-- dump date 20140620_033610 -- class Genbank::misc_feature -- table misc_feature_note -- id note 336407000001 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1806 336407000002 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 336407000003 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 336407000004 catalytic residues [active] 336407000005 ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagH; COG1134 336407000006 ATP-binding cassette component of polysaccharide transport system; Region: ABC_KpsT_Wzt; cd03220 336407000007 Walker A/P-loop; other site 336407000008 ATP binding site [chemical binding]; other site 336407000009 Q-loop/lid; other site 336407000010 ABC transporter signature motif; other site 336407000011 Walker B; other site 336407000012 D-loop; other site 336407000013 H-loop/switch region; other site 336407000014 ABC-type polysaccharide/polyol phosphate export systems, permease component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagG; COG1682 336407000015 ABC-2 type transporter; Region: ABC2_membrane; cl17235 336407000016 putative bifunctional glutamate synthase subunit beta/2-polyprenylphenol hydroxylase; Validated; Region: PRK06567 336407000017 Rickettsial palindromic element RPE4 domain; Region: RPE4; TIGR03777 336407000018 Rickettsial palindromic element RPE4 domain; Region: RPE4; TIGR03777 336407000019 FAD/NAD binding domain (electron transfer subunit) of dihydroorotate dehydrogenase-like proteins. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-dihydroorotate...; Region: DHOD_e_trans_like; cd06192 336407000020 FAD binding pocket [chemical binding]; other site 336407000021 FAD binding motif [chemical binding]; other site 336407000022 phosphate binding motif [ion binding]; other site 336407000023 NAD binding pocket [chemical binding]; other site 336407000024 Iron coordination center [ion binding]; other site 336407000025 SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]; Region: LexA; COG1974 336407000026 Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC...; Region: S24_LexA-like; cd06529 336407000027 Catalytic site [active] 336407000028 Predicted acyltransferases [Lipid metabolism]; Region: COG1835 336407000029 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 336407000030 Protein of unknown function (DUF1016); Region: DUF1016; pfam06250 336407000031 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 336407000032 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 336407000033 membrane protein insertase; Provisional; Region: PRK01318 336407000034 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 336407000035 Mechanosensitive ion channel; Region: MS_channel; pfam00924 336407000036 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 336407000037 prolipoprotein diacylglyceryl transferase; Reviewed; Region: PRK00052 336407000038 Uncharacterized conserved protein [Function unknown]; Region: COG1565 336407000039 Bacterial SH3 domain; Region: SH3_4; pfam06347 336407000040 Bacterial SH3 domain; Region: SH3_4; pfam06347 336407000041 glutathione-regulated potassium-efflux system protein KefB; Provisional; Region: PRK03659 336407000042 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 336407000043 TrkA-N domain; Region: TrkA_N; pfam02254 336407000044 Uncharacterized homolog of plant Iojap protein [Function unknown]; Region: COG0799 336407000045 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 336407000046 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 336407000047 metabolite-proton symporter; Region: 2A0106; TIGR00883 336407000048 putative substrate translocation pore; other site 336407000049 EamA-like transporter family; Region: EamA; pfam00892 336407000050 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 336407000051 EamA-like transporter family; Region: EamA; pfam00892 336407000052 Outer membrane protein W [Cell envelope biogenesis, outer membrane]; Region: OmpW; COG3047 336407000053 Transposase; Region: DEDD_Tnp_IS110; pfam01548 336407000054 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 336407000055 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 336407000056 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; COG1282 336407000057 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 336407000058 Protein of unknown function (DUF1013); Region: DUF1013; cl11533 336407000059 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 336407000060 Colicin V production protein; Region: Colicin_V; pfam02674 336407000061 Putative transcriptional regulator [Transcription]; Region: COG1678 336407000062 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 336407000063 SRP54-type protein, helical bundle domain; Region: SRP54_N; pfam02881 336407000064 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 336407000065 P loop; other site 336407000066 GTP binding site [chemical binding]; other site 336407000067 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 336407000068 SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c...; Region: SCO; cd02968 336407000069 Cu(I) binding site [ion binding]; other site 336407000070 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 336407000071 binding surface 336407000072 TPR motif; other site 336407000073 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK). Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and amino acids as well as formyl-tRNA. Mammalian cells are able to utilize pre-formed folates after...; Region: HPPK; cd00483 336407000074 catalytic center binding site [active] 336407000075 ATP binding site [chemical binding]; other site 336407000076 DHPS subgroup of Pterin binding enzymes. DHPS (dihydropteroate synthase), a functional homodimer, catalyzes the condensation of p-aminobenzoic acid (pABA) in the de novo biosynthesis of folate, which is an essential cofactor in both nucleic acid and...; Region: DHPS; cd00739 336407000077 dihydropteroate synthase; Region: DHPS; TIGR01496 336407000078 substrate binding pocket [chemical binding]; other site 336407000079 dimer interface [polypeptide binding]; other site 336407000080 inhibitor binding site; inhibition site 336407000081 Dihydrofolate reductase [Coenzyme metabolism]; Region: FolA; COG0262 336407000082 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 336407000083 folate binding site [chemical binding]; other site 336407000084 NADP+ binding site [chemical binding]; other site 336407000085 recombination protein F; Reviewed; Region: recF; PRK00064 336407000086 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 336407000087 Walker A/P-loop; other site 336407000088 ATP binding site [chemical binding]; other site 336407000089 Q-loop/lid; other site 336407000090 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 336407000091 ABC transporter signature motif; other site 336407000092 Walker B; other site 336407000093 D-loop; other site 336407000094 H-loop/switch region; other site 336407000095 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 336407000096 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 336407000097 trmE is a tRNA modification GTPase; Region: trmE; cd04164 336407000098 G1 box; other site 336407000099 GTP/Mg2+ binding site [chemical binding]; other site 336407000100 Switch I region; other site 336407000101 G2 box; other site 336407000102 Switch II region; other site 336407000103 G3 box; other site 336407000104 G4 box; other site 336407000105 G5 box; other site 336407000106 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 336407000107 NAD-specific glutamate dehydrogenase [Amino acid transport and metabolism]; Region: COG2902 336407000108 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Region: ELFV_dehydrog; smart00839 336407000109 NAD-specific glutamate dehydrogenase [Amino acid transport and metabolism]; Region: COG2902 336407000110 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]; Region: COG1426 336407000111 Helix-turn-helix domain; Region: HTH_25; pfam13413 336407000112 Cell division protein ZapA (stimulator of FtsZ polymerization and Z-ring component) [Cell cycle control, cell division, chromosome partitioning]; Region: zapA; COG3027 336407000113 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 336407000114 metabolite-proton symporter; Region: 2A0106; TIGR00883 336407000115 putative substrate translocation pore; other site 336407000116 Putative glycosyl/glycerophosphate transferases involved in teichoic acid biosynthesis TagF/TagB/EpsJ/RodC [Cell envelope biogenesis, outer membrane]; Region: TagB; COG1887 336407000117 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 336407000118 Rubrum transdehydrogenase NAD-binding and catalytic domains; Region: Rubrum_tdh; cd05304 336407000119 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 336407000120 ligand binding site [chemical binding]; other site 336407000121 homodimer interface [polypeptide binding]; other site 336407000122 NAD(P) binding site [chemical binding]; other site 336407000123 trimer interface B [polypeptide binding]; other site 336407000124 trimer interface A [polypeptide binding]; other site 336407000125 Outer membrane lipoprotein-sorting protein [Cell envelope biogenesis, outer membrane]; Region: LolA; COG2834 336407000126 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 336407000127 DNA polymerase III subunits gamma and tau; Validated; Region: PRK06645 336407000128 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 336407000129 Walker A motif; other site 336407000130 ATP binding site [chemical binding]; other site 336407000131 Walker B motif; other site 336407000132 arginine finger; other site 336407000133 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 336407000134 hypothetical protein; Validated; Region: PRK00153 336407000135 conserved hypothetical protein (putative transposase or invertase); Region: T_den_put_tspse; TIGR01784 336407000136 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 336407000137 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 336407000138 YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been...; Region: YdcF-like; cl00630 336407000139 lipoate-protein ligase B; Provisional; Region: PRK14347 336407000140 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 336407000141 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 336407000142 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 336407000143 Dolichol kinase [Lipid metabolism]; Region: SEC59; COG0170 336407000144 DNA primase, catalytic core; Region: dnaG; TIGR01391 336407000145 CHC2 zinc finger; Region: zf-CHC2; pfam01807 336407000146 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 336407000147 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 336407000148 active site 336407000149 metal binding site [ion binding]; metal-binding site 336407000150 interdomain interaction site; other site 336407000151 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 336407000152 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 336407000153 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 336407000154 Sigma-70, non-essential region; Region: Sigma70_ner; pfam04546 336407000155 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 336407000156 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 336407000157 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 336407000158 DNA binding residues [nucleotide binding] 336407000159 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 336407000160 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 336407000161 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 336407000162 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 336407000163 dimerization interface 3.5A [polypeptide binding]; other site 336407000164 active site 336407000165 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 336407000166 active site 336407000167 NTP binding site [chemical binding]; other site 336407000168 metal binding triad [ion binding]; metal-binding site 336407000169 Higher Eukarytoes and Prokaryotes Nucleotide-binding domain; Region: HEPN; smart00748 336407000170 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1636 336407000171 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 336407000172 putative transposase; Provisional; Region: PRK09857 336407000173 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 336407000174 metabolite-proton symporter; Region: 2A0106; TIGR00883 336407000175 putative substrate translocation pore; other site 336407000176 NLPC_P60 stabilising domain, N term; Region: N_NLPC_P60; pfam12912 336407000177 SH3 domain of the SH3b1 type; Region: SH3_6; pfam12913 336407000178 SH3 domain of SH3b2 type; Region: SH3_7; pfam12914 336407000179 NlpC/P60 family; Region: NLPC_P60; cl17555 336407000180 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 336407000181 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 336407000182 motif 1; other site 336407000183 active site 336407000184 motif 2; other site 336407000185 motif 3; other site 336407000186 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 336407000187 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 336407000188 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1; Region: PHP_PolIIIA_DnaE1; cd07433 336407000189 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 336407000190 putative active site [active] 336407000191 putative PHP Thumb interface [polypeptide binding]; other site 336407000192 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 336407000193 generic binding surface I; other site 336407000194 generic binding surface II; other site 336407000195 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 336407000196 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 336407000197 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; Region: UDPG_MGDP_dh_C; pfam03720 336407000198 Protein of unknown function; Region: DUF3971; pfam13116 336407000199 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 336407000200 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 336407000201 putative substrate translocation pore; other site 336407000202 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 336407000203 seryl-tRNA synthetase; Provisional; Region: PRK05431 336407000204 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 336407000205 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 336407000206 dimer interface [polypeptide binding]; other site 336407000207 active site 336407000208 motif 1; other site 336407000209 motif 2; other site 336407000210 motif 3; other site 336407000211 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 336407000212 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 336407000213 Integral membrane protein TerC family; Region: TerC; cl10468 336407000214 Methyltransferase domain; Region: Methyltransf_31; pfam13847 336407000215 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 336407000216 S-adenosylmethionine binding site [chemical binding]; other site 336407000217 Predicted regulatory domain of a methyltransferase [General function prediction only]; Region: COG4797 336407000218 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 336407000219 NADH dehydrogenase subunit 6; Provisional; Region: ND6; MTH00213 336407000220 NADH dehydrogenase subunit 6; Provisional; Region: ND6; MTH00213 336407000221 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 336407000222 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 336407000223 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 336407000224 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 336407000225 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 336407000226 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 336407000227 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13541 336407000228 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 336407000229 Walker A/P-loop; other site 336407000230 ATP binding site [chemical binding]; other site 336407000231 Q-loop/lid; other site 336407000232 ABC transporter signature motif; other site 336407000233 Walker B; other site 336407000234 D-loop; other site 336407000235 H-loop/switch region; other site 336407000236 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 336407000237 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 336407000238 dimerization interface [polypeptide binding]; other site 336407000239 DPS ferroxidase diiron center [ion binding]; other site 336407000240 ion pore; other site 336407000241 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06416 336407000242 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; pfam13450 336407000243 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 336407000244 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 336407000245 F0F1 ATP synthase subunit delta; Validated; Region: PRK05758 336407000246 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 336407000247 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 336407000248 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 336407000249 Walker A motif; other site 336407000250 ATP binding site [chemical binding]; other site 336407000251 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 336407000252 Walker B motif; other site 336407000253 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 336407000254 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 336407000255 core domain interface [polypeptide binding]; other site 336407000256 delta subunit interface [polypeptide binding]; other site 336407000257 epsilon subunit interface [polypeptide binding]; other site 336407000258 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 336407000259 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 336407000260 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 336407000261 alpha subunit interaction interface [polypeptide binding]; other site 336407000262 Walker A motif; other site 336407000263 ATP binding site [chemical binding]; other site 336407000264 Walker B motif; other site 336407000265 inhibitor binding site; inhibition site 336407000266 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 336407000267 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK01474 336407000268 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 336407000269 gamma subunit interface [polypeptide binding]; other site 336407000270 epsilon subunit interface [polypeptide binding]; other site 336407000271 LBP interface [polypeptide binding]; other site 336407000272 aconitate hydratase; Validated; Region: PRK09277 336407000273 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 336407000274 substrate binding site [chemical binding]; other site 336407000275 ligand binding site [chemical binding]; other site 336407000276 Aconitase A swivel domain. This is the major form of the TCA cycle enzyme aconitate hydratase, also known as aconitase and citrate hydro-lyase. It includes bacterial and archaeal aconitase A, and the eukaryotic cytosolic form of aconitase. This group...; Region: AcnA_IRP_Swivel; cd01580 336407000277 substrate binding site [chemical binding]; other site 336407000278 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 336407000279 conserved hypothetical protein (putative transposase or invertase); Region: T_den_put_tspse; TIGR01784 336407000280 Predicted membrane protein [Function unknown]; Region: COG3671 336407000281 NADH dehydrogenase subunit G; Validated; Region: PRK09130 336407000282 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 336407000283 catalytic loop [active] 336407000284 iron binding site [ion binding]; other site 336407000285 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 336407000286 MopB_Res_Cmplx1_Nad11: The second domain of the Nad11/75-kDa subunit of the NADH-quinone oxidoreductase/respiratory complex I/NADH dehydrogenase-1(NDH-1) of eukaryotes and the Nqo3/G subunit of alphaproteobacteria NDH-1. The NADH-quinone oxidoreductase...; Region: MopB_Res-Cmplx1_Nad11; cd02773 336407000287 Domain of unknown function (DUF1982); Region: DUF1982; pfam09326 336407000288 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 336407000289 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 336407000290 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 336407000291 4Fe-4S binding domain; Region: Fer4; cl02805 336407000292 4Fe-4S binding domain; Region: Fer4; pfam00037 336407000293 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 336407000294 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 336407000295 Walker A motif; other site 336407000296 ATP binding site [chemical binding]; other site 336407000297 Walker B motif; other site 336407000298 arginine finger; other site 336407000299 Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]; Region: PhrB; COG0415 336407000300 DNA photolyase; Region: DNA_photolyase; pfam00875 336407000301 Beta-lactamase class D [Defense mechanisms]; Region: COG2602 336407000302 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 336407000303 Transglycosylase; Region: Transgly; pfam00912 336407000304 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 336407000305 Antagonist of mitotic exit network protein 1; Region: AMN1; cl15308 336407000306 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 336407000307 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 336407000308 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 336407000309 FeS/SAM binding site; other site 336407000310 TRAM domain; Region: TRAM; pfam01938 336407000311 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 336407000312 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 336407000313 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 336407000314 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 336407000315 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 336407000316 dimer interface [polypeptide binding]; other site 336407000317 active site 336407000318 acyl carrier protein; Provisional; Region: acpP; PRK00982 336407000319 beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs; Region: BKR_SDR_c; cd05333 336407000320 NAD(P) binding site [chemical binding]; other site 336407000321 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 336407000322 homotetramer interface [polypeptide binding]; other site 336407000323 homodimer interface [polypeptide binding]; other site 336407000324 active site 336407000325 recombinase A; Provisional; Region: recA; PRK09354 336407000326 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 336407000327 hexamer interface [polypeptide binding]; other site 336407000328 Walker A motif; other site 336407000329 ATP binding site [chemical binding]; other site 336407000330 Walker B motif; other site 336407000331 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 336407000332 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 336407000333 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 336407000334 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 336407000335 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 336407000336 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 336407000337 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 336407000338 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 336407000339 DNA binding site [nucleotide binding] 336407000340 FxsA cytoplasmic membrane protein; Region: FxsA; cl01148 336407000341 The Delta9 Fatty Acid Desaturase (Delta9-FADS)-like CD includes the delta-9 and delta-11 acyl CoA desaturases found in various eukaryotes including vertebrates, insects, higher plants, and fungi. The delta-9 acyl-lipid desaturases are found in a wide...; Region: Delta9-FADS-like; cd03505 336407000342 Fatty acid desaturase; Region: FA_desaturase; pfam00487 336407000343 Di-iron ligands [ion binding]; other site 336407000344 TPR repeat; Region: TPR_11; pfam13414 336407000345 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 336407000346 TPR motif; other site 336407000347 TPR repeat; Region: TPR_11; pfam13414 336407000348 binding surface 336407000349 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 336407000350 TPR repeat; Region: TPR_11; pfam13414 336407000351 Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]; Region: OlmA; COG2913 336407000352 SmpA / OmlA family; Region: SmpA_OmlA; pfam04355 336407000353 Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]; Region: RpmF; COG0333 336407000354 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 336407000355 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 336407000356 dimer interface [polypeptide binding]; other site 336407000357 active site 336407000358 CoA binding pocket [chemical binding]; other site 336407000359 peptidoglycan-associated outer membrane lipoprotein; Provisional; Region: PRK10802 336407000360 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 336407000361 ligand binding site [chemical binding]; other site 336407000362 Predicted permeases [General function prediction only]; Region: COG0795 336407000363 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 336407000364 rod shape-determining protein MreB; Provisional; Region: PRK13927 336407000365 MreB and similar proteins; Region: MreB_like; cd10225 336407000366 nucleotide binding site [chemical binding]; other site 336407000367 Mg binding site [ion binding]; other site 336407000368 putative protofilament interaction site [polypeptide binding]; other site 336407000369 RodZ interaction site [polypeptide binding]; other site 336407000370 rod shape-determining protein MreC; Provisional; Region: PRK13922 336407000371 rod shape-determining protein MreC; Region: MreC; pfam04085 336407000372 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 336407000373 sequence-specific DNA binding site [nucleotide binding]; other site 336407000374 salt bridge; other site 336407000375 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 336407000376 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 336407000377 catalytic site [active] 336407000378 G-X2-G-X-G-K; other site 336407000379 Part of AAA domain; Region: AAA_19; pfam13245 336407000380 Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair]; Region: COG1112 336407000381 AAA domain; Region: AAA_12; pfam13087 336407000382 PIN domain of ribonucleases (toxins), VapC, FitB, and PAE0151 of bacterial and archaeal toxin/antitoxin-like operons, and other similar homologs; Region: PIN_VapC-like; cd09861 336407000383 putative active site [active] 336407000384 Antidote-toxin recognition MazE; Region: Antitoxin-MazE; cl00877 336407000385 acetyl-CoA acetyltransferase; Provisional; Region: PRK06633 336407000386 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 336407000387 dimer interface [polypeptide binding]; other site 336407000388 active site 336407000389 Poly(3-hydroxyalkanoate) synthetase [Lipid