 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 441768003332 ABC transporter; Region: ABC_tran_2; pfam12848 441768003333 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 441768003334 LrgB-like family; Region: LrgB; pfam04172 441768003335 LrgA family; Region: LrgA; pfam03788 441768003336 riboflavin biosynthesis protein RibD; Region: eubact_ribD; TIGR00326 441768003337 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 441768003338 catalytic motif [active] 441768003339 Zn binding site [ion binding]; other site 441768003340 RibD C-terminal domain; Region: RibD_C; cl17279 441768003341 Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; Region: FixB; COG2025 441768003342 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_alpha; cd01715 441768003343 Electron transfer flavoprotein FAD-binding domain; Region: ETF_alpha; pfam00766 441768003344 The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an...; Region: ETF_beta; cd01714 441768003345 Ligand binding site [chemical binding]; other site 441768003346 Electron transfer flavoprotein domain; Region: ETF; pfam01012 441768003347 Acyl-CoA dehydrogenases [Lipid metabolism]; Region: CaiA; COG1960 441768003348 Acyl-CoA dehydrogenase; Region: ACAD; cl09933 441768003349 active site 441768003350 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]; Region: Crp; COG0664 441768003351 effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO...; Region: CAP_ED; cd00038 441768003352 ligand binding site [chemical binding]; other site 441768003353 flexible hinge region; other site 441768003354 helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family; Region: HTH_CRP; cd00092 441768003355 putative switch regulator; other site 441768003356 non-specific DNA interactions [nucleotide binding]; other site 441768003357 DNA binding site [nucleotide binding] 441768003358 sequence specific DNA binding site [nucleotide binding]; other site 441768003359 putative cAMP binding site [chemical binding]; other site 441768003360 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 441768003361 active site 441768003362 Predicted membrane protein [Function unknown]; Region: COG2855 441768003363 Peptidase_C39 like family; Region: Peptidase_C39_2; pfam13529 441768003364 putative active site [active] 441768003365 Domain of unknown function (DUF2357); Region: DUF2357; pfam09823 441768003366 AAA domain; Region: AAA_22; pfam13401 441768003367 Cadherin-like beta sandwich domain; Region: Cadherin-like; pfam12733 441768003368 Cadherin-like beta sandwich domain; Region: Cadherin-like; pfam12733 441768003369 Cadherin-like beta sandwich domain; Region: Cadherin-like; pfam12733 441768003370 Cadherin-like beta sandwich domain; Region: Cadherin-like; pfam12733 441768003371 Cadherin-like beta sandwich domain; Region: Cadherin-like; pfam12733 441768003372 Cadherin-like beta sandwich domain; Region: Cadherin-like; pfam12733 441768003373 Cadherin-like beta sandwich domain; Region: Cadherin-like; pfam12733 441768003374 Cadherin-like beta sandwich domain; Region: Cadherin-like; pfam12733 441768003375 Cadherin-like beta sandwich domain; Region: Cadherin-like; pfam12733 441768003376 helix_turn_helix, arabinose operon control protein; Region: HTH_ARAC; smart00342 441768003377 Bacterial regulatory helix-turn-helix proteins, AraC family; Region: HTH_AraC; pfam00165 441768003378 Bacterial transcription activator, effector binding domain; Region: AraC_E_bind; smart00871 441768003379 putative rhodanese-related sulfurtransferase; Provisional; Region: PRK00142 441768003380 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 441768003381 active site residue [active] 441768003382 Protein of unknown function (DUF3650); Region: DUF3650; pfam12368 441768003383 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 441768003384 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 441768003385 Walker A motif; other site 441768003386 ATP binding site [chemical binding]; other site 441768003387 Walker B motif; other site 441768003388 arginine finger; other site 441768003389 Domain of unknown function (DUF4355); Region: DUF4355; pfam14265 441768003390 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 441768003391 Walker A motif; other site 441768003392 ATP binding site [chemical binding]; other site 441768003393 Walker B motif; other site 441768003394 arginine finger; other site 441768003395 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 441768003396 exopolyphosphatase; Region: exo_poly_only; TIGR03706 441768003397 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 441768003398 Short C-terminal domain; Region: SHOCT; pfam09851 441768003399 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 441768003400 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 441768003401 metal binding site [ion binding]; metal-binding site 441768003402 active site 441768003403 I-site; other site 441768003404 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 441768003405 Short C-terminal domain; Region: SHOCT; pfam09851 441768003406 Short C-terminal domain; Region: SHOCT; pfam09851 441768003407 A new structural DNA glycosylase; Region: AlkD_like; cl11434 441768003408 active site 441768003409 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 441768003410 metal-binding site [ion binding] 441768003411 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 441768003412 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 441768003413 metal-binding site [ion binding] 441768003414 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 441768003415 Soluble P-type ATPase [General function prediction only]; Region: COG4087 441768003416 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 441768003417 DJ-1 family protein; Region: not_thiJ; TIGR01383 441768003418 conserved cys residue [active] 441768003419 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 441768003420 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Region: MTA/SAH-Nsdase; TIGR01704 441768003421 Uridine kinase [Nucleotide transport and metabolism]; Region: Udk; COG0572 441768003422 Uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway; Region: UMPK; cd02023 441768003423 ATP-binding site [chemical binding]; other site 441768003424 Sugar specificity; other site 441768003425 Pyrimidine base specificity; other site 441768003426 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 441768003427 active site 441768003428 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic...; Region: S2P-M50; cl10020 441768003429 PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated; Region: PDZ; cl00117 441768003430 protein binding site [polypeptide binding]; other site 441768003431 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 441768003432 Zn-dependent proteases [General function prediction only]; Region: SpoIVFB; COG1994 441768003433 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 441768003434 putative substrate binding region [chemical binding]; other site 441768003435 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 441768003436 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 441768003437 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 441768003438 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 441768003439 catalytic residue [active] 441768003440 putative FPP diphosphate binding site; other site 441768003441 putative FPP binding hydrophobic cleft; other site 441768003442 dimer interface [polypeptide binding]; other site 441768003443 putative IPP diphosphate binding site; other site 441768003444 branched-chain amino acid aminotransferase; Provisional; Region: PRK13357 441768003445 BCAT_beta_family: Branched-chain aminotransferase catalyses the transamination of the branched-chain amino acids leusine, isoleucine and valine to their respective alpha-keto acids, alpha-ketoisocaproate, alpha-keto-beta-methylvalerate and...; Region: BCAT_beta_family; cd01557 441768003446 homodimer interface [polypeptide binding]; other site 441768003447 substrate-cofactor binding pocket; other site 441768003448 catalytic residue [active] 441768003449 ribosome recycling factor; Reviewed; Region: frr; PRK00083 441768003450 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 441768003451 hinge region; other site 441768003452 UMP kinase (UMPK)-Ec, the microbial/chloroplast uridine monophosphate kinase (uridylate kinase) enzyme that catalyzes UMP phosphorylation and plays a key role