metabolism]; Region: PhaC; COG3243 336407000390 Uncharacterized conserved protein (DUF2048); Region: DUF2048; pfam09752 336407000391 TLC ATP/ADP transporter; Region: TLC; pfam03219 336407000392 Maf-like protein; Region: Maf; pfam02545 336407000393 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 336407000394 active site 336407000395 dimer interface [polypeptide binding]; other site 336407000396 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 336407000397 rRNA binding site [nucleotide binding]; other site 336407000398 predicted 30S ribosome binding site; other site 336407000399 Autotransporter beta-domain; Region: Autotransporter; smart00869 336407000400 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 336407000401 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 336407000402 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 336407000403 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 336407000404 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 336407000405 Membrane transporters of cations and cationic drugs [Inorganic ion transport and metabolism]; Region: EmrE; COG2076 336407000406 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 336407000407 Sulfatase; Region: Sulfatase; pfam00884 336407000408 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 336407000409 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 336407000410 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 336407000411 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 336407000412 Transposase; Region: DEDD_Tnp_IS110; pfam01548 336407000413 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 336407000414 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 336407000415 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 336407000416 active site 336407000417 hypothetical protein; Reviewed; Region: PRK00024 336407000418 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 336407000419 MPN+ (JAMM) motif; other site 336407000420 Zinc-binding site [ion binding]; other site 336407000421 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 336407000422 The members of this subfamily catalyze the formation of a phosphodiester bond between a membrane-associated undecaprenyl-phosphate (Und-P) molecule and N-acetylhexosamine 1-phosphate, which is usually donated by a soluble UDP-N-acetylhexosamine precursor; Region: GT_WbpL_WbcO_like; cd06854 336407000423 Mg++ binding site [ion binding]; other site 336407000424 putative catalytic motif [active] 336407000425 putative substrate binding site [chemical binding]; other site 336407000426 Protein of unknown function (DUF721); Region: DUF721; pfam05258 336407000427 Hydrolases of the alpha/beta superfamily [General function prediction only]; Region: COG1073 336407000428 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 336407000429 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 336407000430 dimer interface [polypeptide binding]; other site 336407000431 ssDNA binding site [nucleotide binding]; other site 336407000432 tetramer (dimer of dimers) interface [polypeptide binding]; other site 336407000433 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 336407000434 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 336407000435 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 336407000436 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 336407000437 AAA domain; Region: AAA_14; pfam13173 336407000438 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 336407000439 ABC-type metal ion transport system, periplasmic component/surface adhesin [Inorganic ion transport and metabolism]; Region: LraI; COG0803 336407000440 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 336407000441 intersubunit interface [polypeptide binding]; other site 336407000442 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 336407000443 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 336407000444 active site 336407000445 NTP binding site [chemical binding]; other site 336407000446 metal binding triad [ion binding]; metal-binding site 336407000447 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 336407000448 Competence protein; Region: Competence; pfam03772 336407000449 Predicted membrane metal-binding protein [General function prediction only]; Region: ComEC; COG0658 336407000450 Domain of unknown function (DUF4131); Region: DUF4131; pfam13567 336407000451 Competence protein; Region: Competence; pfam03772 336407000452 Autotransporter beta-domain; Region: Autotransporter; pfam03797 336407000453 SurA N-terminal domain; Region: SurA_N_3; cl07813 336407000454 Parvulin-like peptidyl-prolyl isomerase [Posttranslational modification, protein turnover, chaperones]; Region: SurA; COG0760 336407000455 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 336407000456 3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases [Coenzyme metabolism]; Region: UbiD; COG0043 336407000457 Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus; Region: PhaC_N; pfam07167 336407000458 Poly(3-hydroxyalkanoate) synthetase [Lipid metabolism]; Region: PhaC; COG3243 336407000459 Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar proteins; Region: PLDc_Nuc; cd09170 336407000460 PLD-like domain; Region: PLDc_2; pfam13091 336407000461 putative active site [active] 336407000462 catalytic site [active] 336407000463 Phasin protein; Region: Phasin_2; pfam09361 336407000464 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 336407000465 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 336407000466 active site 336407000467 DNA binding site [nucleotide binding] 336407000468 Int/Topo IB signature motif; other site 336407000469 RNA polymerase-binding protein DksA; Region: dksA; TIGR02420 336407000470 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 336407000471 Peroxiredoxin (PRX) family, Bacterioferritin comigratory protein (BCP) subfamily; composed of thioredoxin-dependent thiol peroxidases, widely expressed in pathogenic bacteria, that protect cells against toxicity from reactive oxygen species by reducing...; Region: PRX_BCP; cd03017 336407000472 catalytic triad [active] 336407000473 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 336407000474 IHF dimer interface [polypeptide binding]; other site 336407000475 IHF - DNA interface [nucleotide binding]; other site 336407000476 Beta-glucosidase-related glycosidases [Carbohydrate transport and metabolism]; Region: BglX; COG1472 336407000477 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 336407000478 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 336407000479 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 336407000480 synthetase active site [active] 336407000481 NTP binding site [chemical binding]; other site 336407000482 metal binding site [ion binding]; metal-binding site 336407000483 Rickettsia outer membrane protein B; Region: rOmpB; pfam12334 336407000484 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 336407000485 Autotransporter beta-domain; Region: Autotransporter; smart00869 336407000486 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 336407000487 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 336407000488 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 336407000489 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 336407000490 putative acyl-acceptor binding pocket; other site 336407000491 Tetratricopeptide repeat; Region: TPR_12; pfam13424 336407000492 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 336407000493 Peptidase family M23; Region: Peptidase_M23; pfam01551 336407000494 Protein involved in catabolism of external DNA [General function prediction only]; Region: ComJ; COG2961 336407000495 methyltransferase, FkbM family; Region: fkbM_fam; TIGR01444 336407000496 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 336407000497 Virulence protein RhuM family; Region: Virulence_RhuM; pfam13310 336407000498 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 336407000499 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 336407000500 nucleotide binding pocket [chemical binding]; other site 336407000501 K-X-D-G motif; other site 336407000502 catalytic site [active] 336407000503 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 336407000504 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 336407000505 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 336407000506 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 336407000507 Dimer interface [polypeptide binding]; other site 336407000508 BRCT sequence motif; other site 336407000509 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 336407000510 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 336407000511 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]; Region: CcmF; COG1138 336407000512 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 336407000513 Domain of unknown function DUF21; Region: DUF21; pfam01595 336407000514 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 336407000515 Transporter associated domain; Region: CorC_HlyC; pfam03471 336407000516 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 336407000517 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 336407000518 Walker A/P-loop; other site 336407000519 ATP binding site [chemical binding]; other site 336407000520 Q-loop/lid; other site 336407000521 ABC transporter signature motif; other site 336407000522 Walker B; other site 336407000523 D-loop; other site 336407000524 H-loop/switch region; other site 336407000525 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 336407000526 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 336407000527 FtsX-like permease family; Region: FtsX; pfam02687 336407000528 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 336407000529 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 336407000530 putative substrate translocation pore; other site 336407000531 Protein of unknown function (DUF2673); Region: DUF2673; pfam10880 336407000532 Transposase; Region: DEDD_Tnp_IS110; pfam01548 336407000533 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 336407000534 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 336407000535 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 336407000536 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 336407000537 S-adenosylmethionine binding site [chemical binding]; other site 336407000538 Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: ExoIII-like_AP-endo; cd09086 336407000539 putative catalytic site [active] 336407000540 putative phosphate binding site [ion binding]; other site 336407000541 active site 336407000542 metal binding site A [ion binding]; metal-binding site 336407000543 DNA binding site [nucleotide binding] 336407000544 putative AP binding site [nucleotide binding]; other site 336407000545 putative metal binding site B [ion binding]; other site 336407000546 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 336407000547 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 336407000548 substrate binding pocket [chemical binding]; other site 336407000549 membrane-bound complex binding site; other site 336407000550 hinge residues; other site 336407000551 Exonuclease VII, large subunit [DNA replication, recombination, and repair]; Region: XseA; COG1570 336407000552 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 336407000553 generic binding surface II; other site 336407000554 generic binding surface I; other site 336407000555 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 336407000556 Organic solvent tolerance protein; Region: OstA_C; pfam04453 336407000557 SurA N-terminal domain; Region: SurA_N_3; cl07813 336407000558 Uncharacterized conserved protein [Function unknown]; Region: COG4095 336407000559 GTP-binding protein Der; Reviewed; Region: PRK00093 336407000560 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 336407000561 G1 box; other site 336407000562 GTP/Mg2+ binding site [chemical binding]; other site 336407000563 Switch I region; other site 336407000564 G2 box; other site 336407000565 Switch II region; other site 336407000566 G3 box; other site 336407000567 G4 box; other site 336407000568 G5 box; other site 336407000569 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 336407000570 G1 box; other site 336407000571 GTP/Mg2+ binding site [chemical binding]; other site 336407000572 Switch I region; other site 336407000573 G2 box; other site 336407000574 G3 box; other site 336407000575 Switch II region; other site 336407000576 G4 box; other site 336407000577 G5 box; other site 336407000578 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 336407000579 Transposase; Region: DEDD_Tnp_IS110; pfam01548 336407000580 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 336407000581 Higher Eukarytoes and Prokaryotes Nucleotide-binding domain; Region: HEPN; smart00748 336407000582 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 336407000583 RNA binding site [nucleotide binding]; other site 336407000584 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 336407000585 Ribonuclease E/G family; Region: RNase_E_G; pfam10150 336407000586 Major Facilitator Superfamily; Region: MFS_1; pfam07690 336407000587 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 336407000588 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 336407000589 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 336407000590 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 336407000591 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 336407000592 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 336407000593 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 336407000594 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 336407000595 23S rRNA interface [nucleotide binding]; other site 336407000596 L3 interface [polypeptide binding]; other site 336407000597 PQQ-dependent dehydrogenases and related proteins; Region: PQQ_DH_like; cl11493 336407000598 Trp docking motif [polypeptide binding]; other site 336407000599 active site 336407000600 PQQ-like domain; Region: PQQ_2; pfam13360 336407000601 Protein of unknown function (DUF2659); Region: DUF2659; pfam10858 336407000602 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1729 336407000603 Tetratricopeptide repeat; Region: TPR_6; pfam13174 336407000604 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 336407000605 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 336407000606 dimer interface [polypeptide binding]; other site 336407000607 phosphorylation site [posttranslational modification] 336407000608 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 336407000609 ATP binding site [chemical binding]; other site 336407000610 Mg2+ binding site [ion binding]; other site 336407000611 G-X-G motif; other site 336407000612 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 336407000613 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 336407000614 PDZ domain of C-terminal processing-, tail-specific-, and tricorn proteases, which function in posttranslational protein processing, maturation, and disassembly or degradation, in Bacteria, Archaea, and plant chloroplasts. May be responsible for...; Region: PDZ_CTP_protease; cd00988 336407000615 protein binding site [polypeptide binding]; other site 336407000616 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 336407000617 Catalytic dyad [active] 336407000618 DNA topoisomerase IV subunit B; Reviewed; Region: PRK05559 336407000619 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 336407000620 ATP binding site [chemical binding]; other site 336407000621 Mg2+ binding site [ion binding]; other site 336407000622 G-X-G motif; other site 336407000623 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 336407000624 anchoring element; other site 336407000625 dimer interface [polypeptide binding]; other site 336407000626 ATP binding site [chemical binding]; other site 336407000627 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 336407000628 active site 336407000629 metal binding site [ion binding]; metal-binding site 336407000630 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 336407000631 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 336407000632 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 336407000633 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 336407000634 Transposase; Region: DEDD_Tnp_IS110; pfam01548 336407000635 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 336407000636 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 336407000637 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3827 336407000638 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 336407000639 Protein of unknown function (DUF2660); Region: DUF2660; pfam10859 336407000640 thymidylate kinase; Validated; Region: tmk; PRK00698 336407000641 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 336407000642 TMP-binding site; other site 336407000643 ATP-binding site [chemical binding]; other site 336407000644 methionyl-tRNA synthetase; Reviewed; Region: PRK11893 336407000645 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 336407000646 HIGH motif; other site 336407000647 active site 336407000648 KMSKS motif; other site 336407000649 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 336407000650 tRNA binding surface [nucleotide binding]; other site 336407000651 anticodon binding site; other site 336407000652 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 336407000653 active site 336407000654 Protein of unknown function (DUF511); Region: DUF511; cl01114 336407000655 Protein of unknown function (DUF511); Region: DUF511; cl01114 336407000656 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 336407000657 Cupin domain; Region: Cupin_2; cl17218 336407000658 Mannose-1-phosphate guanylyltransferase [Cell envelope biogenesis, outer membrane]; Region: {ManC}; COG0836 336407000659 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 336407000660 active site 336407000661 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 336407000662 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 336407000663 DNA binding site [nucleotide binding] 336407000664 catalytic residue [active] 336407000665 H2TH interface [polypeptide binding]; other site 336407000666 putative catalytic residues [active] 336407000667 turnover-facilitating residue; other site 336407000668 intercalation triad [nucleotide binding]; other site 336407000669 8OG recognition residue [nucleotide binding]; other site 336407000670 putative reading head residues; other site 336407000671 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 336407000672 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 336407000673 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 336407000674 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 336407000675 S-adenosylmethionine binding site [chemical binding]; other site 336407000676 2-polyprenylphenol 6-hydroxylase; Region: UbiB; TIGR01982 336407000677 ABC1 family; Region: ABC1; pfam03109 336407000678 Aminoglycoside 3'-phosphotransferase (APH) and Choline Kinase (ChoK) family. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs)...; Region: APH_ChoK_like; cd05120 336407000679 active site 336407000680 ATP binding site [chemical binding]; other site 336407000681 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 336407000682 AAA domain; Region: AAA_14; pfam13173 336407000683 Predicted transcription regulator containing HTH domain [Transcription]; Region: COG5499 336407000684 Transposase; Region: DEDD_Tnp_IS110; pfam01548 336407000685 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 336407000686 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 336407000687 Serine hydrolase; Region: Ser_hydrolase; cl17834 336407000688 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 336407000689 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 336407000690 Cytochrome oxidase assembly protein; Region: COX15-CtaA; cl15852 336407000691 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 336407000692 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 336407000693 RNA binding surface [nucleotide binding]; other site 336407000694 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 336407000695 active site 336407000696 Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; Region: AmpC; COG1680 336407000697 Beta-lactamase; Region: Beta-lactamase; pfam00144 336407000698 Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: ExoIII-like_AP-endo; cd09086 336407000699 putative catalytic site [active] 336407000700 putative phosphate binding site [ion binding]; other site 336407000701 active site 336407000702 metal binding site A [ion binding]; metal-binding site 336407000703 DNA binding site [nucleotide binding] 336407000704 putative AP binding site [nucleotide binding]; other site 336407000705 putative metal binding site B [ion binding]; other site 336407000706 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 336407000707 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 336407000708 tetramer interface [polypeptide binding]; other site 336407000709 TPP-binding site [chemical binding]; other site 336407000710 heterodimer interface [polypeptide binding]; other site 336407000711 phosphorylation loop region [posttranslational modification] 336407000712 pyruvate dehydrogenase subunit beta; Validated; Region: PRK09212 336407000713 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 336407000714 alpha subunit interface [polypeptide binding]; other site 336407000715 TPP binding site [chemical binding]; other site 336407000716 heterodimer interface [polypeptide binding]; other site 336407000717 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 336407000718 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 336407000719 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 336407000720 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 336407000721 AAA domain; Region: AAA_14; pfam13173 336407000722 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 336407000723 TolQ protein; Region: tolQ; TIGR02796 336407000724 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 336407000725 TolR protein; Region: tolR; TIGR02801 336407000726 Gram-negative bacterial tonB protein; Region: TonB; cl10048 336407000727 translocation protein TolB; Provisional; Region: tolB; PRK05137 336407000728 TolB amino-terminal domain; Region: TolB_N; pfam04052 336407000729 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 336407000730 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 336407000731 Triacylglycerol lipase-like subfamily of the SGNH hydrolases, 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...; Region: Triacylglycerol_lipase_like; cd01847 336407000732 active site 336407000733 catalytic triad [active] 336407000734 oxyanion hole [active] 336407000735 Autotransporter beta-domain; Region: Autotransporter; smart00869 336407000736 Transposase; Region: DEDD_Tnp_IS110; pfam01548 336407000737 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 336407000738 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 336407000739 Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily; Region: CE4_SF; cl15692 336407000740 Protein of unknown function (DUF1460); Region: DUF1460; pfam07313 336407000741 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 336407000742 Protein of unknown function (DUF1460); Region: DUF1460; pfam07313 336407000743 FAD-dependent thymidylate synthase; Reviewed; Region: thyX; PRK00847 336407000744 Protein of unknown function DUF45; Region: DUF45; pfam01863 336407000745 Peptidase family M23; Region: Peptidase_M23; pfam01551 336407000746 ribose-5-phosphate isomerase B; Provisional; Region: PRK05571 336407000747 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 336407000748 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 336407000749 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 336407000750 ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]; Region: CbiO; COG1122 336407000751 Walker A/P-loop; other site 336407000752 ATP binding site [chemical binding]; other site 336407000753 Q-loop/lid; other site 336407000754 ABC transporter signature motif; other site 336407000755 Walker B; other site 336407000756 D-loop; other site 336407000757 H-loop/switch region; other site 336407000758 Transposase; Region: DEDD_Tnp_IS110; pfam01548 336407000759 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 336407000760 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 336407000761 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 336407000762 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 336407000763 G1 box; other site 336407000764 putative GEF interaction site [polypeptide binding]; other site 336407000765 GTP/Mg2+ binding site [chemical binding]; other site 336407000766 Switch I region; other site 336407000767 G2 box; other site 336407000768 G3 box; other site 336407000769 Switch II region; other site 336407000770 G4 box; other site 336407000771 G5 box; other site 336407000772 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 336407000773 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 336407000774 HAD-hyrolase-like; Region: Hydrolase_like; pfam13242 336407000775 Outer membrane protein (OmpH-like); Region: OmpH; smart00935 336407000776 isocitrate dehydrogenase; Validated; Region: PRK09222 336407000777 Isocitrate/isopropylmalate dehydrogenase [Amino acid transport and metabolism]; Region: LeuB; COG0473 336407000778 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 336407000779 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 336407000780 Recombination protein O N terminal; Region: RecO_N; pfam11967 336407000781 Recombination protein O C terminal; Region: RecO_C; pfam02565 336407000782 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 336407000783 Methyltransferase domain; Region: Methyltransf_31; pfam13847 336407000784 S-adenosylmethionine binding site [chemical binding]; other site 336407000785 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 336407000786 DHH family; Region: DHH; pfam01368 336407000787 DHHA1 domain; Region: DHHA1; pfam02272 336407000788 peptide chain release factor 1; Validated; Region: prfA; PRK00591 336407000789 This domain is found in peptide chain release factors; Region: PCRF; smart00937 336407000790 RF-1 domain; Region: RF-1; pfam00472 336407000791 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 336407000792 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; Region: PDHac_trf_mito; TIGR01349 336407000793 E3 interaction surface; other site 336407000794 lipoyl attachment site [posttranslational modification]; other site 336407000795 e3 binding domain; Region: E3_binding; pfam02817 336407000796 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 336407000797 translation initiation factor IF-3; Reviewed; Region: infC; PRK00028 336407000798 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 336407000799 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 336407000800 Predicted membrane protein [Function unknown]; Region: COG5346 336407000801 Uncharacterized conserved protein (DUF2163); Region: DUF2163; pfam09931 336407000802 phage conserved hypothetical protein BR0599; Region: phg_TIGR02218 336407000803 Phage conserved hypothetical protein BR0599; Region: Phage_BR0599; pfam09356 336407000804 Conserved hypothetical protein 2217 (DUF2460); Region: DUF2460; pfam09343 336407000805 Nucleotidyltransferase substrate binding protein like; Region: NTase_sub_bind; pfam08780 336407000806 Protein of unknown function (DUF3168); Region: DUF3168; pfam11367 336407000807 Phage head-tail joining protein; Region: Phage_H_T_join; pfam05521 336407000808 phage conserved hypothetical protein, phiE125 gp8 family; Region: phage_chp_gp8; TIGR02215 336407000809 Head-Tail Connector Protein gp6 of Bacteriophage HK97 and similar proteins; Region: gp6; cd08054 336407000810 oligomerization interface [polypeptide binding]; other site 336407000811 Caudovirus prohead protease; Region: Peptidase_U35; pfam04586 336407000812 phage major capsid protein, HK97 family; Region: major_cap_HK97; TIGR01554 336407000813 Phage capsid family; Region: Phage_capsid; pfam05065 336407000814 Domain of unknown function (DUF3576); Region: DUF3576; pfam12100 336407000815 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 336407000816 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 336407000817 HIGH motif; other site 336407000818 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 336407000819 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 336407000820 active site 336407000821 KMSKS motif; other site 336407000822 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 336407000823 tRNA binding surface [nucleotide binding]; other site 336407000824 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 336407000825 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 336407000826 active site 336407000827 phosphorylation site [posttranslational modification] 336407000828 intermolecular recognition site; other site 336407000829 dimerization interface [polypeptide binding]; other site 336407000830 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 336407000831 Walker A motif; other site 336407000832 ATP binding site [chemical binding]; other site 336407000833 Walker B motif; other site 336407000834 arginine finger; other site 336407000835 Bacterial regulatory protein, Fis family; Region: HTH_8; cl17420 336407000836 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 336407000837 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 336407000838 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 336407000839 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 336407000840 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 336407000841 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 336407000842 M61 glycyl aminopeptidase; Region: Peptidase_M61; pfam05299 336407000843 Predicted protease with the C-terminal PDZ domain [General function prediction only]; Region: COG3975 336407000844 DNA repair protein RadA; Provisional; Region: PRK11823 336407000845 Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of...; Region: Sms; cd01121 336407000846 Walker A motif/ATP binding site; other site 336407000847 ATP binding site [chemical binding]; other site 336407000848 Walker B motif; other site 336407000849 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 336407000850 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 336407000851 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 336407000852 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 336407000853 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 336407000854 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 336407000855 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 336407000856 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 336407000857 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 336407000858 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 336407000859 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 336407000860 S-adenosylmethionine binding site [chemical binding]; other site 336407000861 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 336407000862 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 336407000863 RNA binding surface [nucleotide binding]; other site 336407000864 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 336407000865 active site 336407000866 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 336407000867 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 336407000868 Predicted periplasmic or secreted lipoprotein [General function prediction only]; Region: OsmY; COG2823 336407000869 BON domain; Region: BON; pfam04972 336407000870 BON domain; Region: BON; pfam04972 336407000871 intracellular septation protein A; Reviewed; Region: PRK00259 336407000872 Iron permease FTR1 family; Region: FTR1; cl00475 336407000873 Cupredoxin-like domain; Region: Cupredoxin_1; pfam13473 336407000874 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 336407000875 Transposase; Region: DEDD_Tnp_IS110; pfam01548 336407000876 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 336407000877 Protocatechuate 3,4-dioxygenase beta subunit [Secondary metabolites biosynthesis, transport, and catabolism]; Region: PcaH; COG3485 336407000878 Intradiol dioxygenases catalyze the critical ring-cleavage step in the conversion of catecholate derivatives to citric acid cycle intermediates. This family contains catechol 1,2-dioxygenases and protocatechuate 3,4-dioxygenases which are mononuclear...; Region: intradiol_dioxygenase; cl17208 336407000879 active site 336407000880 TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a...; Region: TlpA_like_family; cd02966 336407000881 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 336407000882 catalytic residues [active] 336407000883 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 336407000884 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 336407000885 tandem repeat interface [polypeptide binding]; other site 336407000886 oligomer interface [polypeptide binding]; other site 336407000887 active site residues [active] 336407000888 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 336407000889 trimer interface [polypeptide binding]; other site 336407000890 active site 336407000891 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214 336407000892 Glycoprotease family; Region: Peptidase_M22; pfam00814 336407000893 von Willebrand factor (vWF) type A domain; Region: VWA; smart00327 336407000894 metal ion-dependent adhesion site (MIDAS); other site 336407000895 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 336407000896 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 336407000897 tetramerization interface [polypeptide binding]; other site 336407000898 NAD(P) binding site [chemical binding]; other site 336407000899 catalytic residues [active] 336407000900 Transposase; Region: DEDD_Tnp_IS110; pfam01548 336407000901 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 336407000902 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 336407000903 Solute carrier 5 family, sodium/glucose transporters and related proteins; solute-binding domain; Region: SLC5sbd; cd10322 336407000904 Na binding site [ion binding]; other site 336407000905 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 336407000906 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 336407000907 dimer interface [polypeptide binding]; other site 336407000908 phosphorylation site [posttranslational modification] 336407000909 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 336407000910 ATP binding site [chemical binding]; other site 336407000911 Mg2+ binding site [ion binding]; other site 336407000912 G-X-G motif; other site 336407000913 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 336407000914 dimer interface [polypeptide binding]; other site 336407000915 catalytic triad [active] 336407000916 Peptidase MA superfamily; Region: Peptidase_MA_2; pfam13485 336407000917 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 336407000918 Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12. HMBS catalyzes the conversion of...; Region: HMBS; cd00494 336407000919 domain interfaces; other site 336407000920 active site 336407000921 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 336407000922 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 336407000923 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 336407000924 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 336407000925 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 336407000926 dimer interface [polypeptide binding]; other site 336407000927 anticodon binding site; other site 336407000928 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of...; Region: AspRS_core; cd00777 336407000929 homodimer interface [polypeptide binding]; other site 336407000930 motif 1; other site 336407000931 active site 336407000932 motif 2; other site 336407000933 GAD domain; Region: GAD; pfam02938 336407000934 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 336407000935 active site 336407000936 motif 3; other site 336407000937 ATPase MipZ; Region: MipZ; pfam09140 336407000938 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 336407000939 P-loop; other site 336407000940 Magnesium ion binding site [ion binding]; other site 336407000941 multifunctional aminopeptidase A; Provisional; Region: PRK00913 336407000942 Cytosol aminopeptidase family, N-terminal and catalytic domains. Family M17 contains zinc- and manganese-dependent exopeptidases ( EC 3.4.11.1), including leucine aminopeptidase. They catalyze removal of amino acids from the N-terminus of a protein and...; Region: Peptidase_M17; cd00433 336407000943 interface (dimer of trimers) [polypeptide binding]; other site 336407000944 Substrate-binding/catalytic site; other site 336407000945 Zn-binding sites [ion binding]; other site 336407000946 Autotransporter beta-domain; Region: Autotransporter; smart00869 336407000947 Autotransporter beta-domain; Region: Autotransporter; pfam03797 336407000948 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 336407000949 Ankyrin repeats (many copies); Region: Ank_5; pfam13857 336407000950 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 336407000951 Part of AAA domain; Region: AAA_19; pfam13245 336407000952 UvrD/REP helicase N-terminal domain; Region: UvrD-helicase; pfam00580 336407000953 UvrD-like helicase C-terminal domain; Region: UvrD_C; pfam13361 336407000954 Family description; Region: UvrD_C_2; pfam13538 336407000955 SURF1 superfamily. Surf1/Shy1 has been implicated in the posttranslational steps of the biogenesis of the mitochondrially-encoded Cox1 subunit of cytochrome c oxidase (complex IV). Cytochrome c oxidase (complex IV), the terminal electron-transferring...; Region: SURF1; cd06662 336407000956 Uncharacterized conserved protein [Function unknown]; Region: COG4278 336407000957 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 336407000958 DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins; Region: DNA_pol_III_epsilon_Ecoli_like; cd06131 336407000959 active site 336407000960 catalytic site [active] 336407000961 substrate binding site [chemical binding]; other site 336407000962 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 336407000963 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 336407000964 CoA-binding site [chemical binding]; other site 336407000965 ATP-binding [chemical binding]; other site 336407000966 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3494 336407000967 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3814 336407000968 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 336407000969 RNA/DNA hybrid binding site [nucleotide binding]; other site 336407000970 active site 336407000971 hypothetical protein; Provisional; Region: PRK06630 336407000972 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 336407000973 mce related protein; Region: MCE; pfam02470 336407000974 GIY-YIG nuclease domain superfamily; Region: GIY-YIG_SF; cl15257 336407000975 catalytic site [active] 336407000976 metal binding site [ion binding]; metal-binding site 336407000977 UvrB/uvrC motif; Region: UVR; pfam02151 336407000978 Domain of unknown function (DUF4385); Region: DUF4385; pfam14328 336407000979 Bacterial protein of unknown function (DUF883); Region: DUF883; cl01888 336407000980 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 336407000981 Domain of Unknown Function (DUF1543); Region: DUF1543; pfam07566 336407000982 IS1 transposase; Region: DDE_Tnp_IS1; cl00721 336407000983 Aminoglycoside/hydroxyurea antibiotic resistance kinase; Region: APH_6_hur; cl17810 336407000984 Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: CitB; COG2197 336407000985 C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many...; Region: LuxR_C_like; cd06170 336407000986 DNA binding residues [nucleotide binding] 336407000987 dimerization interface [polypeptide binding]; other site 336407000988 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 336407000989 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 336407000990 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 336407000991 Walker A/P-loop; other site 336407000992 ATP binding site [chemical binding]; other site 336407000993 Q-loop/lid; other site 336407000994 ABC transporter signature motif; other site 336407000995 Walker B; other site 336407000996 D-loop; other site 336407000997 H-loop/switch region; other site 336407000998 Mechanosensitive ion channel; Region: MS_channel; pfam00924 336407000999 AAA domain; Region: AAA_14; pfam13173 336407001000 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 336407001001 Autotransporter beta-domain; Region: Autotransporter; pfam03797 336407001002 ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]; Region: Uup; COG0488 336407001003 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 336407001004 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 336407001005 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 336407001006 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 336407001007 Walker A/P-loop; other site 336407001008 ATP binding site [chemical binding]; other site 336407001009 Q-loop/lid; other site 336407001010 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 336407001011 ABC transporter signature motif; other site 336407001012 Walker B; other site 336407001013 D-loop; other site 336407001014 ABC transporter; Region: ABC_tran_2; pfam12848 336407001015 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 336407001016 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 336407001017 MutS domain I; Region: MutS_I; pfam01624 336407001018 MutS domain II; Region: MutS_II; pfam05188 336407001019 MutS domain III; Region: MutS_III; pfam05192 336407001020 ATP-binding cassette domain of MutS1 homolog; Region: ABC_MutS1; cd03284 336407001021 Walker A/P-loop; other site 336407001022 ATP binding site [chemical binding]; other site 336407001023 Q-loop/lid; other site 336407001024 ABC transporter signature motif; other site 336407001025 Walker B; other site 336407001026 D-loop; other site 336407001027 H-loop/switch region; other site 336407001028 Arginase-like and histone-like hydrolases; Region: Arginase_HDAC; cl17011 336407001029 Alkyladenine DNA glycosylase catalyzes the first step in base excision repair; Region: AAG; cd00540 336407001030 active site 336407001031 DNA binding site [nucleotide binding] 336407001032 Haemolytic domain; Region: Haemolytic; cl00506 336407001033 NADH dehydrogenase subunit E; Validated; Region: PRK07539 336407001034 TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes; Region: TRX_Fd_NuoE; cd03064 336407001035 putative dimer interface [polypeptide binding]; other site 336407001036 [2Fe-2S] cluster binding site [ion binding]; other site 336407001037 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; Region: GIY-YIG_unchar_3; cd10448 336407001038 GIY-YIG motif/motif A; other site 336407001039 putative active site [active] 336407001040 putative metal binding site [ion binding]; other site 336407001041 NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]; Region: NuoD; COG0649 336407001042 NADH dehydrogenase subunit D; Validated; Region: PRK06075 336407001043 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 336407001044 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 336407001045 NADH dehydrogenase subunit B; Validated; Region: PRK06411 336407001046 NADH:ubiquinone oxidoreductase subunit A; Validated; Region: PRK06602 336407001047 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 336407001048 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4765 336407001049 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5410 336407001050 Terminase-like family; Region: Terminase_6; pfam03237 336407001051 Phage-related terminase [General function prediction only]; Region: COG5362 336407001052 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 336407001053 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 336407001054 ATP binding site [chemical binding]; other site 336407001055 putative Mg++ binding site [ion binding]; other site 336407001056 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 336407001057 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 336407001058 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 336407001059 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 336407001060 HsdM N-terminal domain; Region: HsdM_N; pfam12161 336407001061 Methyltransferase domain; Region: Methyltransf_26; pfam13659 336407001062 S-adenosylmethionine binding site [chemical binding]; other site 336407001063 4-hydroxybenzoate polyprenyltransferase; Reviewed; Region: ubiA; PRK12847 336407001064 UbiA prenyltransferase family; Region: UbiA; pfam01040 336407001065 Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond...; Region: LRR_RI; cl15309 336407001066 lysozyme_like domain. This contains several members including Soluble Lytic Transglycosylases (SLT), Goose Egg-White Lysozymes (GEWL), Hen Egg-White Lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases; Region: lysozyme_like; cl00222 336407001067 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 336407001068 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 336407001069 oligomer interface [polypeptide binding]; other site 336407001070 active site residues [active] 336407001071 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 336407001072 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 336407001073 RNA binding site [nucleotide binding]; other site 336407001074 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 336407001075 RNA binding site [nucleotide binding]; other site 336407001076 S1_RPS1_repeat_ec3: 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 consists...; Region: S1_RPS1_repeat_ec3; cd05688 336407001077 RNA binding site [nucleotide binding]; other site 336407001078 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 336407001079 RNA binding site [nucleotide binding]; other site 336407001080 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 336407001081 RNA binding site [nucleotide binding]; other site 336407001082 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 336407001083 RNA binding site [nucleotide binding]; other site 336407001084 cytidylate kinase; Provisional; Region: cmk; PRK00023 336407001085 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 336407001086 CMP-binding site; other site 336407001087 The sites determining sugar specificity; other site 336407001088 DnaA N-terminal domain; Region: DnaA_N; pfam11638 336407001089 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; cl17344 336407001090 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 336407001091 His Kinase A (phospho-acceptor) domain; Region: HisKA; pfam00512 336407001092 dimer interface [polypeptide binding]; other site 336407001093 phosphorylation site [posttranslational modification] 336407001094 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 336407001095 ATP binding site [chemical binding]; other site 336407001096 Mg2+ binding site [ion binding]; other site 336407001097 G-X-G motif; other site 336407001098 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 336407001099 HD domain; Region: HD_4; pfam13328 336407001100 helix_turn_helix, Lux Regulon; Region: HTH_LUXR; smart00421 336407001101 DNA binding residues [nucleotide binding] 336407001102 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 336407001103 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 336407001104 synthetase active site [active] 336407001105 NTP binding site [chemical binding]; other site 336407001106 metal binding site [ion binding]; metal-binding site 336407001107 Conjugal transfer protein TraD; Region: TraD; pfam06412 336407001108 Ti-type conjugative transfer relaxase TraA; Region: TraA_Ti; TIGR02768 336407001109 MobA/MobL family; Region: MobA_MobL; pfam03389 336407001110 AAA domain; Region: AAA_30; pfam13604 336407001111 Family description; Region: UvrD_C_2; pfam13538 336407001112 TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG...; Region: TOPRIM_primases; cd01029 336407001113 active site 336407001114 metal binding site [ion binding]; metal-binding site 336407001115 interdomain interaction site; other site 336407001116 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 336407001117 conserved hypothetical protein (putative transposase or invertase); Region: T_den_put_tspse; TIGR01784 336407001118 F sex factor protein N terminal; Region: TraD_N; pfam12615 336407001119 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 336407001120 Type IV secretion-system coupling protein DNA-binding domain; Region: TrwB_AAD_bind; pfam10412 336407001121 Walker A motif; other site 336407001122 ATP binding site [chemical binding]; other site 336407001123 Walker B motif; other site 336407001124 TPR repeat; Region: TPR_11; pfam13414 336407001125 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 336407001126 binding surface 336407001127 TPR motif; other site 336407001128 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 336407001129 binding surface 336407001130 TPR repeat; Region: TPR_11; pfam13414 336407001131 TPR motif; other site 336407001132 TPR repeat; Region: TPR_11; pfam13414 336407001133 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 336407001134 binding surface 336407001135 TPR motif; other site 336407001136 TPR repeat; Region: TPR_11; pfam13414 336407001137 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 336407001138 binding surface 336407001139 TPR repeat; Region: TPR_11; pfam13414 336407001140 TPR motif; other site 336407001141 TPR repeat; Region: TPR_11; pfam13414 336407001142 TraG-like protein, N-terminal region; Region: TraG_N; pfam07916 336407001143 Conjugative relaxosome accessory transposon protein; Region: TraH; pfam06122 336407001144 conjugal transfer protein TrbB; Provisional; Region: PRK13728; cl17283 336407001145 F plasmid transfer operon protein; Region: TraF; pfam13728 336407001146 Type-1V conjugative transfer system mating pair stabilisation; Region: TraN; pfam06986 336407001147 Type-F conjugative transfer system pilin assembly protein; Region: TrbC_Ftype; pfam09673 336407001148 TraU protein; Region: TraU; pfam06834 336407001149 Sex factor F TraW protein N terminal; Region: TraW_N; cl10149 336407001150 F pilus assembly Type-IV secretion system for plasmid transfer; Region: TraC_F_IV; pfam11130 336407001151 type-IV secretion system protein TraC; Region: TraC-F-type; TIGR02746 336407001152 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 336407001153 Walker A motif; other site 336407001154 ATP binding site [chemical binding]; other site 336407001155 Bacterial conjugation TrbI-like protein; Region: TrbI; pfam03743 336407001156 TraE protein; Region: TraE; cl05060 336407001157 Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond...; Region: LRR_RI; cl15309 336407001158 Leucine-rich repeats; other site 336407001159 Substrate binding site [chemical binding]; other site 336407001160 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 336407001161 Integrase [DNA replication, recombination, and repair]; Region: XerC; COG0582 336407001162 active site 336407001163 DNA binding site [nucleotide binding] 336407001164 Int/Topo IB signature motif; other site 336407001165 Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]; Region: PinR; COG1961 336407001166 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 336407001167 catalytic residues [active] 336407001168 catalytic nucleophile [active] 336407001169 Recombinase; Region: Recombinase; pfam07508 336407001170 Predicted permeases [General function prediction only]; Region: COG0679 336407001171 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 336407001172 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 336407001173 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 336407001174 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 336407001175 Methyltransferase domain; Region: Methyltransf_31; pfam13847 336407001176 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 336407001177 S-adenosylmethionine binding site [chemical binding]; other site 336407001178 Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Saccharomyces cerevisiae biotin-apoprotein ligase (ScBLP); Region: GATase1_ScBLP_like; cd03144 336407001179 conserved cys residue [active] 336407001180 Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); Region: DUF2310; pfam10071 336407001181 Uncharacterized conserved protein [Function unknown]; Region: COG5590 336407001182 COQ9; Region: COQ9; pfam08511 336407001183 Ribosomal protein S21 [Translation, ribosomal structure and biogenesis]; Region: RpsU; COG0828 336407001184 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cl00462 336407001185 ABC-type Mn2+/Zn2+ transport systems, permease components [Inorganic ion transport and metabolism]; Region: ZnuB; COG1108 336407001186 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 336407001187 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 336407001188 S-adenosylmethionine binding site [chemical binding]; other site 336407001189 glutamyl-tRNA synthetase; Provisional; Region: gltX; PRK14895 336407001190 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 336407001191 HIGH motif; other site 336407001192 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 336407001193 active site 336407001194 KMSKS motif; other site 336407001195 Invasion associated locus B (IalB) protein; Region: IalB; cl02207 336407001196 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 336407001197 Coenzyme A binding pocket [chemical binding]; other site 336407001198 Fic family protein [Function unknown]; Region: COG3177 336407001199 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 336407001200 Fic/DOC family; Region: Fic; pfam02661 336407001201 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 336407001202 Coenzyme A binding pocket [chemical binding]; other site 336407001203 Acetyltransferase (GNAT) domain; Region: Acetyltransf_3; pfam13302 336407001204 Siderophore biosynthesis protein domain; Region: AlcB; smart01006 336407001205 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 336407001206 acylglycerophosphoethanolamine acyltransferase; Provisional; Region: PRK06814 336407001207 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 336407001208 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 336407001209 putative acyl-acceptor binding pocket; other site 336407001210 C-terminal domain of the acyl-acyl carrier protein synthetase (also called 2-acylglycerophosphoethanolamine acyltransferase, Aas); Region: AAS_C; cd05909 336407001211 acyl-activating enzyme (AAE) consensus motif; other site 336407001212 putative AMP binding site [chemical binding]; other site 336407001213 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]; Region: COG4799 336407001214 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 336407001215 Acetyl-CoA carboxylase alpha subunit [Lipid metabolism]; Region: AccA; cl17345 336407001216 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 336407001217 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 336407001218 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 336407001219 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 336407001220 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 336407001221 carboxyltransferase (CT) interaction site; other site 336407001222 biotinylation site [posttranslational modification]; other site 336407001223 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 336407001224 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 336407001225 dimerization interface [polypeptide binding]; other site 336407001226 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 336407001227 dimer interface [polypeptide binding]; other site 336407001228 phosphorylation site [posttranslational modification] 336407001229 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 336407001230 ATP binding site [chemical binding]; other site 336407001231 Mg2+ binding site [ion binding]; other site 336407001232 G-X-G motif; other site 336407001233 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 336407001234 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 336407001235 Transposase; Region: DEDD_Tnp_IS110; pfam01548 336407001236 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 336407001237 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 336407001238 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 336407001239 Tetratricopeptide repeat; Region: TPR_12; pfam13424 336407001240 binding surface 336407001241 Cephalosporin hydroxylase; Region: CmcI; pfam04989 336407001242 Clavaminic acid synthetase (CAS) -like; CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG oxygenases...; Region: CAS_like; cl00184 336407001243 active site 336407001244 iron coordination sites [ion binding]; other site 336407001245 substrate binding pocket [chemical binding]; other site 336407001246 Chloramphenicol (Cm) phosphotransferase (CPT). Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II; Region: CPT; cl17391 336407001247 AAA domain; Region: AAA_18; pfam13238 336407001248 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 336407001249 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 336407001250 2OG-Fe(II) oxygenase superfamily; Region: 2OG-FeII_Oxy_2; cl17321 336407001251 Xenobiotic acyltransferase (XAT): The XAT class of hexapeptide acyltransferases is composed of a large number of microbial enzymes that catalyze the CoA-dependent acetylation of a variety of hydroxyl-bearing acceptors such as chloramphenicol and...; Region: LbH_XAT; cd03349 336407001252 active site 336407001253 CoA binding site [chemical binding]; other site 336407001254 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 336407001255 Bacterial transcription activator, effector binding domain; Region: AraC_E_bind; smart00871 336407001256 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 336407001257 Coenzyme A binding pocket [chemical binding]; other site 336407001258 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) C-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs' Region: NTP-PPase_MazG_Cterm; cd11529 336407001259 homodimer interface [polypeptide binding]; other site 336407001260 active site 336407001261 putative chemical substrate binding site [chemical binding]; other site 336407001262 metal binding site [ion binding]; metal-binding site 336407001263 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 336407001264 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 336407001265 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 336407001266 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 and contain a highly...; Region: Nudix_Hydrolase_19; cd04678 336407001267 nudix motif; other site 336407001268 Protein of unknown function (DUF2000); Region: DUF2000; pfam09391 336407001269 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 336407001270 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 336407001271 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 336407001272 Walker A/P-loop; other site 336407001273 ATP binding site [chemical binding]; other site 336407001274 Q-loop/lid; other site 336407001275 ABC transporter signature motif; other site 336407001276 Walker B; other site 336407001277 D-loop; other site 336407001278 H-loop/switch region; other site 336407001279 PIN domain; Region: PIN; pfam01850 336407001280 SpoVT / AbrB like domain; Region: SpoVT_AbrB; smart00966 336407001281 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: COG1598 336407001282 HicB family; Region: HicB; pfam05534 336407001283 ExsB is a transcription regulator related protein. It is a subfamily of a Adenosine nucleotide binding superfamily of proteins. This protein family is represented by a single member in nearly every completed large (> 1000 genes) prokaryotic genome. In...; Region: ExsB; cd01995 336407001284 Ligand Binding Site [chemical binding]; other site 336407001285 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 336407001286 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 336407001287 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 336407001288 ClpX C4-type zinc finger; Region: zf-C4_ClpX; pfam06689 336407001289 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 336407001290 Walker A motif; other site 336407001291 ATP binding site [chemical binding]; other site 336407001292 Walker B motif; other site 336407001293 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 336407001294 Dehydroquinate synthase-like (DHQ-like) and iron-containing alcohol dehydrogenases (Fe-ADH); Region: DHQ_Fe-ADH; cl02872 336407001295 Predicted nuclease of restriction endonuclease-like fold, RmuC family [General function prediction only]; Region: COG1322 336407001296 RmuC family; Region: RmuC; pfam02646 336407001297 Glycosyltransferase family 10 (fucosyltransferase); Region: Glyco_transf_10; pfam00852 336407001298 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of...; Region: Glyco_transf_25; cd06532 336407001299 Poly-beta-hydroxyalkanoate depolymerase [Lipid metabolism]; Region: DepA; COG4553 336407001300 PHB de-polymerase C-terminus; Region: PHB_depo_C; pfam06850 336407001301 LicD family; Region: LicD; cl01378 336407001302 valyl-tRNA synthetase; Reviewed; Region: valS; PRK13208 336407001303 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 336407001304 active site 336407001305 HIGH motif; other site 336407001306 nucleotide binding site [chemical binding]; other site 336407001307 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 336407001308 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 336407001309 active site 336407001310 KMSKS motif; other site 336407001311 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 336407001312 tRNA binding surface [nucleotide binding]; other site 336407001313 anticodon binding site; other site 336407001314 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 336407001315 hypothetical protein; Provisional; Region: PRK09956 336407001316 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 336407001317 RNA/DNA hybrid binding site [nucleotide binding]; other site 336407001318 active site 336407001319 co-chaperone HscB; Provisional; Region: hscB; PRK01356 336407001320 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 336407001321 HSP70 interaction site [polypeptide binding]; other site 336407001322 chaperone protein HscA; Provisional; Region: hscA; PRK01433 336407001323 Nucleotide-Binding Domain of the sugar kinase/HSP70/actin superfamily; Region: NBD_sugar-kinase_HSP70_actin; cl17037 336407001324 nucleotide binding site [chemical binding]; other site 336407001325 Ferredoxin [Energy production and conversion]; Region: Fdx; COG0633 336407001326 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 336407001327 catalytic loop [active] 336407001328 iron binding site [ion binding]; other site 336407001329 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 336407001330 TRAP transporter solute receptor, TAXI family; Region: TRAP_TAXI; TIGR02122 336407001331 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 336407001332 Ligand Binding Site [chemical binding]; other site 336407001333 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 336407001334 cytochrome d terminal oxidase subunit 1; Provisional; Region: PRK15097 336407001335 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; pfam01654 336407001336 Protein of unknown function (DUF2671); Region: DUF2671; pfam10877 336407001337 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 336407001338 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 336407001339 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 336407001340 Walker A/P-loop; other site 336407001341 ATP binding site [chemical binding]; other site 336407001342 Q-loop/lid; other site 336407001343 ABC transporter signature motif; other site 336407001344 Walker B; other site 336407001345 D-loop; other site 336407001346 H-loop/switch region; other site 336407001347 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 336407001348 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 336407001349 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 336407001350 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 336407001351 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 336407001352 putative metal binding site; other site 336407001353 toxin-antitoxin system, toxin component, Txe/YoeB family; Region: toxin_Txe_YoeB; TIGR02116 336407001354 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: StbD; COG2161 336407001355 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 336407001356 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 336407001357 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 336407001358 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 336407001359 DNA binding residues [nucleotide binding] 336407001360 Cytochrome oxidase assembly factor [Posttranslational modification, protein turnover, chaperones]; Region: COX11; COG3175 336407001361 SpoVT / AbrB like domain; Region: SpoVT_AbrB; smart00966 336407001362 PIN domain of ribonucleases (toxins), VapC, FitB, and PAE0151 of bacterial and archaeal toxin/antitoxin-like operons, and other similar homologs; Region: PIN_VapC-like; cd09861 336407001363 putative active site [active] 336407001364 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 336407001365 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 336407001366 Ligand Binding Site [chemical binding]; other site 336407001367 amino acid transporter; Region: 2A0306; TIGR00909 336407001368 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 336407001369 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 336407001370 dimer interface [polypeptide binding]; other site 336407001371 motif 1; other site 336407001372 active site 336407001373 motif 2; other site 336407001374 motif 3; other site 336407001375 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 336407001376 anticodon binding site; other site 336407001377 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 336407001378 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 336407001379 ATP binding site [chemical binding]; other site 336407001380 active site 336407001381 substrate binding site [chemical binding]; other site 336407001382 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 336407001383 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 336407001384 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 336407001385 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 336407001386 active site 336407001387 dimer interface [polypeptide binding]; other site 336407001388 motif 1; other site 336407001389 motif 2; other site 336407001390 motif 3; other site 336407001391 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 336407001392 anticodon binding site; other site 336407001393 hypothetical protein; Validated; Region: PRK06620 336407001394 ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]; Region: DnaA; COG0593 336407001395 proline/glycine betaine transporter; Provisional; Region: PRK10642 336407001396 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 336407001397 putative substrate translocation pore; other site 336407001398 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2001 336407001399 MraZ protein; Region: MraZ; pfam02381 336407001400 16S rRNA m(4)C1402 methyltranserfase; Provisional; Region: PRK00050 336407001401 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 336407001402 S-adenosylmethionine binding site [chemical binding]; other site 336407001403 Predicted secreted (periplasmic) protein [Function unknown]; Region: COG5462 336407001404 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 336407001405 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 336407001406 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 336407001407 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 336407001408 120 KDa Rickettsia surface antigen; Region: 120_Rick_ant; pfam12574 336407001409 Transposase; Region: DEDD_Tnp_IS110; pfam01548 336407001410 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 336407001411 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 336407001412 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 336407001413 metabolite-proton symporter; Region: 2A0106; TIGR00883 336407001414 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 336407001415 HD domain; Region: HD_4; pfam13328 336407001416 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 336407001417 AAA domain; Region: AAA_22; pfam13401 336407001418 Walker A/P-loop; other site 336407001419 ATP binding site [chemical binding]; other site 336407001420 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 336407001421 HD domain; Region: HD_4; pfam13328 336407001422 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 336407001423 metabolite-proton symporter; Region: 2A0106; TIGR00883 336407001424 Tetratricopeptide repeat; Region: TPR_12; pfam13424 336407001425 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 336407001426 binding surface 336407001427 TPR motif; other site 336407001428 Tetratricopeptide repeat; Region: TPR_12; pfam13424 336407001429 Tetratricopeptide repeat; Region: TPR_12; pfam13424 336407001430 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 336407001431 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 336407001432 BRO family, N-terminal domain; Region: Bro-N; smart01040 336407001433 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 336407001434 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 336407001435 non-specific DNA binding site [nucleotide binding]; other site 336407001436 salt bridge; other site 336407001437 sequence-specific DNA binding site [nucleotide binding]; other site 336407001438 Iron-sulphur cluster assembly; Region: Fe-S_assembly; pfam04384 336407001439 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 336407001440 active site 336407001441 catalytic residues [active] 336407001442 metal binding site [ion binding]; metal-binding site 336407001443 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 336407001444 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 336407001445 putative active site [active] 336407001446 substrate binding site [chemical binding]; other site 336407001447 putative cosubstrate binding site; other site 336407001448 catalytic site [active] 336407001449 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 336407001450 substrate binding site [chemical binding]; other site 336407001451 Protein of unknown function (DUF563); Region: DUF563; cl15705 336407001452 Predicted ATPase [General function prediction only]; Region: COG1485 336407001453 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 336407001454 Walker A motif; other site 336407001455 ATP binding site [chemical binding]; other site 336407001456 Walker B motif; other site 336407001457 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 336407001458 HD domain; Region: HD_4; pfam13328 336407001459 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 336407001460 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 336407001461 Substrate binding site; other site 336407001462 Mg++ binding site; other site 336407001463 hypothetical protein; Validated; Region: PRK00110 336407001464 50S ribosomal protein L36; Validated; Region: rpmJ; PRK00831 336407001465 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 336407001466 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 336407001467 N-acetyl-D-glucosamine binding site [chemical binding]; other site 336407001468 Protein of unknown function (DUF2532); Region: DUF2532; pfam10811 336407001469 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 336407001470 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 336407001471 S-adenosylmethionine binding site [chemical binding]; other site 336407001472 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 336407001473 Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]; Region: GlpB; cl17730 336407001474 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 336407001475 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 336407001476 Tetratricopeptide repeat; Region: TPR_12; pfam13424 336407001477 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 336407001478 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 336407001479 N-acetyl-D-glucosamine binding site [chemical binding]; other site 336407001480 catalytic residue [active] 336407001481 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 336407001482 dimer interface [polypeptide binding]; other site 336407001483 catalytic triad [active] 336407001484 RecB family exonuclease [DNA replication, recombination, and repair]; Region: COG2887 336407001485 Ankyrin repeats (many copies); Region: Ank_5; pfam13857 336407001486 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 336407001487 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 336407001488 DNA polymerase III PolC; Validated; Region: polC; PRK00448 336407001489 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 336407001490 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 336407001491 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 336407001492 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 336407001493 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 336407001494 ring oligomerisation interface [polypeptide binding]; other site 336407001495 ATP/Mg binding site [chemical binding]; other site 336407001496 stacking interactions; other site 336407001497 hinge regions; other site 336407001498 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 336407001499 oligomerisation interface [polypeptide binding]; other site 336407001500 mobile loop; other site 336407001501 roof hairpin; other site 336407001502 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 336407001503 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 336407001504 synthetase active site [active] 336407001505 NTP binding site [chemical binding]; other site 336407001506 metal binding site [ion binding]; metal-binding site 336407001507 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 336407001508 HD domain; Region: HD_4; pfam13328 336407001509 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 336407001510 active site 336407001511 peptide chain release factor 2; Validated; Region: prfB; PRK00578 336407001512 PCRF domain; Region: PCRF; pfam03462 336407001513 RF-1 domain; Region: RF-1; pfam00472 336407001514 Elongation factor Tu GTP binding domain; Region: GTP_EFTU; pfam00009 336407001515 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 336407001516 G1 box; other site 336407001517 putative GEF interaction site [polypeptide binding]; other site 336407001518 GTP/Mg2+ binding site [chemical binding]; other site 336407001519 Switch I region; other site 336407001520 G2 box; other site 336407001521 G3 box; other site 336407001522 Switch II region; other site 336407001523 G4 box; other site 336407001524 G5 box; other site 336407001525 Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to...; Region: Translation_Factor_II_like; cl02787 336407001526 Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to...; Region: Translation_Factor_II_like; cl02787 336407001527 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 336407001528 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 336407001529 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 336407001530 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 336407001531 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 336407001532 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 336407001533 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK06039 336407001534 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 336407001535 HIGH motif; other site 336407001536 Rickettsial palindromic element RPE4 domain; Region: RPE4; TIGR03777 336407001537 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 336407001538 active site 336407001539 KMSKS motif; other site 336407001540 Anticodon-binding domain of archaeal, bacterial, and eukaryotic cytoplasmic isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_ABEc; cd07961 336407001541 tRNA binding surface [nucleotide binding]; other site 336407001542 anticodon binding site; other site 336407001543 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; pfam02592 336407001544 PIN domain of ribonucleases (toxins), VapC, FitB, and PAE0151 of bacterial and archaeal toxin/antitoxin-like operons, and other similar homologs; Region: PIN_VapC-like; cd09861 336407001545 putative active site [active] 336407001546 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 336407001547 Domain of unknown function DUF20; Region: UPF0118; pfam01594 336407001548 GrpE; Region: GrpE; pfam01025 336407001549 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 336407001550 dimer interface [polypeptide binding]; other site 336407001551 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 336407001552 ribonuclease PH; Reviewed; Region: rph; PRK00173 336407001553 Ribonuclease PH; Region: RNase_PH_bact; cd11362 336407001554 hexamer interface [polypeptide binding]; other site 336407001555 active site 336407001556 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 336407001557 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 336407001558 RNA binding surface [nucleotide binding]; other site 336407001559 FtsJ-like methyltransferase; Region: FtsJ; pfam01728 336407001560 Transcriptional regulator; Region: Rrf2; cl17282 336407001561 Rrf2 family protein; Region: rrf2_super; TIGR00738 336407001562 Globins are heme proteins, which bind and transport oxygen. This family summarizes a diverse set of homologous protein domains, including: (1) tetrameric vertebrate hemoglobins, which are the major protein component of erythrocytes and transport oxygen...; Region: globin; cd01040 336407001563 bifunctional nitric oxide dioxygenase/dihydropteridine reductase 2; Provisional; Region: PRK13289 336407001564 heme-binding site [chemical binding]; other site 336407001565 Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport...; Region: FNR_like; cl06868 336407001566 FAD binding pocket [chemical binding]; other site 336407001567 conserved FAD binding motif [chemical binding]; other site 336407001568 phosphate binding motif [ion binding]; other site 336407001569 beta-alpha-beta structure motif; other site 336407001570 NAD binding pocket [chemical binding]; other site 336407001571 ribosome maturation protein RimP; Reviewed; Region: PRK00092 336407001572 Sm and related proteins; Region: Sm_like; cl00259 336407001573 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 336407001574 putative oligomer interface [polypeptide binding]; other site 336407001575 putative RNA binding site [nucleotide binding]; other site 336407001576 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 336407001577 NusA N-terminal domain; Region: NusA_N; pfam08529 336407001578 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 336407001579 RNA binding site [nucleotide binding]; other site 336407001580 homodimer interface [polypeptide binding]; other site 336407001581 NusA-like KH domain; Region: KH_5; pfam13184 336407001582 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 336407001583 G-X-X-G motif; other site 336407001584 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 336407001585 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 336407001586 Translation initiation factor 2 (IF-2; GTPase) [Translation, ribosomal structure and biogenesis]; Region: InfB; COG0532 336407001587 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 336407001588 G1 box; other site 336407001589 putative GEF interaction site [polypeptide binding]; other site 336407001590 GTP/Mg2+ binding site [chemical binding]; other site 336407001591 Switch I region; other site 336407001592 G2 box; other site 336407001593 G3 box; other site 336407001594 Switch II