in pyrimidine nucleotide biosynthesis; regulation of this process is via feed-back control and...; Region: AAK_UMPK-PyrH-Ec; cd04254 441768003453 putative nucleotide binding site [chemical binding]; other site 441768003454 uridine monophosphate binding site [chemical binding]; other site 441768003455 homohexameric interface [polypeptide binding]; other site 441768003456 elongation factor Ts; Provisional; Region: tsf; PRK09377 441768003457 UBA/TS-N domain; Region: UBA; pfam00627 441768003458 Elongation factor TS; Region: EF_TS; pfam00889 441768003459 Elongation factor TS; Region: EF_TS; pfam00889 441768003460 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 441768003461 rRNA interaction site [nucleotide binding]; other site 441768003462 S8 interaction site; other site 441768003463 putative laminin-1 binding site; other site 441768003464 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 441768003465 trimer interface [polypeptide binding]; other site 441768003466 active site 441768003467 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cl00447 441768003468 nudix motif; other site 441768003469 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 441768003470 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 441768003471 active site 441768003472 DNA binding site [nucleotide binding] 441768003473 Int/Topo IB signature motif; other site 441768003474 tRNA (uracil-5-)-methyltransferase Gid; Reviewed; Region: PRK05335 441768003475 Glucose inhibited division protein A; Region: GIDA; pfam01134 441768003476 Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-terminal...; Region: MIP; cl00200 441768003477 amphipathic channel; other site 441768003478 Asn-Pro-Ala signature motifs; other site 441768003479 ECF-type riboflavin transporter, S component; Region: ECF-ribofla_trS; cl17272 441768003480 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 441768003481 ligand binding site [chemical binding]; other site 441768003482 active site 441768003483 UGI interface [polypeptide binding]; other site 441768003484 catalytic site [active] 441768003485 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the...; Region: Peptidase_S24_S26; cd06462 441768003486 Catalytic site [active] 441768003487 ATP synthase subunit D; Region: ATP-synt_D; pfam01813 441768003488 V-type ATP synthase subunit B; Provisional; Region: PRK04196 441768003489 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 441768003490 V/A-type ATP synthase (non-catalytic) subunit B. These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi...; Region: V_A-ATPase_B; cd01135 441768003491 Walker A motif homologous position; other site 441768003492 Walker B motif; other site 441768003493 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 441768003494 V-type ATP synthase subunit A; Provisional; Region: PRK04192 441768003495 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 441768003496 V/A-type ATP synthase catalytic subunit A. These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi...; Region: V_A-ATPase_A; cd01134 441768003497 Walker A motif/ATP binding site; other site 441768003498 Walker B motif; other site 441768003499 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 441768003500 ATP synthase (F/14-kDa) subunit; Region: ATP-synt_F; pfam01990 441768003501 ATP synthase subunit C; Region: ATP-synt_C; cl00466 441768003502 V-type ATP synthase subunit I; Validated; Region: PRK05771 441768003503 ATP synthase (C/AC39) subunit; Region: vATP-synt_AC39; pfam01992 441768003504 V-type ATP synthase subunit C; Provisional; Region: PRK01198; cl00660 441768003505 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; pfam00044 441768003506 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 441768003507 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 441768003508 Uncharacterized subgroup 1 of the CYTH-like superfamily; Region: CYTH-like_Pase_1; cd07762 441768003509 putative active site [active] 441768003510 putative metal binding residues [ion binding]; other site 441768003511 signature motif; other site 441768003512 putative triphosphate binding site [ion binding]; other site 441768003513 Nuclease-related domain; Region: NERD; pfam08378 441768003514 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 441768003515 salt bridge; other site 441768003516 non-specific DNA binding site [nucleotide binding]; other site 441768003517 sequence-specific DNA binding site [nucleotide binding]; other site 441768003518 Arsenate Reductase (ArsC) family, Spx subfamily; Spx is a unique RNA polymerase (RNAP)-binding protein present in bacilli and some mollicutes. It inhibits transcription by binding to the C-terminal domain of the alpha subunit of RNAP, disrupting complex...; Region: ArsC_Spx; cd03032 441768003519 ArsC family; Region: ArsC; pfam03960 441768003520 putative catalytic residues [active] 441768003521 thiol/disulfide switch; other site 441768003522 oligoendopeptidase F; Region: pepF; TIGR00181 441768003523 Peptidase family M3B Oligopeptidase F (PepF); Region: M3B_PepF_3; cd09608 441768003524 active site 441768003525 Zn binding site [ion binding]; other site 441768003526 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 441768003527 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 441768003528 active site 441768003529 HIGH motif; other site 441768003530 dimer interface [polypeptide binding]; other site 441768003531 KMSKS motif; other site 441768003532 Domain of unknown function (DUF4118); Region: DUF4118; pfam13493 441768003533 Class III nucleotidyl cyclases; Region: Nucleotidyl_cyc_III; cl11967 441768003534 metal binding site [ion binding]; metal-binding site 441768003535 nucleotidyl binding site; other site 441768003536 EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second...; Region: EAL; cd01948 441768003537 Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only]; Region: LCB5; COG1597 441768003538 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; pfam00781 441768003539 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 441768003540 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 441768003541 active site 441768003542 HIGH motif; other site 441768003543 dimer interface [polypeptide binding]; other site 441768003544 KMSKS motif; other site 441768003545 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 441768003546 RNA binding surface [nucleotide binding]; other site 441768003547 catabolite control protein A; Region: ccpA; TIGR01481 441768003548 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 441768003549 DNA binding site [nucleotide binding] 441768003550 domain linker motif; other site 441768003551 Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation; Region: PBP1_CcpA_like; cd06298 441768003552 dimerization interface [polypeptide binding]; other site 441768003553 effector binding site; other site 441768003554 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 441768003555 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 441768003556 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 441768003557 RimM N-terminal domain; Region: RimM; pfam01782 441768003558 PRC-barrel domain; Region: PRC; pfam05239 441768003559 KH domain; Region: KH_4; pfam13083 441768003560 Predicted RNA-binding protein (contains KH domain) [General function prediction only]; Region: COG1837 441768003561 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 441768003562 Uncharacterized protein conserved in bacteria (DUF2129); Region: DUF2129; cl11453 441768003563 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 441768003564 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 441768003565 RNA binding surface [nucleotide binding]; other site 441768003566 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 441768003567 active site 441768003568 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 441768003569 active site 441768003570 catalytic residues [active] 441768003571 metal binding site [ion binding]; metal-binding site 441768003572 Glycosyl hydrolase family 20 (GH20) catalytic domain of N-acetyl-beta-D-glucosaminidase (GcnA, also known as BhsA) and related proteins. GcnA is an exoglucosidase which cleaves N-acetyl-beta-D-galactosamine (NAG) and N-acetyl-beta-D-galactosamine...; Region: GH20_GcnA-like; cd06565 441768003573 putative active site [active] 441768003574 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 441768003575 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 441768003576 thiamine biosynthesis protein ThiI; Provisional; Region: PRK01565 441768003577 THUMP domain of thiamine biosynthesis protein ThiI; Region: THUMP_ThiI; cd11716 441768003578 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 441768003579 Ligand Binding Site [chemical binding]; other site 441768003580 GAF domain-containing protein [Signal transduction mechanisms]; Region: COG1956 441768003581 GAF domain; Region: GAF_2; pfam13185 441768003582 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 441768003583 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 441768003584 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 441768003585 RNA binding surface [nucleotide binding]; other site 441768003586 GlcNAc-PI de-N-acetylase; Region: PIG-L; cl00929 441768003587 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 441768003588 Coenzyme A binding pocket [chemical binding]; other site 441768003589 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 441768003590 Coenzyme A binding pocket [chemical binding]; other site 441768003591 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 441768003592 Glutaredoxin-like domain protein; Region: GlrX_arch; TIGR02187 441768003593 Thioredoxin (TRX)-Glutaredoxin (GRX)-like family; composed of archaeal and bacterial proteins that show similarity to both TRX and GRX, including the C-terminal TRX-fold subdomain of Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO). All...; Region: TRX_GRX_like; cd02973 441768003594 catalytic residues [active] 441768003595 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 441768003596 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox_3; pfam13738 441768003597 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 441768003598 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 441768003599 triosephosphate isomerase; Provisional; Region: PRK14565 441768003600 substrate binding site [chemical binding]; other site 441768003601 dimer interface [polypeptide binding]; other site 441768003602 catalytic triad [active] 441768003603 Histidine-containing phosphocarrier protein (HPr)-like proteins. HPr is a central component of the bacterial phosphoenolpyruvate sugar phosphotransferase system (PTS). The PTS catalyses the phosphorylation of sugar substrates during their translocation...; Region: PTS-HPr_like; cd00367 441768003604 dimerization domain swap beta strand [polypeptide binding]; other site 441768003605 regulatory protein interface [polypeptide binding]; other site 441768003606 active site 441768003607 regulatory phosphorylation site [posttranslational modification]; other site 441768003608 DNA-binding transcriptional repressor PuuR; Provisional; Region: PRK09943 441768003609 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 441768003610 non-specific DNA binding site [nucleotide binding]; other site 441768003611 salt bridge; other site 441768003612 sequence-specific DNA binding site [nucleotide binding]; other site 441768003613 Cupin domain; Region: Cupin_2; pfam07883 441768003614 Phosphoglycerate kinase; Region: PGK; pfam00162 441768003615 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; cd00318 441768003616 substrate binding site [chemical binding]; other site 441768003617 hinge regions; other site 441768003618 ADP binding site [chemical binding]; other site 441768003619 catalytic site [active] 441768003620 ComK protein; Region: ComK; cl11560 441768003621 Bacterial Ig-like domain (group 2); Region: Big_2; cl02708 441768003622 cysteine desulfurase activator complex subunit SufB; Provisional; Region: PRK11814; cl03223 441768003623 FeS assembly protein SufB; Region: sufB; TIGR01980 441768003624 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 441768003625 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 441768003626 trimerization site [polypeptide binding]; other site 441768003627 active site 441768003628 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 441768003629 Cysteine desulfurase (SufS)-like. This family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to cysteine desulfurase (SufS) and selenocysteine lyase. SufS...; Region: SufS_like; cd06453 441768003630 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 441768003631 catalytic residue [active] 441768003632 Uncharacterized protein family (UPF0051); Region: UPF0051; pfam01458 441768003633 cysteine desulfurase activator complex subunit SufB; Provisional; Region: PRK11814; cl03223 441768003634 Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]; Region: sufC; COG0396 441768003635 ABC-type transport system involved in Fe-S cluster assembly, ATPase component; Region: ABC_FeS_Assembly; cd03217 441768003636 Walker A/P-loop; other site 441768003637 ATP binding site [chemical binding]; other site 441768003638 Q-loop/lid; other site 441768003639 ABC transporter signature motif; other site 441768003640 Walker B; other site 441768003641 D-loop; other site 441768003642 H-loop/switch region; other site 441768003643 nickel import ATP-binding protein NikE; Region: nickel_nikE; TIGR02769 441768003644 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 441768003645 Walker A/P-loop; other site 441768003646 ATP binding site [chemical binding]; other site 441768003647 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 441768003648 Q-loop/lid; other site 441768003649 ABC transporter signature motif; other site 441768003650 Walker B; other site 441768003651 D-loop; other site 441768003652 H-loop/switch region; other site 441768003653 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 441768003654 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppD; COG0444 441768003655 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 441768003656 Walker A/P-loop; other site 441768003657 ATP binding site [chemical binding]; other site 441768003658 Q-loop/lid; other site 441768003659 ABC transporter signature motif; other site 441768003660 Walker B; other site 441768003661 D-loop; other site 441768003662 H-loop/switch region; other site 441768003663 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; pfam08352 441768003664 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 441768003665 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppC; COG1173 441768003666 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 441768003667 dimer interface [polypeptide binding]; other site 441768003668 conserved gate region; other site 441768003669 putative PBP binding loops; other site 441768003670 ABC-ATPase subunit interface; other site 441768003671 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 441768003672 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 441768003673 dimer interface [polypeptide binding]; other site 441768003674 conserved gate region; other site 441768003675 putative PBP binding loops; other site 441768003676 ABC-ATPase subunit interface; other site 441768003677 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 441768003678 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; cd00995 441768003679 Bacterial extracellular solute-binding proteins, family 5 Middle; Region: SBP_bac_5; pfam00496 441768003680 Domain of unknown function (DUF3899); Region: DUF3899; pfam13038 441768003681 Listeria-Bacteroides repeat domain (List_Bact_rpt); Region: Flg_new; cl09714 441768003682 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 441768003683 Active site serine [active] 441768003684 Transcriptional regulator [Transcription]; Region: AcrR; COG1309 441768003685 Bacterial regulatory proteins, tetR family; Region: TetR_N; pfam00440 441768003686 asparagine synthetase AsnA; Provisional; Region: PRK05425 441768003687 motif 1; other site 441768003688 dimer interface [polypeptide binding]; other site 441768003689 active site 441768003690 motif 2; other site 441768003691 motif 3; other site 441768003692 Sulfatase; Region: Sulfatase; cl17466 441768003693 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; Region: Glyoxalase; pfam00903 441768003694 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases; Region: Glo_EDI_BRP_like_10; cd07251 441768003695 hypothetical protein; Provisional; Region: PRK04164 441768003696 Uncharacterized protein conserved in bacteria (DUF2179); Region: DUF2179; pfam10035 441768003697 ABC-2 family transporter protein; Region: ABC2_membrane_6; cl01496 441768003698 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4587 