region; other site 336407001595 G4 box; other site 336407001596 G5 box; other site 336407001597 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 336407001598 Translation-initiation factor 2; Region: IF-2; pfam11987 336407001599 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 336407001600 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 336407001601 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 336407001602 GIY-YIG motif/motif A; other site 336407001603 active site 336407001604 catalytic site [active] 336407001605 putative DNA binding site [nucleotide binding]; other site 336407001606 metal binding site [ion binding]; metal-binding site 336407001607 UvrB/uvrC motif; Region: UVR; pfam02151 336407001608 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 336407001609 Zeta toxin; Region: Zeta_toxin; pfam06414 336407001610 Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond...; Region: LRR_RI; cl15309 336407001611 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3328 336407001612 Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond...; Region: LRR_RI; cl15309 336407001613 Substrate binding site [chemical binding]; other site 336407001614 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 336407001615 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 336407001616 30S subunit binding site; other site 336407001617 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 336407001618 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 336407001619 putative monovalent cation/H+ antiporter subunit F; Reviewed; Region: PRK12612 336407001620 2-octaprenyl-6-methoxyphenyl hydroxylase; Validated; Region: PRK06617 336407001621 ubiquinone biosynthesis hydroxylase family protein; Provisional; Region: PRK07608; cl17314 336407001622 Apolipoprotein L; Region: ApoL; pfam05461 336407001623 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 336407001624 pyridoxal phosphate-dependent acyltransferase, putative; Region: gly_Cac_T_rel; TIGR01825 336407001625 KBL_like; this family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to serine palmitoyltransferase (SPT), 5-aminolevulinate synthase (ALAS); Region: KBL_like; cd06454 336407001626 substrate-cofactor binding pocket; other site 336407001627 pyridoxal 5'-phosphate binding site [chemical binding]; other site 336407001628 catalytic residue [active] 336407001629 heat shock protein 90; Provisional; Region: PRK05218 336407001630 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 336407001631 ATP binding site [chemical binding]; other site 336407001632 Mg2+ binding site [ion binding]; other site 336407001633 G-X-G motif; other site 336407001634 hypothetical protein; Reviewed; Region: PRK01530 336407001635 AAA domain; Region: AAA_22; pfam13401 336407001636 AAA domain; Region: AAA_14; pfam13173 336407001637 Tetratricopeptide repeat; Region: TPR_12; pfam13424 336407001638 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 336407001639 binding surface 336407001640 TPR motif; other site 336407001641 Tetratricopeptide repeat; Region: TPR_12; pfam13424 336407001642 Tetratricopeptide repeat; Region: TPR_12; pfam13424 336407001643 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 336407001644 binding surface 336407001645 TPR motif; other site 336407001646 Tetratricopeptide repeat; Region: TPR_12; pfam13424 336407001647 GTA TIM-barrel-like domain; Region: GTA_TIM; pfam13547 336407001648 Putative phage tail protein; Region: Phage-tail_3; pfam13550 336407001649 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 336407001650 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 336407001651 CysQ, a 3'-Phosphoadenosine-5'-phosphosulfate (PAPS) 3'-phosphatase, is a bacterial member of the inositol monophosphatase family. It has been proposed that CysQ helps control intracellular levels of PAPS, which is an intermediate in...; Region: CysQ; cd01638 336407001652 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 336407001653 active site 336407001654 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3755 336407001655 TMPIT-like protein; Region: TMPIT; pfam07851 336407001656 malate dehydrogenase; Reviewed; Region: PRK06223 336407001657 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 336407001658 NAD(P) binding site [chemical binding]; other site 336407001659 dimer interface [polypeptide binding]; other site 336407001660 tetramer (dimer of dimers) interface [polypeptide binding]; other site 336407001661 substrate binding site [chemical binding]; other site 336407001662 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 336407001663 non-specific DNA binding site [nucleotide binding]; other site 336407001664 salt bridge; other site 336407001665 sequence-specific DNA binding site [nucleotide binding]; other site 336407001666 Protein of unknown function (DUF1044); Region: DUF1044; cl01955 336407001667 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 336407001668 H(+) -translocating inorganic pyrophosphatase; Region: PLN02255; cl11452 336407001669 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 336407001670 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 336407001671 HlyD family secretion protein; Region: HlyD_3; pfam13437 336407001672 Outer membrane efflux protein; Region: OEP; pfam02321 336407001673 Outer membrane efflux protein; Region: OEP; pfam02321 336407001674 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 336407001675 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 336407001676 diaminopimelate epimerase; Region: DapF; TIGR00652 336407001677 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 336407001678 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 336407001679 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 336407001680 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 336407001681 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 336407001682 FeS/SAM binding site; other site 336407001683 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 336407001684 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 336407001685 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 336407001686 dimer interface [polypeptide binding]; other site 336407001687 motif 1; other site 336407001688 active site 336407001689 motif 2; other site 336407001690 motif 3; other site 336407001691 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 336407001692 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 336407001693 putative tRNA-binding site [nucleotide binding]; other site 336407001694 B3/4 domain; Region: B3_4; pfam03483 336407001695 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 336407001696 tRNA synthetase B5 domain; Region: B5; smart00874 336407001697 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 336407001698 dimer interface [polypeptide binding]; other site 336407001699 motif 1; other site 336407001700 motif 3; other site 336407001701 motif 2; other site 336407001702 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 336407001703 Beta clamp domain. The beta subunit (processivity factor) of DNA polymerase III holoenzyme, refered to as the beta clamp, forms a ring shaped dimer that encircles dsDNA (sliding clamp) in bacteria. The beta-clamp is structurally similar to the trimeric...; Region: beta_clamp; cd00140 336407001704 DNA polymerase III subunit beta; Validated; Region: PRK05643 336407001705 putative DNA binding surface [nucleotide binding]; other site 336407001706 dimer interface [polypeptide binding]; other site 336407001707 beta-clamp/clamp loader binding surface; other site 336407001708 beta-clamp/translesion DNA polymerase binding surface; other site 336407001709 AAA domain; Region: AAA_14; pfam13173 336407001710 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 336407001711 Orientia OTT_1508-like deaminase; Region: OTT_1508_deam; pfam14441 336407001712 Large extracellular alpha-helical protein [General function prediction only]; Region: COG2373 336407001713 MG2 domain; Region: A2M_N; pfam01835 336407001714 Alpha-2-macroglobulin family; Region: A2M; pfam00207 336407001715 Proteins similar to alpha2-macroglobulin (alpha (2)-M). Alpha (2)-M is a major carrier protein in serum. It is a broadly specific proteinase inhibitor. The structural thioester of alpha (2)-M, is involved in the immobilization and entrapment of...; Region: A2M_like; cd02891 336407001716 surface patch; other site 336407001717 thioester region; other site 336407001718 specificity defining residues; other site 336407001719 Domain of unknown function DUF11; Region: DUF11; pfam01345 336407001720 Predicted glutamine amidotransferases [General function prediction only]; Region: COG2071 336407001721 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 336407001722 conserved cys residue [active] 336407001723 arginine:agmatin antiporter; Provisional; Region: PRK10644 336407001724 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 336407001725 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 336407001726 active site 336407001727 catalytic residues [active] 336407001728 metal binding site [ion binding]; metal-binding site 336407001729 Protein of unknown function (DUF497); Region: DUF497; pfam04365 336407001730 Domain of unknown function (DUF4415); Region: DUF4415; cl01401 336407001731 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 336407001732 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 336407001733 Ribonuclease BN family enzyme [Replication, recombination, and repair]; Region: Rbn; COG1295 336407001734 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 336407001735 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 336407001736 non-specific DNA binding site [nucleotide binding]; other site 336407001737 salt bridge; other site 336407001738 sequence-specific DNA binding site [nucleotide binding]; other site 336407001739 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 336407001740 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 336407001741 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 336407001742 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 336407001743 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 336407001744 active site 336407001745 catalytic residues [active] 336407001746 metal binding site [ion binding]; metal-binding site 336407001747 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 336407001748 Part of AAA domain; Region: AAA_19; pfam13245 336407001749 Family description; Region: UvrD_C_2; pfam13538 336407001750 Transposase; Region: DEDD_Tnp_IS110; pfam01548 336407001751 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 336407001752 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 336407001753 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 336407001754 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 336407001755 active site 336407001756 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 336407001757 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 336407001758 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 336407001759 Uncharacterized conserved protein [Function unknown]; Region: COG1723 336407001760 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 336407001761 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 336407001762 catalytic site [active] 336407001763 putative active site [active] 336407001764 putative substrate binding site [chemical binding]; other site 336407001765 HRDC domain; Region: HRDC; cl02578 336407001766 Copper(I)-binding protein [Inorganic ion transport and metabolism]; Region: COG2847 336407001767 DNA alkylation repair enzyme; Region: DNA_alkylation; pfam08713 336407001768 A new structural DNA glycosylase; Region: AlkD_like; cd06561 336407001769 active site 336407001770 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 336407001771 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 336407001772 DNA binding site [nucleotide binding] 336407001773 active site 336407001774 TraX protein; Region: TraX; cl05434 336407001775 TraX protein; Region: TraX; cl05434 336407001776 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 336407001777 MviN-like protein; Region: MVIN; pfam03023 336407001778 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 336407001779 dimer interface [polypeptide binding]; other site 336407001780 substrate binding site [chemical binding]; other site 336407001781 metal binding sites [ion binding]; metal-binding site 336407001782 cytochrome c-type biogenesis protein CcmE; Reviewed; Region: PRK13254 336407001783 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 336407001784 SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c...; Region: SCO; cd02968 336407001785 Cu(I) binding site [ion binding]; other site 336407001786 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 336407001787 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 336407001788 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 336407001789 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 336407001790 This family is most closely related to the GT1 family of glycosyltransferases. WavL in Vibrio cholerae has been shown to be involved in the biosynthesis of the lipopolysaccharide core; Region: GT1_WavL_like; cd03819 336407001791 putative ADP-binding pocket [chemical binding]; other site 336407001792 Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]; Region: MhpC; COG0596 336407001793 Putative lysophospholipase; Region: Hydrolase_4; pfam12146 336407001794 Novel bacterial esterase that cleaves esters on halogenated cyclic compounds; Region: Esterase_713_like; cl17303 336407001795 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 336407001796 catalytic site [active] 336407001797 Protein of unknown function (DUF2608); Region: DUF2608; pfam11019 336407001798 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 336407001799 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 336407001800 HlyD family secretion protein; Region: HlyD_3; pfam13437 336407001801 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 336407001802 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 336407001803 active site 336407001804 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cd00761 336407001805 active site 336407001806 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 336407001807 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4627 336407001808 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 336407001809 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 336407001810 active site 336407001811 homodimer interface [polypeptide binding]; other site 336407001812 UDP-N-acetylglucosamine 4,6-dehydratase/5-epimerase; Region: FnlA; TIGR04130 336407001813 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 336407001814 NAD(P) binding site [chemical binding]; other site 336407001815 homodimer interface [polypeptide binding]; other site 336407001816 substrate binding site [chemical binding]; other site 336407001817 active site 336407001818 Polysaccharide biosynthesis protein C-terminal; Region: Polysacc_syn_2C; pfam08485 336407001819 dTDP-4-dehydrorhamnose reductase [Cell envelope biogenesis, outer membrane]; Region: RfbD; COG1091 336407001820 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 336407001821 NADP binding site [chemical binding]; other site 336407001822 active site 336407001823 putative substrate binding site [chemical binding]; other site 336407001824 glutamyl-tRNA synthetase; Provisional; Region: PRK12558 336407001825 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 336407001826 active site 336407001827 HIGH motif; other site 336407001828 nucleotide binding site [chemical binding]; other site 336407001829 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 336407001830 active site 336407001831 KMSKS motif; other site 336407001832 DNA topoisomerase I; Validated; Region: PRK06599 336407001833 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 336407001834 active site 336407001835 interdomain interaction site; other site 336407001836 putative metal-binding site [ion binding]; other site 336407001837 nucleotide binding site [chemical binding]; other site 336407001838 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 336407001839 domain I; other site 336407001840 DNA binding groove [nucleotide binding] 336407001841 phosphate binding site [ion binding]; other site 336407001842 domain II; other site 336407001843 domain III; other site 336407001844 nucleotide binding site [chemical binding]; other site 336407001845 catalytic site [active] 336407001846 domain IV; other site 336407001847 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 336407001848 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 336407001849 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 336407001850 DNA protecting protein DprA; Region: dprA; TIGR00732 336407001851 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 336407001852 Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic hydroperoxides; Region: PRX_Typ2cys; cd03015 336407001853 dimer interface [polypeptide binding]; other site 336407001854 decamer (pentamer of dimers) interface [polypeptide binding]; other site 336407001855 catalytic triad [active] 336407001856 peroxidatic and resolving cysteines [active] 336407001857 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 336407001858 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 336407001859 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 336407001860 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 336407001861 substrate binding pocket [chemical binding]; other site 336407001862 chain length determination region; other site 336407001863 substrate-Mg2+ binding site; other site 336407001864 catalytic residues [active] 336407001865 aspartate-rich region 1; other site 336407001866 active site lid residues [active] 336407001867 aspartate-rich region 2; other site 336407001868 Helix-turn-helix domain; Region: HTH_37; pfam13744 336407001869 non-specific DNA binding site [nucleotide binding]; other site 336407001870 salt bridge; other site 336407001871 sequence-specific DNA binding site [nucleotide binding]; other site 336407001872 Phage derived protein Gp49-like (DUF891); Region: Gp49; pfam05973 336407001873 TLC ATP/ADP transporter; Region: TLC; pfam03219 336407001874 A4GalT_like proteins catalyze the addition of galactose or glucose residues to the lipooligosaccharide (LOS) or lipopolysaccharide (LPS) of the bacterial cell surface; Region: GT8_A4GalT_like; cd04194 336407001875 Glycosyl transferase family 8; Region: Glyco_transf_8; pfam01501 336407001876 Ligand binding site; other site 336407001877 metal-binding site 336407001878 AmpG-like permease; Region: 2A0125; TIGR00901 336407001879 LysE type translocator; Region: LysE; cl00565 336407001880 Lysine efflux permease [General function prediction only]; Region: COG1279 336407001881 Uroporphyrinogen-III synthase [Coenzyme metabolism]; Region: HemD; COG1587 336407001882 Uroporphyrinogen-III synthase (HemD) catalyzes the asymmetrical cyclization of tetrapyrrole (linear) to uroporphyrinogen-III, the fourth step in the biosynthesis of heme. This ubiquitous enzyme is present in eukaryotes, bacteria and archaea. Mutations in...; Region: HemD; cd06578 336407001883 active site 336407001884 HemY protein N-terminus; Region: HemY_N; pfam07219 336407001885 isopentenyl pyrophosphate isomerase; Provisional; Region: PRK05437 336407001886 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 336407001887 homotetramer interface [polypeptide binding]; other site 336407001888 FMN binding site [chemical binding]; other site 336407001889 homodimer contacts [polypeptide binding]; other site 336407001890 putative active site [active] 336407001891 putative substrate binding site [chemical binding]; other site 336407001892 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 336407001893 dimer interface [polypeptide binding]; other site 336407001894 putative radical transfer pathway; other site 336407001895 diiron center [ion binding]; other site 336407001896 tyrosyl radical; other site 336407001897 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09102 336407001898 Class I ribonucleotide reductase; Region: RNR_I; cd01679 336407001899 active site 336407001900 dimer interface [polypeptide binding]; other site 336407001901 catalytic residues [active] 336407001902 effector binding site; other site 336407001903 R2 peptide binding site; other site 336407001904 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; cl00257 336407001905 IHF - DNA interface [nucleotide binding]; other site 336407001906 IHF dimer interface [polypeptide binding]; other site 336407001907 Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: SppA; COG0616 336407001908 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 336407001909 tandem repeat interface [polypeptide binding]; other site 336407001910 oligomer interface [polypeptide binding]; other site 336407001911 active site residues [active] 336407001912 transcription termination factor Rho; Provisional; Region: rho; PRK09376 336407001913 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 336407001914 Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA...; Region: Rho_CSD; cd04459 336407001915 RNA binding site [nucleotide binding]; other site 336407001916 Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase. It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the...; Region: rho_factor; cd01128 336407001917 multimer interface [polypeptide binding]; other site 336407001918 Walker A motif; other site 336407001919 ATP binding site [chemical binding]; other site 336407001920 Walker B motif; other site 336407001921 DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a CXXC...; Region: DsbA_Com1_like; cd03023 336407001922 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 336407001923 catalytic residues [active] 336407001924 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 336407001925 SmpB-tmRNA interface; other site 336407001926 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 336407001927 dihydrodipicolinate synthase; Region: dapA; TIGR00674 336407001928 dimer interface [polypeptide binding]; other site 336407001929 active site 336407001930 catalytic residue [active] 336407001931 branched-chain amino acid aminotransferase; Validated; Region: PRK06606 336407001932 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 336407001933 homodimer interface [polypeptide binding]; other site 336407001934 substrate-cofactor binding pocket; other site 336407001935 pyridoxal 5'-phosphate binding site [chemical binding]; other site 336407001936 catalytic residue [active] 336407001937 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 336407001938 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 336407001939 active site 336407001940 phosphorylation site [posttranslational modification] 336407001941 intermolecular recognition site; other site 336407001942 dimerization interface [polypeptide binding]; other site 336407001943 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 336407001944 DNA binding site [nucleotide binding] 336407001945 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 336407001946 dimer interface [polypeptide binding]; other site 336407001947 phosphorylation site [posttranslational modification] 336407001948 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 336407001949 ATP binding site [chemical binding]; other site 336407001950 Mg2+ binding site [ion binding]; other site 336407001951 G-X-G motif; other site 336407001952 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 336407001953 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 336407001954 catalytic residue [active] 336407001955 putative FPP diphosphate binding site; other site 336407001956 putative FPP binding hydrophobic cleft; other site 336407001957 dimer interface [polypeptide binding]; other site 336407001958 putative IPP diphosphate binding site; other site 336407001959 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 336407001960 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 336407001961 Septum formation initiator [Cell division and chromosome partitioning]; Region: COG2919 336407001962 Septum formation initiator; Region: DivIC; pfam04977 336407001963 Ribonuclease D [Translation, ribosomal structure and biogenesis]; Region: Rnd; COG0349 336407001964 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 336407001965 catalytic site [active] 336407001966 putative active site [active] 336407001967 putative substrate binding site [chemical binding]; other site 336407001968 Solute carrier families 5 and 6-like; solute binding domain; Region: SLC5-6-like_sbd; cl00456 336407001969 Solute carrier 5 family, sodium/glucose transporters and related proteins; solute-binding domain; Region: SLC5sbd; cd10322 336407001970 Na binding site [ion binding]; other site 336407001971 Fic family protein [Function unknown]; Region: COG3177 336407001972 Fic/DOC family N-terminal; Region: Fic_N; pfam13784 336407001973 Fic/DOC family; Region: Fic; pfam02661 336407001974 Fic family protein [Function unknown]; Region: COG3177 336407001975 Domain of unknown function (DUF4172); Region: DUF4172; pfam13776 336407001976 Fic/DOC family; Region: Fic; pfam02661 336407001977 CESA_like_2 is a member of the cellulose synthase superfamily; Region: CESA_like_2; cd06427 336407001978 Glycosyltransferase like family 2; Region: Glyco_tranf_2_3; pfam13641 336407001979 DXD motif; other site 336407001980 PemK-like protein; Region: PemK; pfam02452 336407001981 Ribbon-helix-helix protein, copG family; Region: RHH_1; pfam01402 336407001982 Phage portal protein; Region: Phage_portal; pfam04860 336407001983 Phage-related protein [Function unknown]; Region: COG4695 336407001984 ABC-type anion transport system, duplicated permease component [Inorganic ion transport and metabolism]; Region: COG4986 336407001985 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 336407001986 dimer interface [polypeptide binding]; other site 336407001987 conserved gate region; other site 336407001988 putative PBP binding loops; other site 336407001989 ABC-ATPase subunit interface; other site 336407001990 ABC-type anion transport system, duplicated permease component [Inorganic ion transport and metabolism]; Region: COG4986 336407001991 Protein of unknown function (DUF4239); Region: DUF4239; pfam14023 336407001992 exodeoxyribonuclease VII, small subunit; Region: xseB; TIGR01280 336407001993 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 336407001994 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 336407001995 RimM N-terminal domain; Region: RimM; pfam01782 336407001996 PRC-barrel domain; Region: PRC; pfam05239 336407001997 120 KDa Rickettsia surface antigen; Region: 120_Rick_ant; pfam12574 336407001998 120 KDa Rickettsia surface antigen; Region: 120_Rick_ant; pfam12574 336407001999 TLC ATP/ADP transporter; Region: TLC; pfam03219 336407002000 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK01528 336407002001 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 336407002002 RNA binding site [nucleotide binding]; other site 336407002003 active site 336407002004 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 336407002005 16S/18S rRNA binding site [nucleotide binding]; other site 336407002006 S13e-L30e interaction site [polypeptide binding]; other site 336407002007 25S rRNA binding site [nucleotide binding]; other site 336407002008 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 336407002009 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 336407002010 RNase E interface [polypeptide binding]; other site 336407002011 trimer interface [polypeptide binding]; other site 336407002012 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 336407002013 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 336407002014 RNase E interface [polypeptide binding]; other site 336407002015 trimer interface [polypeptide binding]; other site 336407002016 active site 336407002017 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 336407002018 putative nucleic acid binding region [nucleotide binding]; other site 336407002019 G-X-X-G motif; other site 336407002020 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 336407002021 RNA binding site [nucleotide binding]; other site 336407002022 domain interface; other site 336407002023 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 336407002024 KpsF-like protein. KpsF is an arabinose-5-phosphate isomerase which contains SIS (Sugar ISomerase) domains. SIS domains are found in many phosphosugar isomerases and phosphosugar binding proteins. KpsF catalyzes the reversible reaction of ribulose...; Region: SIS_Kpsf; cd05014 336407002025 putative active site [active] 336407002026 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with KpsF/GutQ domains in the API [A5P (D-arabinose 5-phosphate) isomerase] protein. These APIs catalyze the conversion of the pentose pathway...; Region: CBS_pair_KpsF_GutQ_assoc; cd04604 336407002027 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5375 336407002028 OstA-like protein; Region: OstA; pfam03968 336407002029 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 336407002030 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 336407002031 Walker A/P-loop; other site 336407002032 ATP binding site [chemical binding]; other site 336407002033 Q-loop/lid; other site 336407002034 ABC transporter signature motif; other site 336407002035 Walker B; other site 336407002036 D-loop; other site 336407002037 H-loop/switch region; other site 336407002038 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 336407002039 The phosphomannomutase/phosphoglucomutase (PMM/PGM) bifunctional enzyme catalyzes the reversible conversion of 1-phospho to 6-phospho-sugars (e.g. between mannose-1-phosphate and mannose-6-phosphate or glucose-1-phosphate and glucose-6-phosphate) via a...; Region: PMM_PGM; cd03089 336407002040 active site 336407002041 substrate binding site [chemical binding]; other site 336407002042 metal binding site [ion binding]; metal-binding site 336407002043 tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed; Region: miaA; PRK00091 336407002044 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 336407002045 NADH:ubiquinone oxidoreductase subunit N; Provisional; Region: PRK05777 336407002046 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 336407002047 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 336407002048 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 336407002049 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 336407002050 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 336407002051 Protein required for attachment to host cells; Region: Host_attach; cl02398 336407002052 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 336407002053 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 336407002054 putative acyl-acceptor binding pocket; other site 336407002055 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 336407002056 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 336407002057 active site 336407002058 HIGH motif; other site 336407002059 dimer interface [polypeptide binding]; other site 336407002060 KMSKS motif; other site 336407002061 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 336407002062 binding surface 336407002063 TPR motif; other site 336407002064 Tetratricopeptide repeat; Region: TPR_12; pfam13424 336407002065 Tetratricopeptide repeat; Region: TPR_12; pfam13424 336407002066 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 336407002067 Walker A/P-loop; other site 336407002068 ATP binding site [chemical binding]; other site 336407002069 DNA gyrase subunit A; Validated; Region: PRK05560 336407002070 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 336407002071 CAP-like domain; other site 336407002072 active site 336407002073 primary dimer interface [polypeptide binding]; other site 336407002074 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 336407002075 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 336407002076 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 336407002077 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 336407002078 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 336407002079 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 336407002080 Found in ATP-dependent protease La (LON); Region: LON; smart00464 336407002081 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 336407002082 Walker A motif; other site 336407002083 ATP binding site [chemical binding]; other site 336407002084 Walker B motif; other site 336407002085 arginine finger; other site 336407002086 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 336407002087 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 336407002088 Threonine dehydratase: The first step in amino acid degradation is the removal of nitrogen. Although the nitrogen atoms of most amino acids are transferred to alpha-ketoglutarate before removal, the alpha-amino group of threonine can be directly...; Region: Thr-dehyd; cd01562 336407002089 tetramer interface [polypeptide binding]; other site 336407002090 pyridoxal 5'-phosphate binding site [chemical binding]; other site 336407002091 catalytic residue [active] 336407002092 Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan...; Region: Trp-synth-beta_II; cl00342 336407002093 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 336407002094 Rickettsial palindromic element RPE4 domain; Region: RPE4; TIGR03777 336407002095 GTP cyclohydrolase I; Provisional; Region: folE; PRK09347 336407002096 GTP cyclohydrolase I; Provisional; Region: PLN03044 336407002097 active site 336407002098 prolyl-tRNA synthetase; Provisional; Region: PRK12325 336407002099 Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: ProRS_core_prok; cd00779 336407002100 dimer interface [polypeptide binding]; other site 336407002101 motif 1; other site 336407002102 active site 336407002103 motif 2; other site 336407002104 motif 3; other site 336407002105 ProRS Prolyl-anticodon binding domain, short version found predominantly in bacteria. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding; Region: ProRS_anticodon_short; cd00861 336407002106 anticodon binding site; other site 336407002107 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 336407002108 metabolite-proton symporter; Region: 2A0106; TIGR00883 336407002109 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 336407002110 HD domain; Region: HD_4; pfam13328 336407002111 Uncharacterized protein family (UPF0081); Region: UPF0081; pfam03652 336407002112 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 336407002113 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 336407002114 Sulfatase; Region: Sulfatase; pfam00884 336407002115 frataxin-like protein; Provisional; Region: cyaY; PRK01379 336407002116 putative iron binding site [ion binding]; other site 336407002117 Aminodeoxychorismate lyase [Coenzyme transport and metabolism]; Region: COG1559 336407002118 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 336407002119 dimerization interface [polypeptide binding]; other site 336407002120 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 336407002121 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 336407002122 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 336407002123 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 336407002124 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 336407002125 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 336407002126 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 336407002127 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 336407002128 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 336407002129 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 336407002130 Walker A motif; other site 336407002131 ATP binding site [chemical binding]; other site 336407002132 AAA domain (Cdc48 subfamily); Region: AAA_2; pfam07724 336407002133 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 336407002134 Protease HslV and the ATPase/chaperone HslU are part of an ATP-dependent proteolytic system that is the prokaryotic homolog of the proteasome. HslV is a dimer of hexamers (a dodecamer) that forms a central proteolytic chamber with active sites on the...; Region: protease_HslV; cd01913 336407002135 active site 336407002136 HslU subunit interaction site [polypeptide binding]; other site 336407002137 Protein of unknown function (DUF2628); Region: DUF2628; pfam10947 336407002138 HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the basis...; Region: HIT_like; cl00228 336407002139 nucleotide binding site/active site [active] 336407002140 HIT family signature motif; other site 336407002141 catalytic residue [active] 336407002142 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 336407002143 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 336407002144 type I secretion system ABC transporter, PrtD family; Region: type_I_sec_PrtD; TIGR01842 336407002145 ATP-binding cassette domain of PrtD, subfamily C; Region: ABCC_Protease_Secretion; cd03246 336407002146 Walker A/P-loop; other site 336407002147 ATP binding site [chemical binding]; other site 336407002148 Q-loop/lid; other site 336407002149 ABC transporter signature motif; other site 336407002150 Walker B; other site 336407002151 D-loop; other site 336407002152 H-loop/switch region; other site 336407002153 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 336407002154 Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl; Region: Biotinyl_lipoyl_domains; cl11404 336407002155 HlyD family secretion protein; Region: HlyD_3; pfam13437 336407002156 Predicted periplasmic protein (DUF2233); Region: DUF2233; pfam09992 336407002157 putative monovalent cation/H+ antiporter subunit G; Reviewed; Region: PRK12674 336407002158 putative monovalent cation/H+ antiporter subunit B; Reviewed; Region: PRK12507 336407002159 Predicted subunit of the Multisubunit Na+/H+ antiporter [Inorganic ion transport and metabolism]; Region: COG1563 336407002160 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 336407002161 Protein of unknown function (DUF2670); Region: DUF2670; pfam10875 336407002162 Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; Region: UCR_Fe-S_N; pfam10399 336407002163 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 336407002164 Iron-sulfur protein (ISP) component of the bc(1) complex family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The bc(1) complex is a multisubunit enzyme found in many different organisms including...; Region: Rieske_cytochrome_bc1; cd03470 336407002165 [2Fe-2S] cluster binding site [ion binding]; other site 336407002166 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cd00284 336407002167 Qi binding site; other site 336407002168 cytochrome b; Provisional; Region: CYTB; MTH00191 336407002169 intrachain domain interface; other site 336407002170 interchain domain interface [polypeptide binding]; other site 336407002171 heme bH binding site [chemical binding]; other site 336407002172 heme bL binding site [chemical binding]; other site 336407002173 Qo binding site; other site 336407002174 Cytochrome b(C-terminus)/b6/petD: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: cytochrome_b_C; cd00290 336407002175 interchain domain interface [polypeptide binding]; other site 336407002176 intrachain domain interface; other site 336407002177 Qi binding site; other site 336407002178 Qo binding site; other site 336407002179 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 336407002180 Transposase; Region: DEDD_Tnp_IS110; pfam01548 336407002181 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 336407002182 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 336407002183 Protein of unknown function (DUF3154); Region: DUF3154; pfam11351 336407002184 Molecular chaperone (small heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: IbpA; COG0071 336407002185 Alpha-crystallin domain (ACD) of alpha-crystallin-type small(s) heat shock proteins (Hsps). sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is the Alpha-crystallin domain (ACD). sHsps are generally...; Region: ACD_sHsps-like; cd06464 336407002186 putative dimer interface [polypeptide binding]; other site 336407002187 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 336407002188 AsmA-like C-terminal region; Region: AsmA_2; pfam13502 336407002189 protoheme IX farnesyltransferase; Provisional; Region: PRK04375 336407002190 UbiA prenyltransferase family; Region: UbiA; pfam01040 336407002191 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 336407002192 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 336407002193 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 336407002194 RNA binding surface [nucleotide binding]; other site 336407002195 Patatin [General function prediction only]; Region: COG3621 336407002196 Patatin-like phospholipase; includes PNPLA8, PNPLA9, and Pat17; Region: Pat17_PNPLA8_PNPLA9_like; cd07199 336407002197 active site 336407002198 nucleophile elbow; other site 336407002199 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 336407002200 DnaA N-terminal domain; Region: DnaA_N; pfam11638 336407002201 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 336407002202 Walker A motif; other site 336407002203 ATP binding site [chemical binding]; other site 336407002204 Walker B motif; other site 336407002205 arginine finger; other site 336407002206 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 336407002207 DnaA box-binding interface [nucleotide binding]; other site 336407002208 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; cl00125 336407002209 Uncharacterized conserved protein [Function unknown]; Region: COG2938 336407002210 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 336407002211 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 336407002212 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 336407002213 ATP binding site [chemical binding]; other site 336407002214 putative Mg++ binding site [ion binding]; other site 336407002215 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 336407002216 nucleotide binding region [chemical binding]; other site 336407002217 ATP-binding site [chemical binding]; other site 336407002218 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 336407002219 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 336407002220 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 336407002221 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 336407002222 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 336407002223 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 336407002224 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Region: murF; TIGR01143 336407002225 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 336407002226 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 336407002227 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 336407002228 Phospho-N-acetylmuramoyl-pentapeptide-transferase (mraY) is an enzyme responsible for the formation of the first lipid intermediate in the synthesis of bacterial cell wall peptidoglycan. It catalyzes the formation of...; Region: GT_MraY; cd06852 336407002229 Mg++ binding site [ion binding]; other site 336407002230 putative catalytic motif [active] 336407002231 putative substrate binding site [chemical binding]; other site 336407002232 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 336407002233 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 336407002234 putative substrate translocation pore; other site 336407002235 GTP-binding protein YchF; Reviewed; Region: PRK09601 336407002236 YchF GTPase; Region: YchF; cd01900 336407002237 G1 box; other site 336407002238 GTP/Mg2+ binding site [chemical binding]; other site 336407002239 Switch I region; other site 336407002240 G2 box; other site 336407002241 Switch II region; other site 336407002242 G3 box; other site 336407002243 G4 box; other site 336407002244 G5 box; other site 336407002245 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 336407002246 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 336407002247 Methyltransferase domain; Region: Methyltransf_26; pfam13659 336407002248 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 336407002249 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl14958 336407002250 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 336407002251 Acetyltransferases [General function prediction only]; Region: RimI; COG0456 336407002252 Coenzyme A binding pocket [chemical binding]; other site 336407002253 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 336407002254 putative active site [active] 336407002255 catalytic residue [active] 336407002256 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 336407002257 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 336407002258 5S rRNA interface [nucleotide binding]; other site 336407002259 CTC domain interface [polypeptide binding]; other site 336407002260 L16 interface [polypeptide binding]; other site 336407002261 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 336407002262 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 336407002263 FeS/SAM binding site; other site 336407002264 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 336407002265 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 336407002266 23S rRNA binding site [nucleotide binding]; other site 336407002267 L21 binding site [polypeptide binding]; other site 336407002268 L13 binding site [polypeptide binding]; other site 336407002269 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 336407002270 ribonuclease P; Reviewed; Region: rnpA; PRK01492 336407002271 Sec7 domain; Domain named after the S. cerevisiae SEC7 gene product. The Sec7 domain is the central domain of the guanine-nucleotide-exchange factors (GEFs) of the ADP-ribosylation factor family of small GTPases (ARFs) . It carries the exchange factor...; Region: Sec7; cd00171 336407002272 active site/putative ARF binding site [active] 336407002273 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 336407002274 Malic enzyme, N-terminal domain; Region: malic; pfam00390 336407002275 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 336407002276 putative NAD(P) binding site [chemical binding]; other site 336407002277 Phosphotransacetylase [Energy production and conversion]; Region: Pta; COG0280 336407002278 Predicted permeases [General function prediction only]; Region: COG0679 336407002279 lysyl-tRNA synthetase; Reviewed; Region: lysK; PRK00750 336407002280 catalytic core domain of class I lysyl tRNA synthetase; Region: LysRS_core_class_I; cd00674 336407002281 active site 336407002282 HIGH motif; other site 336407002283 KMSKS motif; other site 336407002284 Disulfide bond formation protein DsbB [Posttranslational modification, protein turnover, chaperones]; Region: DsbB; COG1495 336407002285 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: PhnK; COG1101 336407002286 First domain of the ATP-binding cassette component of cobalt transport system; Region: ABC_cobalt_CbiO_domain1; cd03225 336407002287 Walker A/P-loop; other site 336407002288 ATP binding site [chemical binding]; other site 336407002289 Q-loop/lid; other site 336407002290 ABC transporter signature motif; other site 336407002291 Walker B; other site 336407002292 D-loop; other site 336407002293 H-loop/switch region; other site 336407002294 Branched-chain amino acid transport system / permease component; Region: BPD_transp_2; pfam02653 336407002295 Transmembrane subunit (TM) of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which are involved in the uptake of branched-chain amino acids (AAs), as well as TMs of transporters involved in the uptake of...; Region: TM_PBP1_branched-chain-AA_like; cd06574 336407002296 TM-ABC transporter signature motif; other site 336407002297 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: COG2984 336407002298 Protein of unknown function (DUF328); Region: DUF328; pfam03883 336407002299 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 336407002300 MurG is an N-acetylglucosaminyltransferase, the last enzyme involved in the intracellular phase of peptidoglycan biosynthesis. It transfers N-acetyl-D-glucosamine (GlcNAc) from UDP-GlcNAc to the C4 hydroxyl of a lipid-linked N-acetylmuramoyl pentapeptide...; Region: GT1_MurG; cd03785 336407002301 active site 336407002302 homodimer interface [polypeptide binding]; other site 336407002303 cell division protein FtsW; Region: ftsW; TIGR02614 336407002304 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK01368 336407002305 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 336407002306 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 336407002307 DNA binding site [nucleotide binding] 336407002308 substrate interaction site [chemical binding]; other site 336407002309 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 336407002310 cofactor binding site; other site 336407002311 Protein of unknown function (DUF3035); Region: DUF3035; pfam11233 336407002312 lipoprotein signal peptidase; Reviewed; Region: lspA; PRK00376 336407002313 putative peptidase; Provisional; Region: PRK11649 336407002314 Peptidase family M23; Region: Peptidase_M23; pfam01551 336407002315 Cytidylyltransferase [Cell envelope biogenesis, outer membrane / Lipid metabolism]; Region: TagD; COG0615 336407002316 active site 336407002317 nucleotide binding site [chemical binding]; other site 336407002318 HIGH motif; other site 336407002319 KMSKS motif; other site 336407002320 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 336407002321 cytochrome c oxidase subunit II; Provisional; Region: COX2; MTH00154 336407002322 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; pfam00116 336407002323 cytochrome c oxidase subunit I; Validated; Region: COX1; MTH00007 336407002324 Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of...; Region: Cyt_c_Oxidase_I; cd01663 336407002325 Subunit I/III interface [polypeptide binding]; other site 336407002326 D-pathway; other site 336407002327 Subunit I/VIIc interface [polypeptide binding]; other site 336407002328 Subunit I/IV interface [polypeptide binding]; other site 336407002329 Subunit I/II interface [polypeptide binding]; other site 336407002330 Low-spin heme (heme a) binding site [chemical binding]; other site 336407002331 Subunit I/VIIa interface [polypeptide binding]; other site 336407002332 Subunit I/VIa interface [polypeptide binding]; other site 336407002333 Dimer interface; other site 336407002334 Putative water exit pathway; other site 336407002335 Binuclear center (heme a3/CuB) [ion binding]; other site 336407002336 K-pathway; other site 336407002337 Subunit I/Vb interface [polypeptide binding]; other site 336407002338 Putative proton exit pathway; other site 336407002339 Subunit I/VIb interface; other site 336407002340 Subunit I/VIc interface [polypeptide binding]; other site 336407002341 Electron transfer pathway; other site 336407002342 Subunit I/VIIIb interface [polypeptide binding]; other site 336407002343 Subunit I/VIIb interface [polypeptide binding]; other site 336407002344 RDD family; Region: RDD; pfam06271 336407002345 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212 336407002346 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; pfam01812 336407002347 Predicted glutamine amidotransferases [General function prediction only]; Region: COG2071 336407002348 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 336407002349 catalytic triad [active] 336407002350 Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond...; Region: LRR_RI; cl15309 336407002351 Leucine-rich repeats; other site 336407002352 Substrate binding site [chemical binding]; other site 336407002353 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 336407002354 DEAD/DEAH box helicase; Region: DEAD; pfam00270 336407002355 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 336407002356 SEC-C motif; Region: SEC-C; pfam02810 336407002357 peptidylprolyl isomerase; Reviewed; Region: prsA; PRK03002 336407002358 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 336407002359 Transposase; Region: DEDD_Tnp_IS110; pfam01548 336407002360 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 336407002361 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 336407002362 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 336407002363 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 336407002364 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 336407002365 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 336407002366 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 336407002367 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 336407002368 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 336407002369 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 336407002370 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 336407002371 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: PRK01424 336407002372 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 336407002373 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06589 336407002374 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 336407002375 Transposase; Region: DEDD_Tnp_IS110; pfam01548 336407002376 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 336407002377 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 