441768003699 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4587 441768003700 ABC-2 family transporter protein; Region: ABC2_membrane_6; cl01496 441768003701 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: COG4586 441768003702 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 441768003703 Walker A/P-loop; other site 441768003704 ATP binding site [chemical binding]; other site 441768003705 Q-loop/lid; other site 441768003706 ABC transporter signature motif; other site 441768003707 Walker B; other site 441768003708 D-loop; other site 441768003709 H-loop/switch region; other site 441768003710 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 441768003711 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 441768003712 ATP-binding cassette domain of glucan transporter and related proteins, subfamily C; Region: ABCC_Glucan_exporter_like; cd03254 441768003713 Walker A/P-loop; other site 441768003714 ATP binding site [chemical binding]; other site 441768003715 Q-loop/lid; other site 441768003716 ABC transporter signature motif; other site 441768003717 Walker B; other site 441768003718 D-loop; other site 441768003719 H-loop/switch region; other site 441768003720 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 441768003721 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 441768003722 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 441768003723 Walker A/P-loop; other site 441768003724 ATP binding site [chemical binding]; other site 441768003725 Q-loop/lid; other site 441768003726 ABC transporter signature motif; other site 441768003727 Walker B; other site 441768003728 D-loop; other site 441768003729 H-loop/switch region; other site 441768003730 Transcriptional regulators [Transcription]; Region: MarR; COG1846 441768003731 MarR family; Region: MarR_2; pfam12802 441768003732 Lamin Tail Domain; Region: LTD; pfam00932 441768003733 Lamin Tail Domain; Region: LTD; pfam00932 441768003734 Uncharacterized conserved protein (DUF2161); Region: DUF2161; cl02298 441768003735 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional; Region: fabG; PRK05565 441768003736 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 441768003737 NAD(P) binding site [chemical binding]; other site 441768003738 active site 441768003739 MutT homolog-1 (MTH1) is a member of the Nudix hydrolase superfamily. MTH1, the mammalian counterpart of MutT, hydrolyzes oxidized purine nucleoside triphosphates, such as 8-oxo-dGTP and 2-hydroxy-ATP, to monophosphates, thereby preventing the...; Region: MTH1; cd03427 441768003740 putative active site [active] 441768003741 nucleotide binding site [chemical binding]; other site 441768003742 nudix motif; other site 441768003743 putative metal binding site [ion binding]; other site 441768003744 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 441768003745 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 441768003746 ring oligomerisation interface [polypeptide binding]; other site 441768003747 ATP/Mg binding site [chemical binding]; other site 441768003748 stacking interactions; other site 441768003749 hinge regions; other site 441768003750 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 441768003751 oligomerisation interface [polypeptide binding]; other site 441768003752 mobile loop; other site 441768003753 roof hairpin; other site 441768003754 Protein of unknown function (DUF1295); Region: DUF1295; cl17837 441768003755 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 441768003756 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 441768003757 Walker A/P-loop; other site 441768003758 ATP binding site [chemical binding]; other site 441768003759 Q-loop/lid; other site 441768003760 ABC transporter signature motif; other site 441768003761 Walker B; other site 441768003762 D-loop; other site 441768003763 H-loop/switch region; other site 441768003764 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 441768003765 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 441768003766 substrate binding pocket [chemical binding]; other site 441768003767 membrane-bound complex binding site; other site 441768003768 hinge residues; other site 441768003769 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 441768003770 dimer interface [polypeptide binding]; other site 441768003771 conserved gate region; other site 441768003772 putative PBP binding loops; other site 441768003773 ABC-ATPase subunit interface; other site 441768003774 copper-(or silver)-translocating P-type ATPase; Region: ATPase-IB1_Cu; TIGR01511 441768003775 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 441768003776 Soluble P-type ATPase [General function prediction only]; Region: COG4087 441768003777 Restriction endonuclease; Region: Mrr_cat; pfam04471 441768003778 AAA domain; Region: AAA_11; pfam13086 441768003779 Part of AAA domain; Region: AAA_19; pfam13245 441768003780 Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair]; Region: COG1112 441768003781 AAA domain; Region: AAA_12; pfam13087 441768003782 Protein of unknown function (DUF2726); Region: DUF2726; pfam10881 441768003783 Restriction endonuclease; Region: Mrr_cat; pfam04471 441768003784 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 441768003785 Uncharacterized conserved protein (DUF2075); Region: DUF2075; pfam09848 441768003786 Walker A motif; other site 441768003787 ATP binding site [chemical binding]; other site 441768003788 Walker B motif; other site 441768003789 Uncharacterized conserved protein [Function unknown]; Region: COG3410 441768003790 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 441768003791 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 441768003792 metal-binding site [ion binding] 441768003793 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 441768003794 Soluble P-type ATPase [General function prediction only]; Region: COG4087 441768003795 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 441768003796 dimerization interface [polypeptide binding]; other site 441768003797 putative DNA binding site [nucleotide binding]; other site 441768003798 putative Zn2+ binding site [ion binding]; other site 441768003799 Domain of unknown function (DU1801); Region: DUF1801; pfam08818 441768003800 YolD-like protein; Region: YolD; pfam08863 441768003801 DNA polymerase IV; Reviewed; Region: PRK03103 441768003802 umuC subunit of DNA Polymerase V; Region: PolY_Pol_V_umuC; cd01700 441768003803 active site 441768003804 DNA binding site [nucleotide binding] 441768003805 Domain of unknown function (DUF4113); Region: DUF4113; pfam13438 441768003806 type I site-specific deoxyribonuclease, HsdR family; Region: hsdR; TIGR00348 441768003807 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 441768003808 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 441768003809 ATP binding site [chemical binding]; other site 441768003810 putative Mg++ binding site [ion binding]; other site 441768003811 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 441768003812 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 441768003813 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 441768003814 HsdM N-terminal domain; Region: HsdM_N; pfam12161 441768003815 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 441768003816 Methyltransferase domain; Region: Methyltransf_26; pfam13659 441768003817 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 441768003818 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 441768003819 non-specific DNA binding site [nucleotide binding]; other site 441768003820 salt bridge; other site 441768003821 sequence-specific DNA binding site [nucleotide binding]; other site 441768003822 magnesium-transporting ATPase MgtA; Provisional; Region: PRK10517 441768003823 Cation transporter/ATPase, N-terminus; Region: Cation_ATPase_N; smart00831 441768003824 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 441768003825 Putative hydrolase of sodium-potassium ATPase alpha subunit; Region: Hydrolase_like2; pfam13246 441768003826 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 441768003827 motif II; other site 441768003828 Cation transporting ATPase, C-terminus; Region: Cation_ATPase_C; pfam00689 441768003829 Glyco_18 domain; Region: Glyco_18; smart00636 441768003830 The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods. Chitinases have...; Region: GH18_chitinase-like; cl10447 441768003831 active site 441768003832 ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]; Region: PotA; COG3842 441768003833 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 441768003834 Walker A/P-loop; other site 441768003835 ATP binding site [chemical binding]; other site 441768003836 Q-loop/lid; other site 441768003837 ABC transporter signature motif; other site 441768003838 Walker B; other site 441768003839 D-loop; other site 441768003840 H-loop/switch region; other site 441768003841 TOBE domain; Region: TOBE_2; pfam08402 441768003842 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 441768003843 dimer interface [polypeptide binding]; other site 441768003844 conserved gate region; other site 441768003845 putative PBP binding loops; other site 441768003846 ABC-ATPase subunit interface; other site 441768003847 ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; Region: PotC; COG1177 441768003848 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 441768003849 dimer interface [polypeptide binding]; other site 441768003850 conserved gate region; other site 441768003851 putative PBP binding loops; other site 441768003852 ABC-ATPase subunit interface; other site 441768003853 Bacterial extracellular solute-binding protein; Region: SBP_bac_8; pfam13416 441768003854 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; pfam01547 441768003855 Uncharacterized conserved protein [Function unknown]; Region: COG5646 441768003856 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 441768003857 ribonucleotide-diphosphate reductase subunit beta; Provisional; Region: nrdF2; PRK13966 441768003858 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 441768003859 dimer interface [polypeptide binding]; other site 441768003860 putative radical transfer pathway; other site 441768003861 diiron center [ion binding]; other site 441768003862 tyrosyl radical; other site 441768003863 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK07632 441768003864 Ribonucleotide reductase N-terminal; Region: RNR_N; pfam08343 441768003865 Class I ribonucleotide reductase; Region: RNR_I; cd01679 441768003866 active site 441768003867 dimer interface [polypeptide binding]; other site 441768003868 catalytic residues [active] 441768003869 effector binding site; other site 441768003870 R2 peptide binding site; other site 441768003871 NrdI Flavodoxin like; Region: Flavodoxin_NdrI; pfam07972 441768003872 4Fe-4S single cluster domain; Region: Fer4_12; pfam13353 441768003873 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 441768003874 FeS/SAM binding site; other site 441768003875 anaerobic ribonucleoside triphosphate reductase; Provisional; Region: PRK07111 441768003876 ATP cone domain; Region: ATP-cone; pfam03477 441768003877 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 441768003878 Ribonucleotide reductase and Pyruvate formate lyase; Region: RNR_PFL; cl09939 441768003879 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 441768003880 Beta-lactamase; Region: Beta-lactamase; pfam00144 441768003881 Protein of unknown function (DUF975); Region: DUF975; cl10504 441768003882 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 441768003883 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 441768003884 dimer interface [polypeptide binding]; other site 441768003885 phosphorylation site [posttranslational modification] 441768003886 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 441768003887 ATP binding site [chemical binding]; other site 441768003888 Mg2+ binding site [ion binding]; other site 441768003889 G-X-G motif; other site 441768003890 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 441768003891 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 441768003892 active site 441768003893 phosphorylation site [posttranslational modification] 441768003894 intermolecular recognition site; other site 441768003895 dimerization interface [polypeptide binding]; other site 441768003896 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 441768003897 DNA binding site [nucleotide binding] 441768003898 phosphate transport system regulatory protein PhoU; Region: phoU_full; TIGR02135 441768003899 PhoU domain; Region: PhoU; pfam01895 441768003900 PhoU domain; Region: PhoU; pfam01895 441768003901 ABC-type phosphate transport system, ATPase component [Inorganic ion transport and metabolism]; Region: PstB; COG1117 441768003902 ATP-binding cassette domain of the phosphate transport system; Region: ABC_PstB_phosphate_transporter; cd03260 441768003903 Walker A/P-loop; other site 441768003904 ATP binding site [chemical binding]; other site 441768003905 Q-loop/lid; other site 441768003906 ABC transporter signature motif; other site 441768003907 Walker B; other site 441768003908 D-loop; other site 441768003909 H-loop/switch region; other site 441768003910 ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]; Region: PstA; COG0581 441768003911 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 441768003912 dimer interface [polypeptide binding]; other site 441768003913 conserved gate region; other site 441768003914 putative PBP binding loops; other site 441768003915 ABC-ATPase subunit interface; other site 441768003916 phosphate ABC transporter, permease protein PstC; Region: phosphate_pstC; TIGR02138 441768003917 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 441768003918 conserved gate region; other site 441768003919 putative PBP binding loops; other site 441768003920 ABC-ATPase subunit interface; other site 441768003921 PBP superfamily domain; Region: PBP_like_2; cl17296 441768003922 PBP superfamily domain; Region: PBP_like_2; cl17296 441768003923 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 441768003924 ABC-type multidrug transport system, ATPase component [Defense mechanisms]; Region: CcmA; COG1131 441768003925 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 441768003926 Walker A/P-loop; other site 441768003927 ATP binding site [chemical binding]; other site 441768003928 Q-loop/lid; other site 441768003929 ABC transporter signature motif; other site 441768003930 Walker B; other site 441768003931 D-loop; other site 441768003932 H-loop/switch region; other site 441768003933 Domain of unknown function (DUF4162); Region: DUF4162; pfam13732 441768003934 Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only]; Region: LCB5; COG1597 441768003935 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; pfam00781 441768003936 Lipoate-protein ligase A [Coenzyme metabolism]; Region: LplA; COG0095 441768003937 Predicted membrane protein [Function unknown]; Region: COG2364 441768003938 dihydrolipoamide dehydrogenase; Region: lipoamide_DH; TIGR01350 441768003939 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 441768003940 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 441768003941 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 441768003942 E3 interaction surface; other site 441768003943 lipoyl attachment site [posttranslational modification]; other site 441768003944 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed; Region: PRK11856 441768003945 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 441768003946 E3 interaction surface; other site 441768003947 lipoyl attachment site [posttranslational modification]; other site 441768003948 e3 binding domain; Region: E3_binding; pfam02817 441768003949 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 441768003950 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit [Energy production and conversion]; Region: AcoB; COG0022 441768003951 Pyrimidine (PYR) binding domain of the beta subunits of the E1 components of human pyruvate dehydrogenase complex (E1- PDHc) and related proteins; Region: TPP_PYR_E1-PDHc-beta_like; cd07036 441768003952 alpha subunit interface [polypeptide binding]; other site 441768003953 TPP binding site [chemical binding]; other site 441768003954 heterodimer interface [polypeptide binding]; other site 441768003955 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 441768003956 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_x; TIGR03181 441768003957 Thiamine pyrophosphate (TPP) family, E1 of PDC_ADC_BCADC subfamily, TPP-binding module; composed of proteins similar to the E1 components of the human pyruvate dehydrogenase complex (PDC), the acetoin dehydrogenase complex (ADC) and the branched chain...; Region: TPP_E1_PDC_ADC_BCADC; cd02000 441768003958 tetramer interface [polypeptide binding]; other site 441768003959 TPP-binding site [chemical binding]; other site 441768003960 heterodimer interface [polypeptide binding]; other site 441768003961 phosphorylation loop region [posttranslational modification] 441768003962 Fic/DOC family; Region: Fic; cl00960 441768003963 DNA-damage-inducible protein J [DNA replication, recombination, and repair]; Region: RelB; COG3077 441768003964 agmatinase; Region: agmatinase; TIGR01230 441768003965 Agmatinase and related proteins; Region: Agmatinase-like_2; cd11593 441768003966 putative active site [active] 441768003967 Mn binding site [ion binding]; other site 441768003968 Arginine/lysine/ornithine decarboxylases [Amino acid transport and metabolism]; Region: LdcC; COG1982 441768003969 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 441768003970 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 441768003971 catalytic residue [active] 441768003972 Orn/Lys/Arg decarboxylase, C-terminal domain; Region: OKR_DC_1_C; pfam03711 441768003973 Uncharacterized subfamily of Uracil-DNA glycosylases; Region: UDG_like_1; cd10033 441768003974 putative uracil binding site [chemical binding]; other site 441768003975 putative active site [active] 441768003976 Listeria-Bacteroides repeat domain (List_Bact_rpt); Region: Flg_new; cl09714 441768003977 Listeria-Bacteroides repeat domain (List_Bact_rpt); Region: Flg_new; cl09714 441768003978 Bacterial cellulose synthase subunit; Region: BcsB; cl15851 441768003979 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional; Region: PRK09311 441768003980 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: DHBP_synthase; cl00336 441768003981 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 441768003982 dimerization interface [polypeptide binding]; other site 441768003983 active site 441768003984 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins; Region: SRPBCC_CalC_Aha1-like_4; cd08897 441768003985 putative hydrophobic ligand binding site [chemical binding]; other site 441768003986 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 441768003987 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 441768003988 substrate binding pocket [chemical binding]; other site 441768003989 membrane-bound complex binding site; other site 441768003990 hinge residues; other site 441768003991 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 441768003992 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 441768003993 dimer interface [polypeptide binding]; other site 441768003994 conserved gate region; other site 441768003995 putative PBP binding loops; other site 441768003996 ABC-ATPase subunit interface; other site 441768003997 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 441768003998 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 441768003999 Walker A/P-loop; other site 441768004000 ATP binding site [chemical binding]; other site 441768004001 Q-loop/lid; other site 441768004002 ABC transporter signature motif; other site 441768004003 Walker B; other site 441768004004 D-loop; other site 441768004005 H-loop/switch region; other site 441768004006 Trp repressor protein; Region: Trp_repressor; cl17266 441768004007 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 441768004008 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 441768004009 substrate binding pocket [chemical binding]; other site 441768004010 chain length determination region; other site 441768004011 substrate-Mg2+ binding site; other site 441768004012 catalytic residues [active] 441768004013 aspartate-rich region 1; other site 441768004014 active site lid residues [active] 441768004015 aspartate-rich region 2; other site 441768004016 PAS fold; Region: PAS_3; pfam08447 441768004017 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 441768004018 putative active site [active] 441768004019 heme pocket [chemical binding]; other site 441768004020 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 441768004021 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 441768004022 metal binding site [ion binding]; metal-binding site 441768004023 active site 441768004024 I-site; other site 441768004025 aldehyde dehydrogenase family protein; Provisional; Region: PTZ00381 441768004026 Bacillus subtilis aldehyde dehydrogenase ywdH-like; Region: ALDH_YwdH-P39616; cd07136 441768004027 NAD(P) binding site [chemical binding]; other site 441768004028 catalytic residues [active] 441768004029 K+-dependent Na+/Ca+ exchanger related-protein; Region: TIGR00367 441768004030 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 441768004031 Sodium/calcium exchanger protein; Region: Na_Ca_ex; pfam01699 441768004032 adenylosuccinate lyase; Provisional; Region: PRK07492 441768004033 Adenylsuccinate lyase (ASL)_subgroup 1; Region: Adenylsuccinate_lyase_1; cd01360 441768004034 tetramer interface [polypeptide binding]; other site 441768004035 active site 441768004036 Adenylosuccinate lyase C-terminus; Region: ADSL_C; smart00998 441768004037 NAD(P)+-dependent aldehyde dehydrogenase superfamily; Region: ALDH-SF; cl11961 441768004038 NAD(P) binding site [chemical binding]; other site 441768004039 catalytic residues [active] 441768004040 Leucine rich repeats (6 copies); Region: LRR_5; pfam13306 441768004041 Transcriptional accessory protein [Transcription]; Region: Tex; COG2183 441768004042 Tex-like protein N-terminal domain; Region: Tex_N; pfam09371 441768004043 Likely ribonuclease with RNase H fold; Region: YqgFc; smart00732 441768004044 S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression; Region: S1_Tex; cd05685 441768004045 RNA binding site [nucleotide binding]; other site 441768004046 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 441768004047 Sporulation Regulator WhiA N terminal; Region: WhiA_N; pfam10298 441768004048 Sporulation Regulator WhiA C terminal domain; Region: HTH_WhiA; pfam02650 441768004049 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 441768004050 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 441768004051 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 441768004052 Prolipoprotein diacylglyceryl transferase; Region: LGT; pfam01790 441768004053 pyrophosphatase PpaX; Provisional; Region: PRK13288 441768004054 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 441768004055 motif II; other site 441768004056 HPr Serine kinase N terminus; Region: Hpr_kinase_N; pfam02603 441768004057 Hpr(Ser) kinase/phosphatase; Region: hpr-ser; TIGR00679 441768004058 HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent...; Region: HprK_C; cd01918 441768004059 Hpr binding site; other site 441768004060 active site 441768004061 homohexamer subunit interaction site [polypeptide binding]; other site 441768004062 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 441768004063 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 441768004064 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 441768004065 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 441768004066 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 441768004067 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 441768004068 nucleotide binding pocket [chemical binding]; other site 441768004069 K-X-D-G motif; other site 441768004070 catalytic site [active] 441768004071 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 441768004072 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 441768004073 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 441768004074 Dimer interface [polypeptide binding]; other site 441768004075 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 441768004076 Part of AAA domain; Region: AAA_19; pfam13245 441768004077 Family description; Region: UvrD_C_2; pfam13538 441768004078 Listeria-Bacteroides repeat domain (List_Bact_rpt); Region: Flg_new; pfam09479 441768004079 Immune inhibitor A peptidase M6; Region: Peptidase_M6; cl11525 441768004080 ATP-dependent DNA helicase PcrA; Region: pcrA; TIGR01073 441768004081 Part of AAA domain; Region: AAA_19; pfam13245 441768004082 AAA domain; Region: AAA_12; pfam13087 441768004083 Family description; Region: UvrD_C_2; pfam13538 441768004084 glutaminyl-tRNA synthetase; Provisional; Region: PRK05347 441768004085 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 441768004086 active site 441768004087 HIGH motif; other site 441768004088 nucleotide binding site [chemical binding]; other site 441768004089 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 