336407002378 Multimeric flavodoxin WrbA [General function prediction only]; Region: WrbA; COG0655 336407002379 NADPH-dependent FMN reductase; Region: FMN_red; pfam03358 336407002380 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 336407002381 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 336407002382 active site 336407002383 HIGH motif; other site 336407002384 dimer interface [polypeptide binding]; other site 336407002385 KMSKS motif; other site 336407002386 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 336407002387 RNA binding surface [nucleotide binding]; other site 336407002388 Transposase, Mutator family; Region: Transposase_mut; pfam00872 336407002389 Transposase, Mutator family; Region: Transposase_mut; pfam00872 336407002390 Transposase, Mutator family; Region: Transposase_mut; pfam00872 336407002391 MULE transposase domain; Region: MULE; pfam10551 336407002392 Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond...; Region: LRR_RI; cl15309 336407002393 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 336407002394 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 336407002395 X-Prolyl Aminopeptidase 2. E.C. 3.4.11.9. Also known as X-Pro aminopeptidase, proline aminopeptidase, aminopeptidase P, and aminoacylproline aminopeptidase. Catalyses release of any N-terminal amino acid, including proline, that is linked with proline; Region: APP; cd01085 336407002396 active site 336407002397 Transposase; Region: DEDD_Tnp_IS110; pfam01548 336407002398 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 336407002399 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 336407002400 Autotransporter beta-domain; Region: Autotransporter; smart00869 336407002401 Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the...; Region: ALAD_PBGS_aspartate_rich; cd04823 336407002402 dimer interface [polypeptide binding]; other site 336407002403 allosteric magnesium binding site [ion binding]; other site 336407002404 active site 336407002405 aspartate-rich active site metal binding site; other site 336407002406 Schiff base residues; other site 336407002407 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 336407002408 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 336407002409 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 336407002410 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 336407002411 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 336407002412 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 336407002413 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 336407002414 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 336407002415 primosome assembly protein PriA; Validated; Region: PRK05580 336407002416 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 336407002417 ATP binding site [chemical binding]; other site 336407002418 putative Mg++ binding site [ion binding]; other site 336407002419 helicase superfamily c-terminal domain; Region: HELICc; smart00490 336407002420 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Provisional; Region: PRK06029 336407002421 Flavoprotein; Region: Flavoprotein; pfam02441 336407002422 SpoVT / AbrB like domain; Region: SpoVT_AbrB; smart00966 336407002423 PIN domain of ribonucleases (toxins), VapC, FitB, and PAE0151 of bacterial and archaeal toxin/antitoxin-like operons, and other similar homologs; Region: PIN_VapC-like; cd09861 336407002424 putative active site [active] 336407002425 replicative DNA helicase; Provisional; Region: PRK09165 336407002426 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 336407002427 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 336407002428 Walker A motif; other site 336407002429 ATP binding site [chemical binding]; other site 336407002430 Walker B motif; other site 336407002431 DNA binding loops [nucleotide binding] 336407002432 Tryptophan/tyrosine permease family; Region: Trp_Tyr_perm; cl17316 336407002433 Beta-lactamase enzyme family; Region: Beta-lactamase2; cl17872 336407002434 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 336407002435 muropeptide transporter; Reviewed; Region: ampG; PRK11902 336407002436 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 336407002437 putative substrate translocation pore; other site 336407002438 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 336407002439 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 336407002440 ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C; Region: ABCC_MsbA; cd03251 336407002441 Walker A/P-loop; other site 336407002442 ATP binding site [chemical binding]; other site 336407002443 Q-loop/lid; other site 336407002444 ABC transporter signature motif; other site 336407002445 Walker B; other site 336407002446 D-loop; other site 336407002447 H-loop/switch region; other site 336407002448 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 336407002449 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 336407002450 Walker A motif; other site 336407002451 ATP binding site [chemical binding]; other site 336407002452 Walker B motif; other site 336407002453 arginine finger; other site 336407002454 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 336407002455 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 336407002456 RuvA N terminal domain; Region: RuvA_N; pfam01330 336407002457 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 336407002458 Fic family protein [Function unknown]; Region: COG3177 336407002459 Domain of unknown function (DUF4172); Region: DUF4172; pfam13776 336407002460 Fic/DOC family; Region: Fic; pfam02661 336407002461 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 336407002462 putative substrate translocation pore; other site 336407002463 Iron-sulfur cluster assembly accessory protein; Region: TIGR00049 336407002464 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 336407002465 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 336407002466 trimerization site [polypeptide binding]; other site 336407002467 active site 336407002468 cysteine desulfurase; Provisional; Region: PRK14012 336407002469 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 336407002470 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 336407002471 catalytic residue [active] 336407002472 Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]; Region: NifS; COG1104 336407002473 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 336407002474 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 336407002475 catalytic residue [active] 336407002476 iron-sulfur cluster assembly transcription factor IscR; Region: IscR; TIGR02010 336407002477 Rrf2 family protein; Region: rrf2_super; TIGR00738 336407002478 hypothetical protein; Provisional; Region: PRK06661 336407002479 intersubunit interface [polypeptide binding]; other site 336407002480 active site 336407002481 Zn2+ binding site [ion binding]; other site 336407002482 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 336407002483 AAA domain; Region: AAA_14; pfam13173 336407002484 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase; Reviewed; Region: lpxC; PRK13186 336407002485 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 336407002486 Cytochrome c2 [Energy production and conversion]; Region: COG3474 336407002487 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: COG1585 336407002488 cell division protein FtsA; Region: ftsA; TIGR01174 336407002489 Cell division protein FtsA; Region: FtsA; smart00842 336407002490 Cell division protein FtsA; Region: FtsA; pfam14450 336407002491 Transposase; Region: DEDD_Tnp_IS110; pfam01548 336407002492 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 336407002493 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 336407002494 Cell division septal protein [Cell envelope biogenesis, outer membrane]; Region: FtsQ; COG1589 336407002495 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 336407002496 Cell division protein FtsQ; Region: FtsQ; pfam03799 336407002497 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 336407002498 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 336407002499 ATP-grasp domain; Region: ATP-grasp_4; cl17255 336407002500 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 336407002501 FAD binding domain; Region: FAD_binding_4; pfam01565 336407002502 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 336407002503 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 336407002504 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 336407002505 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 336407002506 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 336407002507 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 336407002508 Stress-induced morphogen (activity unknown) [Signal transduction mechanisms]; Region: BolA; COG0271 336407002509 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 336407002510 HlyD family secretion protein; Region: HlyD_3; pfam13437 336407002511 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 336407002512 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 336407002513 CDP-alcohol phosphatidyltransferase 2; Region: CDP-OH_P_tran_2; pfam08009 336407002514 phosphatidylserine decarboxylase; Provisional; Region: PRK05305 336407002515 Domain of unknown function (DUF2610); Region: DUF2610; pfam11020 336407002516 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]; Region: SuhB; COG0483 336407002517 Inositol-monophosphatase-like domains. This family of phosphatases is dependent on bivalent metal ions such as Mg++, and many members are inhibited by Li+ (which is thought to displace a bivalent ion in the active site). Substrates include fructose-1; Region: IMPase_like; cd01637 336407002518 active site 336407002519 elongation factor P; Validated; Region: PRK00529 336407002520 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 336407002521 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 336407002522 RNA binding site [nucleotide binding]; other site 336407002523 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 336407002524 RNA binding site [nucleotide binding]; other site 336407002525 response regulator PleD; Reviewed; Region: pleD; PRK09581 336407002526 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 336407002527 active site 336407002528 phosphorylation site [posttranslational modification] 336407002529 intermolecular recognition site; other site 336407002530 dimerization interface [polypeptide binding]; other site 336407002531 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 336407002532 active site 336407002533 phosphorylation site [posttranslational modification] 336407002534 intermolecular recognition site; other site 336407002535 dimerization interface [polypeptide binding]; other site 336407002536 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 336407002537 metal binding site [ion binding]; metal-binding site 336407002538 active site 336407002539 I-site; other site 336407002540 Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the Nudix hydrolase superfamily. Members of this family are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant...; Region: Ap4A_hydrolase_plant_like; cd03671 336407002541 putative active site [active] 336407002542 Ap4A binding site [chemical binding]; other site 336407002543 nudix motif; other site 336407002544 putative metal binding site [ion binding]; other site 336407002545 BRO family, N-terminal domain; Region: Bro-N; smart01040 336407002546 Spore Coat Protein U domain; Region: SCPU; pfam05229 336407002547 P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimD; COG3188 336407002548 Type VII secretion system (T7SS), usher protein; Region: Usher; pfam00577 336407002549 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 336407002550 Gram-negative pili assembly chaperone, N-terminal domain; Region: Pili_assembly_N; pfam00345 336407002551 Spore Coat Protein U domain; Region: SCPU; pfam05229 336407002552 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 336407002553 PIN domain of the VapC-like Sll0205 protein and homologs; Region: PIN_Sll0205; cd09872 336407002554 putative active site [active] 336407002555 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 336407002556 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 336407002557 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 336407002558 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14171 336407002559 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 336407002560 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 336407002561 homodimer interface [polypeptide binding]; other site 336407002562 NADP binding site [chemical binding]; other site 336407002563 substrate binding site [chemical binding]; other site 336407002564 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 336407002565 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 336407002566 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 336407002567 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; cl02529 336407002568 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 336407002569 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 336407002570 Ligand binding site; other site 336407002571 oligomer interface; other site 336407002572 CTP synthetase; Validated; Region: pyrG; PRK05380 336407002573 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 336407002574 Catalytic site [active] 336407002575 active site 336407002576 UTP binding site [chemical binding]; other site 336407002577 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 336407002578 active site 336407002579 putative oxyanion hole; other site 336407002580 catalytic triad [active] 336407002581 TLC ATP/ADP transporter; Region: TLC; pfam03219 336407002582 4'-phosphopantetheinyl transferase; Provisional; Region: acpS; PRK00070 336407002583 DNA-directed RNA polymerase, omega subunit; Region: rpoZ; TIGR00690 336407002584 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 336407002585 UDP-N-acetylglucosamine enolpyruvyl transferase catalyzes enolpyruvyl transfer as part of the first step in the biosynthesis of peptidoglycan, a component of the bacterial cell wall. The reaction is phosphoenolpyruvate + UDP-N-acetyl-D-glucosamine =...; Region: UdpNAET; cd01555 336407002586 hinge; other site 336407002587 active site 336407002588 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 336407002589 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 336407002590 Mg2+ binding site [ion binding]; other site 336407002591 G-X-G motif; other site 336407002592 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 336407002593 anchoring element; other site 336407002594 dimer interface [polypeptide binding]; other site 336407002595 ATP binding site [chemical binding]; other site 336407002596 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 336407002597 active site 336407002598 putative metal-binding site [ion binding]; other site 336407002599 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 336407002600 HAD-superfamily class IIA hydrolase, TIGR01459; Region: HAD-SF-IIA-hyp4 336407002601 Haloacid dehalogenase-like hydrolase; Region: Hydrolase_6; pfam13344 336407002602 Peptidase domain in the S8 and S53 families; Region: Peptidases_S8_S53; cl10459 336407002603 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 336407002604 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 336407002605 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 336407002606 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 336407002607 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 336407002608 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 336407002609 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 336407002610 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 336407002611 Type 1 glutamine amidotransferase (GATase1)-like domain; Region: GAT_1; cl00020 336407002612 conserved cys residue [active] 336407002613 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 336407002614 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 336407002615 MgtE intracellular N domain; Region: MgtE_N; pfam03448 336407002616 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 336407002617 Divalent cation transporter; Region: MgtE; pfam01769 336407002618 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 336407002619 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 336407002620 active site 336407002621 DNA binding site [nucleotide binding] 336407002622 Int/Topo IB signature motif; other site 336407002623 RecG-like helicase [DNA replication, recombination, and repair / Transcription]; Region: RecG; COG1200 336407002624 RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a...; Region: RecG_wedge_OBF; cd04488 336407002625 generic binding surface II; other site 336407002626 ssDNA binding site; other site 336407002627 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 336407002628 ATP binding site [chemical binding]; other site 336407002629 putative Mg++ binding site [ion binding]; other site 336407002630 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 336407002631 nucleotide binding region [chemical binding]; other site 336407002632 ATP-binding site [chemical binding]; other site 336407002633 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 336407002634 Coenzyme A transferase; Region: CoA_trans; cl17247 336407002635 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 336407002636 Transposase; Region: DEDD_Tnp_IS110; pfam01548 336407002637 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 336407002638 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 336407002639 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06591 336407002640 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 336407002641 putative monovalent cation/H+ antiporter subunit C; Reviewed; Region: PRK07375 336407002642 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 336407002643 VirB7 interaction site; other site 336407002644 VirB8 protein; Region: VirB8; cl01500 336407002645 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 336407002646 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cl11423 336407002647 Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion]; Region: VirB10; COG2948 336407002648 type IV secretion system ATPase VirB11; Provisional; Region: PRK13900 336407002649 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 336407002650 Walker A motif; other site 336407002651 hexamer interface [polypeptide binding]; other site 336407002652 ATP binding site [chemical binding]; other site 336407002653 Walker B motif; other site 336407002654 type IV secretion system component VirD4; Provisional; Region: PRK13897 336407002655 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion. These proteins aid the transfer of DNA from the plasmid into the host bacterial chromosome. They contain an ATP binding domain. VirD4 is involved in DNA transfer...; Region: TraG_VirD4; cd01126 336407002656 Walker A motif; other site 336407002657 ATP binding site [chemical binding]; other site 336407002658 Walker B motif; other site 336407002659 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 336407002660 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 336407002661 PIN domain of ribonucleases (toxins), VapC and FitB, of prokaryotic toxin/antitoxin operons, Pyrococcus horikoshii protein PH0500, and other similar bacterial and archaeal homologs; Region: PIN_VapC-FitB; cd09881 336407002662 oligomeric interface; other site 336407002663 putative active site [active] 336407002664 homodimer interface [polypeptide binding]; other site 336407002665 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06588 336407002666 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 336407002667 Prolyl oligopeptidase, N-terminal beta-propeller domain; Region: Peptidase_S9_N; pfam02897 336407002668 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 336407002669 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 336407002670 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 336407002671 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 336407002672 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 336407002673 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 336407002674 uncharacterized subgroup of the Escherichia coli Mg2+ transporter CorA_like subfamily; Region: EcCorA-like_u1; cd12837 336407002675 Cl binding site [ion binding]; other site 336407002676 oligomer interface [polypeptide binding]; other site 336407002677 Bacterial PH domain; Region: DUF304; pfam03703 336407002678 Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond...; Region: LRR_RI; cl15309 336407002679 Leucine-rich repeats; other site 336407002680 Substrate binding site [chemical binding]; other site 336407002681 metabolite-proton symporter; Region: 2A0106; TIGR00883 336407002682 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 336407002683 putative substrate translocation pore; other site 336407002684 Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]; Region: SpoT; COG0317 336407002685 HD domain; Region: HD_4; pfam13328 336407002686 DnaA N-terminal domain; Region: DnaA_N; pfam11638 336407002687 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 336407002688 50S ribosomal protein L17; Validated; Region: rplQ; PRK05591 336407002689 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 336407002690 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 336407002691 alphaNTD - beta interaction site [polypeptide binding]; other site 336407002692 alphaNTD homodimer interface [polypeptide binding]; other site 336407002693 alphaNTD - beta' interaction site [polypeptide binding]; other site 336407002694 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 336407002695 30S ribosomal protein S11; Validated; Region: PRK05309 336407002696 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 336407002697 30S ribosomal protein S13; Region: bact_S13; TIGR03631 336407002698 adenylate kinase; Reviewed; Region: adk; PRK00279 336407002699 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 336407002700 AMP-binding site [chemical binding]; other site 336407002701 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 336407002702 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 336407002703 SecY translocase; Region: SecY; pfam00344 336407002704 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 336407002705 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 336407002706 23S rRNA binding site [nucleotide binding]; other site 336407002707 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 336407002708 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 336407002709 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 336407002710 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 336407002711 23S rRNA interface [nucleotide binding]; other site 336407002712 L21e interface [polypeptide binding]; other site 336407002713 5S rRNA interface [nucleotide binding]; other site 336407002714 L27 interface [polypeptide binding]; other site 336407002715 L5 interface [polypeptide binding]; other site 336407002716 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 336407002717 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 336407002718 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 336407002719 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 336407002720 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08881 336407002721 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 336407002722 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 336407002723 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 336407002724 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 336407002725 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 336407002726 RNA binding site [nucleotide binding]; other site 336407002727 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 336407002728 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 336407002729 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 336407002730 23S rRNA interface [nucleotide binding]; other site 336407002731 putative translocon interaction site; other site 336407002732 signal recognition particle (SRP54) interaction site; other site 336407002733 L23 interface [polypeptide binding]; other site 336407002734 trigger factor interaction site; other site 336407002735 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 336407002736 23S rRNA interface [nucleotide binding]; other site 336407002737 5S rRNA interface [nucleotide binding]; other site 336407002738 putative antibiotic binding site [chemical binding]; other site 336407002739 L25 interface [polypeptide binding]; other site 336407002740 L27 interface [polypeptide binding]; other site 336407002741 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 336407002742 KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional...; Region: KH-II; cl00098 336407002743 G-X-X-G motif; other site 336407002744 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 336407002745 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 336407002746 putative translocon binding site; other site 336407002747 protein-rRNA interface [nucleotide binding]; other site 336407002748 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 336407002749 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 336407002750 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 336407002751 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 336407002752 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 336407002753 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 336407002754 50S ribosomal protein L3, bacterial; Region: L3_bact; TIGR03625 336407002755 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 336407002756 elongation factor Tu; Reviewed; Region: PRK00049 336407002757 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 336407002758 G1 box; other site 336407002759 GEF interaction site [polypeptide binding]; other site 336407002760 GTP/Mg2+ binding site [chemical binding]; other site 336407002761 Switch I region; other site 336407002762 G2 box; other site 336407002763 G3 box; other site 336407002764 Switch II region; other site 336407002765 G4 box; other site 336407002766 G5 box; other site 336407002767 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 336407002768 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 336407002769 Antibiotic Binding Site [chemical binding]; other site 336407002770 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 336407002771 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 336407002772 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 336407002773 fumarate hydratase; Reviewed; Region: fumC; PRK00485 