441768004090 active site 441768004091 KMSKS motif; other site 441768004092 tRNA synthetases class I (E and Q), anti-codon binding domain; Region: tRNA-synt_1c_C; pfam03950 441768004093 UGMP family protein; Validated; Region: PRK09604 441768004094 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 441768004095 ribosomal-protein-alanine acetyltransferase; Region: rimI; TIGR01575 441768004096 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 441768004097 Coenzyme A binding pocket [chemical binding]; other site 441768004098 tRNA threonylcarbamoyl adenosine modification protein YeaZ; Region: T6A_YeaZ; TIGR03725 441768004099 Glycoprotease family; Region: Peptidase_M22; pfam00814 441768004100 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 441768004101 glucose-6-phosphate isomerase; Provisional; Region: pgi; PRK14097 441768004102 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 441768004103 active site 441768004104 dimer interface [polypeptide binding]; other site 441768004105 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 441768004106 dimer interface [polypeptide binding]; other site 441768004107 active site 441768004108 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cd00164 441768004109 RNA binding site [nucleotide binding]; other site 441768004110 Divergent PAP2 family; Region: DUF212; pfam02681 441768004111 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 441768004112 Protein of unknown function (DUF1027); Region: DUF1027; cl09961 441768004113 5,10-methenyltetrahydrofolate synthetase; Region: MTHFS_bact; TIGR02727 441768004114 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 441768004115 PAS domain; Region: PAS_9; pfam13426 441768004116 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]; Region: COG2199 441768004117 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 441768004118 metal binding site [ion binding]; metal-binding site 441768004119 active site 441768004120 I-site; other site 441768004121 Uncharacterized conserved protein [Function unknown]; Region: COG1624 441768004122 DisA bacterial checkpoint controller nucleotide-binding; Region: DisA_N; pfam02457 441768004123 Predicted transcriptional regulators [Transcription]; Region: COG1733 441768004124 HxlR-like helix-turn-helix; Region: HxlR; pfam01638 441768004125 GTP-binding protein HflX; Region: GTP_HflX; TIGR03156 441768004126 GTP-binding GTPase N-terminal; Region: GTP-bdg_N; pfam13167 441768004127 HflX GTPase family; Region: HflX; cd01878 441768004128 G1 box; other site 441768004129 GTP/Mg2+ binding site [chemical binding]; other site 441768004130 Switch I region; other site 441768004131 G2 box; other site 441768004132 G3 box; other site 441768004133 Switch II region; other site 441768004134 G4 box; other site 441768004135 G5 box; other site 441768004136 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 441768004137 nuc_hydro_IU_UC_XIUA: inosine-uridine preferring, xanthosine-inosine-uridine-adenosine-preferring and, uridine-cytidine preferring nucleoside hydrolases. Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the...; Region: nuc_hydro_IU_UC_XIUA; cd02651 441768004138 active site 441768004139 tetramer interface [polypeptide binding]; other site 441768004140 Sugar kinases, ribokinase family [Carbohydrate transport and metabolism]; Region: RbsK; COG0524 441768004141 Ribokinase catalyses the phosphorylation of ribose to ribose-5-phosphate using ATP. This reaction is the first step in the ribose metabolism. It traps ribose within the cell after uptake and also prepares the sugar for use in the synthesis of nucleotides...; Region: ribokinase; cd01174 441768004142 substrate binding site [chemical binding]; other site 441768004143 dimer interface [polypeptide binding]; other site 441768004144 ATP binding site [chemical binding]; other site 441768004145 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 441768004146 Coenzyme A binding pocket [chemical binding]; other site 441768004147 Transcriptional regulators [Transcription]; Region: PurR; COG1609 441768004148 Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators; Region: HTH_LacI; cd01392 441768004149 DNA binding site [nucleotide binding] 441768004150 domain linker motif; other site 441768004151 Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily; Region: PBP1_LacI_sugar_binding_like; cd06267 441768004152 dimerization interface [polypeptide binding]; other site 441768004153 ligand binding site [chemical binding]; other site 441768004154 Permease family; Region: Xan_ur_permease; pfam00860 441768004155 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 441768004156 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 441768004157 FMN binding site [chemical binding]; other site 441768004158 active site 441768004159 catalytic residues [active] 441768004160 substrate binding site [chemical binding]; other site 441768004161 Hsp33-like chaperonin; Reviewed; Region: hslO; PRK00114 441768004162 Heat shock protein 33 (Hsp33): Cytosolic protein that acts as a molecular chaperone under oxidative conditions. In normal (reducing) cytosolic conditions, four conserved Cys residues are coordinated by a Zn ion. Under oxidative stress (such as heat...; Region: Hsp33; cd00498 441768004163 dimerization interface [polypeptide binding]; other site 441768004164 domain crossover interface; other site 441768004165 redox-dependent activation switch; other site 441768004166 Uncharacterized conserved protein [Function unknown]; Region: COG3595 441768004167 Domain of unknown function (DUF4098); Region: DUF4098; pfam13345 441768004168 Predicted membrane protein [Function unknown]; Region: COG4709 441768004169 Predicted transcriptional regulators [Transcription]; Region: COG1695 441768004170 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cd00090 441768004171 putative DNA binding site [nucleotide binding]; other site 441768004172 putative Zn2+ binding site [ion binding]; other site 441768004173 Maf-like protein; Region: Maf; pfam02545 441768004174 Nucleotide binding protein Maf. Maf has been implicated in inhibition of septum formation in eukaryotes, bacteria and archaea, but homologs in B.subtilis and S.cerevisiae are nonessential for cell division. Maf has been predicted to be a nucleotide- or...; Region: Maf; cd00555 441768004175 active site 441768004176 dimer interface [polypeptide binding]; other site 441768004177 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 441768004178 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 441768004179 Ligand Binding Site [chemical binding]; other site 441768004180 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 441768004181 active site 441768004182 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 441768004183 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 441768004184 Walker A motif; other site 441768004185 ATP binding site [chemical binding]; other site 441768004186 Walker B motif; other site 441768004187 arginine finger; other site 441768004188 Peptidase family M41; Region: Peptidase_M41; pfam01434 441768004189 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 441768004190 RNA binding surface [nucleotide binding]; other site 441768004191 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 441768004192 LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop; Region: LysRS_N; cd04322 441768004193 dimer interface [polypeptide binding]; other site 441768004194 putative anticodon binding site; other site 441768004195 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 441768004196 motif 1; other site 441768004197 active site 441768004198 motif 2; other site 441768004199 motif 3; other site 441768004200 Protein of unknown function (DUF4256); Region: DUF4256; pfam14066 441768004201 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 441768004202 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 441768004203 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 441768004204 Domain of unknown function (DUF1730); Region: DUF1730; pfam08331 441768004205 4Fe-4S double cluster binding domain; Region: Fer4_16; pfam13484 441768004206 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 441768004207 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 441768004208 intersubunit interface [polypeptide binding]; other site 441768004209 active site 441768004210 zinc binding site [ion binding]; other site 441768004211 Na+ binding site [ion binding]; other site 441768004212 CTP synthetase; Validated; Region: pyrG; PRK05380 441768004213 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 441768004214 Catalytic site [active] 441768004215 active site 441768004216 UTP binding site [chemical binding]; other site 441768004217 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 441768004218 active site 441768004219 putative oxyanion hole; other site 441768004220 catalytic triad [active] 441768004221 Tocopherol cyclase; Region: Tocopherol_cycl; cl14571 441768004222 DNA-directed RNA polymerase subunit delta; Reviewed; Region: PRK02363 441768004223 recombination protein RecR; Reviewed; Region: recR; PRK00076 441768004224 RecR protein; Region: RecR; pfam02132 441768004225 TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in Escherichia coli RecR. RecR participates in the RecFOR pathway of homologous recombinational repair in prokaryotes. This pathway provides a...; Region: TOPRIM_recR; cd01025 441768004226 putative active site [active] 441768004227 putative metal-binding site [ion binding]; other site 441768004228 tetramer interface [polypeptide binding]; other site 441768004229 hypothetical protein; Validated; Region: PRK00153 441768004230 DNA polymerase III subunits gamma and tau; Validated; Region: PRK05563 441768004231 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 441768004232 Walker A motif; other site 441768004233 ATP binding site [chemical binding]; other site 441768004234 Walker B motif; other site 441768004235 arginine finger; other site 441768004236 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 441768004237 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 441768004238 trmE is a tRNA modification GTPase; Region: trmE; cd04164 441768004239 G1 box; other site 441768004240 GTP/Mg2+ binding site [chemical binding]; other site 441768004241 Switch I region; other site 441768004242 G2 box; other site 441768004243 Switch II region; other site 441768004244 G3 box; other site 441768004245 G4 box; other site 441768004246 G5 box; other site 441768004247 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 441768004248 MgtC family; Region: MgtC; pfam02308 441768004249 DHH family; Region: DHH; pfam01368 441768004250 Exopolyphosphatase-related proteins [General function prediction only]; Region: COG0618 441768004251 DHHA1 domain; Region: DHHA1; pfam02272 441768004252 Exopolyphosphatase-related proteins [General function prediction only]; Region: COG0618 441768004253 DHH family; Region: DHH; pfam01368 441768004254 DHHA1 domain; Region: DHHA1; pfam02272 441768004255 Staphylococcal nuclease homologues; Region: SNc; smart00318 441768004256 Catalytic site; other site 441768004257 Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds; Region: SNc; cl00140 441768004258 ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; Region: UgpB; COG1653 441768004259 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 441768004260 ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]; Region: UgpE; COG0395 441768004261 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 441768004262 dimer interface [polypeptide binding]; other site 441768004263 conserved gate region; other site 441768004264 putative PBP binding loops; other site 441768004265 ABC-ATPase subunit interface; other site 441768004266 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 441768004267 dimer interface [polypeptide binding]; other site 441768004268 conserved gate region; other site 441768004269 putative PBP binding loops; other site 441768004270 ABC-ATPase subunit interface; other site 441768004271 ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]; Region: MalK; COG3839 441768004272 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 441768004273 Walker A/P-loop; other site 441768004274 ATP binding site [chemical binding]; other site 441768004275 Q-loop/lid; other site 441768004276 ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]; Region: MalK; COG3839 441768004277 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 441768004278 ABC transporter signature motif; other site 441768004279 Walker B; other site 441768004280 D-loop; other site 441768004281 H-loop/switch region; other site 441768004282 Integral membrane protein DUF92; Region: DUF92; pfam01940 441768004283 Trans-Isoprenyl Diphosphate Synthases, head-to-head; Region: Trans_IPPS_HH; cd00683 441768004284 active site lid residues [active] 441768004285 substrate binding pocket [chemical binding]; other site 441768004286 catalytic residues [active] 441768004287 substrate-Mg2+ binding site; other site 441768004288 aspartate-rich region 1; other site 441768004289 aspartate-rich region 2; other site 441768004290 phytoene desaturase; Region: crtI_fam; TIGR02734 441768004291 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 441768004292 Dolichol kinase [Lipid metabolism]; Region: SEC59; COG0170 441768004293 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 441768004294 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 441768004295 Walker A/P-loop; other site 441768004296 ATP binding site [chemical binding]; other site 441768004297 Q-loop/lid; other site 441768004298 ABC transporter signature motif; other site 441768004299 Walker B; other site 441768004300 D-loop; other site 441768004301 H-loop/switch region; other site 441768004302 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 441768004303 Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue per...; Region: GSH_Peroxidase; cd00340 441768004304 catalytic residues [active] 441768004305 dimer interface [polypeptide binding]; other site 441768004306 Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; Region: LytT; COG3279 441768004307 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 441768004308 active site 441768004309 phosphorylation site [posttranslational modification] 441768004310 intermolecular recognition site; other site 441768004311 dimerization interface [polypeptide binding]; other site 441768004312 LytTr DNA-binding domain; Region: LytTR; pfam04397 441768004313 Protein of unknown function (DUF1295); Region: DUF1295; cl17837 441768004314 Predicted kinase related to dihydroxyacetone kinase [General function prediction only]; Region: COG1461 441768004315 DAK2 domain; Region: Dak2; pfam02734 441768004316 EDD domain protein, DegV family; Region: DegV; TIGR00762 441768004317 Uncharacterized protein, DegV family COG1307; Region: DegV; pfam02645 441768004318 Predicted membrane protein (DUF2177); Region: DUF2177; pfam09945 441768004319 photolyase PhrII; Region: phr2; TIGR00591 441768004320 DNA photolyase; Region: DNA_photolyase; pfam00875 441768004321 asparaginyl-tRNA synthetase; Validated; Region: asnC; PRK03932 441768004322 EcAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli asparaginyl-tRNA synthetase (AsnRS) and, in Arabidopsis thaliana and Saccharomyces cerevisiae mitochondrial (mt) AsnRS. This domain is a beta-barrel domain (OB...; Region: EcAsnRS_like_N; cd04318 441768004323 putative dimer interface [polypeptide binding]; other site 441768004324 putative anticodon binding site; other site 441768004325 Asx tRNA synthetase (AspRS/AsnRS) class II core domain. Assignment to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs in the core domain. This family includes AsnRS as well as...; Region: AsxRS_core; cd00776 441768004326 homodimer interface [polypeptide binding]; other site 441768004327 motif 1; other site 441768004328 motif 2; other site 441768004329 active site 441768004330 motif 3; other site 441768004331 RmuC family; Region: RmuC; pfam02646 441768004332 Predicted RNA-binding protein [General function prediction only]; Region: Jag; COG1847 441768004333 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 441768004334 G-X-X-G motif; other site 441768004335 R3H domain found in proteins homologous to Bacillus subtilus Jag, which is associated with SpoIIIJ. SpoIIIJ is necessary for the third stage of sporulation. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine...; Region: R3H_jag; cd02644 441768004336 RxxxH motif; other site 441768004337 Preprotein translocase subunit YidC [Intracellular trafficking and secretion]; Region: YidC; COG0706 441768004338 60Kd inner membrane protein; Region: 60KD_IMP; pfam02096 441768004339 Ribonuclease P; Region: Ribonuclease_P; cl00457 441768004340 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399