336407002774 Class II fumarases; Region: Fumarase_classII; cd01362 336407002775 active site 336407002776 tetramer interface [polypeptide binding]; other site 336407002777 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: Phd; COG4118 336407002778 Transposase; Region: DEDD_Tnp_IS110; pfam01548 336407002779 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 336407002780 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 336407002781 cell division protein FtsZ; Validated; Region: PRK09330 336407002782 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 336407002783 nucleotide binding site [chemical binding]; other site 336407002784 SulA interaction site; other site 336407002785 Serine protease inhibitor ecotin [General function prediction only]; Region: Eco; COG4574 336407002786 secondary substrate binding site; other site 336407002787 primary substrate binding site; other site 336407002788 inhibition loop; other site 336407002789 dimerization interface [polypeptide binding]; other site 336407002790 Scaffold protein Nfu/NifU N terminal; Region: Nfu_N; smart00932 336407002791 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 336407002792 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5304 336407002793 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 336407002794 putative substrate translocation pore; other site 336407002795 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 336407002796 ATP-dependent RNA helicase RhlE; Provisional; Region: PRK10590 336407002797 ATP binding site [chemical binding]; other site 336407002798 Mg++ binding site [ion binding]; other site 336407002799 motif III; other site 336407002800 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 336407002801 nucleotide binding region [chemical binding]; other site 336407002802 ATP-binding site [chemical binding]; other site 336407002803 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 336407002804 DNA-binding site [nucleotide binding]; DNA binding site 336407002805 RNA-binding motif; other site 336407002806 Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond...; Region: LRR_RI; cl15309 336407002807 Predicted transcriptional regulator [Transcription]; Region: COG3636; cl17681 336407002808 Phage derived protein Gp49-like (DUF891); Region: Gp49; cl01470 336407002809 Ribbon-helix-helix protein, copG family; Region: RHH_1; pfam01402 336407002810 PemK-like protein; Region: PemK; pfam02452 336407002811 Methyltransferase domain; Region: Methyltransf_31; pfam13847 336407002812 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 336407002813 S-adenosylmethionine binding site [chemical binding]; other site 336407002814 Endolysins and autolysins are found in viruses and bacteria, respectively. The ds DNA phages of eubacteria use endolysins or muralytic enzymes in conjunction with hollin, a small membrane protein, to degrade the peptidoglycan found in bacterial cell...; Region: endolysin_autolysin; cd00737 336407002815 catalytic residues [active] 336407002816 Membrane carboxypeptidase/penicillin-binding protein PbpC [Cell envelope biogenesis, outer membrane]; Region: PbpC; COG4953 336407002817 Transglycosylase; Region: Transgly; pfam00912 336407002818 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 336407002819 Penicillin-Binding Protein C-terminus Family; Region: BiPBP_C; pfam06832 336407002820 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 336407002821 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 336407002822 ATP-binding cassette domain of iron-sulfur clusters transporter, subfamily C; Region: ABCC_ATM1_transporter; cd03253 336407002823 Walker A/P-loop; other site 336407002824 ATP binding site [chemical binding]; other site 336407002825 Q-loop/lid; other site 336407002826 ABC transporter signature motif; other site 336407002827 Walker B; other site 336407002828 D-loop; other site 336407002829 H-loop/switch region; other site 336407002830 Glutaredoxin (GRX) family, GRX bacterial class 1 and 3 (b_1_3)-like subfamily; composed of bacterial GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the...; Region: GRX_GRXb_1_3_like; cd03418 336407002831 GSH binding site [chemical binding]; other site 336407002832 catalytic residues [active] 336407002833 excinuclease ABC subunit B; Provisional; Region: PRK05298 336407002834 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 336407002835 ATP binding site [chemical binding]; other site 336407002836 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 336407002837 nucleotide binding region [chemical binding]; other site 336407002838 ATP-binding site [chemical binding]; other site 336407002839 Ultra-violet resistance protein B; Region: UvrB; pfam12344 336407002840 UvrB/uvrC motif; Region: UVR; pfam02151 336407002841 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 336407002842 Sodium:dicarboxylate symporter family; Region: SDF; pfam00375 336407002843 Uncharacterized protein involved in tolerance to divalent cations [Inorganic ion transport and metabolism]; Region: CutA; COG1324 336407002844 6-pyruvoyl-tetrahydropterin synthase [Coenzyme metabolism]; Region: COG0720 336407002845 active site 336407002846 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 336407002847 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 336407002848 E3 interaction surface; other site 336407002849 lipoyl attachment site [posttranslational modification]; other site 336407002850 e3 binding domain; Region: E3_binding; pfam02817 336407002851 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; pfam00198 336407002852 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 336407002853 Thiamine pyrophosphate (TPP) family, E1 of OGDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the 2-oxoglutarate dehydrogenase multienzyme complex (OGDC). OGDC catalyzes the oxidative decarboxylation of...; Region: TPP_E1_OGDC_like; cd02016 336407002854 TPP-binding site [chemical binding]; other site 336407002855 Transketolase, pyrimidine binding domain; Region: Transket_pyr; pfam02779 336407002856 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]; Region: COG2317 336407002857 Peptidase family M32 includes thermostable carboxypeptidases TaqCP and PfuCP; Region: M32_Taq; cd06460 336407002858 active site 336407002859 Zn binding site [ion binding]; other site 336407002860 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 336407002861 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 336407002862 Walker A/P-loop; other site 336407002863 ATP binding site [chemical binding]; other site 336407002864 Q-loop/lid; other site 336407002865 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 336407002866 ABC transporter signature motif; other site 336407002867 Walker B; other site 336407002868 D-loop; other site 336407002869 H-loop/switch region; other site 336407002870 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 336407002871 Type IV secretory pathway, VirB2 components (pilins) [Intracellular trafficking and secretion]; Region: VirB2; COG3838 336407002872 Cytochrome c oxidase subunit III. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of...; Region: Cyt_c_Oxidase_III; cd01665 336407002873 Subunit III/VIIa interface [polypeptide binding]; other site 336407002874 Phospholipid binding site [chemical binding]; other site 336407002875 Subunit I/III interface [polypeptide binding]; other site 336407002876 Subunit III/VIb interface [polypeptide binding]; other site 336407002877 Subunit III/VIa interface; other site 336407002878 Subunit III/Vb interface [polypeptide binding]; other site 336407002879 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 336407002880 diiron binding motif [ion binding]; other site 336407002881 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK06585 336407002882 Lipopolysaccharide-assembly; Region: LptE; cl01125 336407002883 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 336407002884 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 336407002885 Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]; Region: DegQ; COG0265 336407002886 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 336407002887 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 336407002888 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 336407002889 Nucleotide-binding domain of human HSPA9, Escherichia coli DnaK, and similar proteins; Region: HSPA9-like_NBD; cd11733 336407002890 nucleotide binding site [chemical binding]; other site 336407002891 NEF interaction site [polypeptide binding]; other site 336407002892 SBD interface [polypeptide binding]; other site 336407002893 chaperone protein DnaJ; Provisional; Region: PRK14300 336407002894 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 336407002895 HSP70 interaction site [polypeptide binding]; other site 336407002896 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 336407002897 substrate binding site [polypeptide binding]; other site 336407002898 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 336407002899 Zn binding sites [ion binding]; other site 336407002900 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 336407002901 dimer interface [polypeptide binding]; other site 336407002902 Putative cation transport regulator [General function prediction only]; Region: ChaB; COG4572 336407002903 Outer membrane protein/protective antigen OMA87 [Cell envelope biogenesis, outer membrane]; Region: COG4775 336407002904 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 336407002905 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 336407002906 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 336407002907 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 336407002908 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 336407002909 Surface antigen; Region: Bac_surface_Ag; pfam01103 336407002910 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]; Region: COG0750 336407002911 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 336407002912 active site 336407002913 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 336407002914 protein binding site [polypeptide binding]; other site 336407002915 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 336407002916 putative substrate binding region [chemical binding]; other site 336407002917 transcription antitermination protein NusB; Reviewed; Region: nusB; PRK00202 336407002918 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 336407002919 FtsJ-like methyltransferase; Region: FtsJ; pfam01728 336407002920 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 336407002921 putative coenzyme Q binding site [chemical binding]; other site 336407002922 Protein of unknown function (DUF2674); Region: DUF2674; pfam10879 336407002923 AAA domain; Region: AAA_22; pfam13401 336407002924 Tetratricopeptide repeat; Region: TPR_12; pfam13424 336407002925 Tetratricopeptide repeat; Region: TPR_12; pfam13424 336407002926 Tetratricopeptide repeat; Region: TPR_12; pfam13424 336407002927 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 336407002928 non-specific DNA binding site [nucleotide binding]; other site 336407002929 salt bridge; other site 336407002930 sequence-specific DNA binding site [nucleotide binding]; other site 336407002931 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 336407002932 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 336407002933 putative monovalent cation/H+ antiporter subunit E; Reviewed; Region: PRK06580 336407002934 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 336407002935 putative nucleotide binding site [chemical binding]; other site 336407002936 uridine monophosphate binding site [chemical binding]; other site 336407002937 homohexameric interface [polypeptide binding]; other site 336407002938 ribosome recycling factor; Reviewed; Region: frr; PRK00083 336407002939 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 336407002940 hinge region; other site 336407002941 aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed; Region: gatC; PRK00034 336407002942 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 336407002943 aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed; Region: gatA; PRK00012 336407002944 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 336407002945 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 336407002946 GatB domain; Region: GatB_Yqey; smart00845 336407002947 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 336407002948 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 336407002949 substrate binding pocket [chemical binding]; other site 336407002950 membrane-bound complex binding site; other site 336407002951 hinge residues; other site 336407002952 Flavin reductase like domain; Region: Flavin_Reduct; smart00903 336407002953 dihydrodipicolinate reductase; Provisional; Region: PRK00048 336407002954 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 336407002955 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 336407002956 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 336407002957 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 336407002958 Uncharacterized conserved small protein [Function unknown]; Region: COG5508 336407002959 Protein of unknown function (DUF1674); Region: DUF1674; pfam07896 336407002960 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385 336407002961 RNA methyltransferase, RsmE family; Region: TIGR00046 336407002962 MJ0042 family finger-like domain; Region: MJ0042_CXXC; TIGR02098 336407002963 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 336407002964 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate (THDP) N-succinyltransferase (also called THP succinyltransferase): THDP N-succinyltransferase catalyzes the conversion of tetrahydrodipicolinate and succinyl-CoA to N-succinyltetrahydrodipicolinate and CoA; Region: LbH_THP_succinylT; cd03350 336407002965 trimer interface [polypeptide binding]; other site 336407002966 active site 336407002967 substrate binding site [chemical binding]; other site 336407002968 CoA binding site [chemical binding]; other site 336407002969 Domain of unknown function (DUF2383); Region: DUF2383; pfam09537 336407002970 coproporphyrinogen III oxidase; Provisional; Region: PRK06582 336407002971 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 336407002972 FeS/SAM binding site; other site 336407002973 HemN C-terminal domain; Region: HemN_C; pfam06969 336407002974 putative transposase; Provisional; Region: PRK09857 336407002975 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 336407002976 signal recognition particle protein; Provisional; Region: PRK10867 336407002977 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 336407002978 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 336407002979 P loop; other site 336407002980 GTP binding site [chemical binding]; other site 336407002981 Signal peptide binding domain; Region: SRP_SPB; pfam02978 336407002982 DNA polymerase III subunit delta'; Validated; Region: PRK06581 336407002983 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 336407002984 IHF dimer interface [polypeptide binding]; other site 336407002985 IHF - DNA interface [nucleotide binding]; other site 336407002986 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 336407002987 Protein export membrane protein; Region: SecD_SecF; cl14618 336407002988 Uncharacterized conserved protein [Function unknown]; Region: COG2155 336407002989 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 336407002990 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 336407002991 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 336407002992 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 336407002993 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 336407002994 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 336407002995 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 336407002996 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 336407002997 PTS_IIA, PTS system, glucose/sucrose 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 family...; Region: PTS_IIA_glc; cl00162 336407002998 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 336407002999 DNA binding site [nucleotide binding] 336407003000 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 336407003001 DNA-directed RNA polymerase subunit beta; Reviewed; Region: rpoB; PRK00405 336407003002 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 336407003003 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 336407003004 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 336407003005 RNA polymerase Rpb2, domain 6; Region: RNA_pol_Rpb2_6; pfam00562 336407003006 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 336407003007 RPB3 interaction site [polypeptide binding]; other site 336407003008 RPB1 interaction site [polypeptide binding]; other site 336407003009 RPB11 interaction site [polypeptide binding]; other site 336407003010 RPB10 interaction site [polypeptide binding]; other site 336407003011 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 336407003012 core dimer interface [polypeptide binding]; other site 336407003013 peripheral dimer interface [polypeptide binding]; other site 336407003014 L10 interface [polypeptide binding]; other site 336407003015 L11 interface [polypeptide binding]; other site 336407003016 putative EF-Tu interaction site [polypeptide binding]; other site 336407003017 putative EF-G interaction site [polypeptide binding]; other site 336407003018 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 336407003019 23S rRNA interface [nucleotide binding]; other site 336407003020 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 336407003021 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 336407003022 mRNA/rRNA interface [nucleotide binding]; other site 336407003023 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 336407003024 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 336407003025 23S rRNA interface [nucleotide binding]; other site 336407003026 L7/L12 interface [polypeptide binding]; other site 336407003027 putative thiostrepton binding site; other site 336407003028 L25 interface [polypeptide binding]; other site 336407003029 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 336407003030 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 336407003031 putative homodimer interface [polypeptide binding]; other site 336407003032 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 336407003033 heterodimer interface [polypeptide binding]; other site 336407003034 homodimer interface [polypeptide binding]; other site 336407003035 preprotein translocase subunit SecE; Reviewed; Region: secE; PRK07597 336407003036 elongation factor G; Reviewed; Region: PRK00007 336407003037 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 336407003038 G1 box; other site 336407003039 putative GEF interaction site [polypeptide binding]; other site 336407003040 GTP/Mg2+ binding site [chemical binding]; other site 336407003041 Switch I region; other site 336407003042 G2 box; other site 336407003043 G3 box; other site 336407003044 Switch II region; other site 336407003045 G4 box; other site 336407003046 G5 box; other site 336407003047 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 336407003048 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 336407003049 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 336407003050 30S ribosomal protein S7; Validated; Region: PRK05302 336407003051 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 336407003052 S17 interaction site [polypeptide binding]; other site 336407003053 S8 interaction site; other site 336407003054 16S rRNA interaction site [nucleotide binding]; other site 336407003055 streptomycin interaction site [chemical binding]; other site 336407003056 23S rRNA interaction site [nucleotide binding]; other site 336407003057 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 336407003058 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 336407003059 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 336407003060 dimer interface [polypeptide binding]; other site 336407003061 conserved gate region; other site 336407003062 putative PBP binding loops; other site 336407003063 ABC-ATPase subunit interface; other site 336407003064 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK09078 336407003065 L-aspartate oxidase; Provisional; Region: PRK06175 336407003066 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 336407003067 Plasmid stabilization system protein [General function prediction only]; Region: ParE; COG3668 336407003068 Uncharacterized protein family (UPF0156); Region: RHH_2; cl17383 336407003069 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase D (SdhD) subunit-like; composed of predominantly uncharacterized bacterial proteins with similarity to the E. coli SdhD subunit. One characterized protein is the respiratory...; Region: SQR_TypeC_SdhD_like; cd03495 336407003070 putative SdhC subunit interface [polypeptide binding]; other site 336407003071 putative proximal heme binding site [chemical binding]; other site 336407003072 putative Iron-sulfur protein interface [polypeptide binding]; other site 336407003073 putative proximal quinone binding site; other site 336407003074 Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase C (SdhC) subunit; composed of bacterial SdhC and eukaryotic large cytochrome b binding (CybL) proteins. SQR catalyzes the oxidation of succinate to fumarate coupled to the...; Region: SQR_TypeC_SdhC; cd03499 336407003075 Iron-sulfur protein interface; other site 336407003076 proximal quinone binding site [chemical binding]; other site 336407003077 SdhD (CybS) interface [polypeptide binding]; other site 336407003078 proximal heme binding site [chemical binding]; other site 336407003079 hypothetical protein; Validated; Region: PRK01415 336407003080 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 336407003081 active site residue [active] 336407003082 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 336407003083 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 336407003084 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 336407003085 protein binding site [polypeptide binding]; other site 336407003086 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 336407003087 protein binding site [polypeptide binding]; other site 336407003088 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 336407003089 Band_7_HflC: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfC (High frequency of lysogenization C). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflC; cd03405 336407003090 Band_7_HflK: The band 7 domain of flotillin (reggie) like proteins. This group includes proteins similar to prokaryotic HlfK (High frequency of lysogenization K). Although many members of the band 7 family are lipid raft associated, prokaryote plasma...; Region: Band_7_HflK; cd03404 336407003091 HflK protein; Region: hflK; TIGR01933 336407003092 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Mrp; COG0489 336407003093 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 336407003094 Walker A motif; other site 336407003095 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 336407003096 Predicted nucleoside-diphosphate-sugar epimerase [Cell envelope biogenesis, outer membrane]; Region: COG3660 336407003097 Mitochondrial fission ELM1; Region: Mito_fiss_Elm1; pfam06258 336407003098 Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; Region: NT_KNTase_like; cd05403 336407003099 active site 336407003100 NTP binding site [chemical binding]; other site 336407003101 metal binding triad [ion binding]; metal-binding site 336407003102 antibiotic binding site [chemical binding]; other site 336407003103 nucleotidyltransferase substrate binding protein, HI0074 family; Region: HI0074; TIGR01987 336407003104 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 336407003105 SpoU rRNA Methylase family; Region: SpoU_methylase; cl17307 336407003106 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD...; Region: RuvC_resolvase; cd00529 336407003107 active site 336407003108 putative DNA-binding cleft [nucleotide binding]; other site 336407003109 dimer interface [polypeptide binding]; other site 336407003110 GTPase Era; Reviewed; Region: era; PRK00089 336407003111 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 336407003112 G1 box; other site 336407003113 GTP/Mg2+ binding site [chemical binding]; other site 336407003114 Switch I region; other site 336407003115 G2 box; other site 336407003116 Switch II region; other site 336407003117 G3 box; other site 336407003118 G4 box; other site 336407003119 G5 box; other site 336407003120 KH domain; Region: KH_2; pfam07650 336407003121 TPR repeat; Region: TPR_11; pfam13414 336407003122 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 336407003123 binding surface 336407003124 TPR motif; other site 336407003125 TPR repeat; Region: TPR_11; pfam13414 336407003126 ribonuclease III; Reviewed; Region: rnc; PRK00102 336407003127 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 336407003128 dimerization interface [polypeptide binding]; other site 336407003129 active site 336407003130 metal binding site [ion binding]; metal-binding site 336407003131 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 336407003132 dsRNA binding site [nucleotide binding]; other site 336407003133 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 336407003134 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 336407003135 Catalytic site [active] 336407003136 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 336407003137 NADH dehydrogenase I subunit F; Provisional; Region: PRK13596 336407003138 SLBB domain; Region: SLBB; pfam10531 336407003139 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; smart00928 336407003140 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 336407003141 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 336407003142 Protein export membrane protein; Region: SecD_SecF; pfam02355 336407003143 hypothetical protein; Provisional; Region: PRK13694 336407003144 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 336407003145 UDP-N-acetylglucosamine O-acyltransferase (UDP-GlcNAc acyltransferase): Proteins in this family catalyze the transfer of (R)-3-hydroxymyristic acid from its acyl carrier protein thioester to UDP-GlcNAc. It is the first enzyme in the lipid A biosynthetic...; Region: LbH_UDP-GlcNAc_AT; cd03351 336407003146 active site 336407003147 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 336407003148 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 336407003149 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 336407003150 UDP-3-O-acyl-glucosamine N-acyltransferase (LpxD): The enzyme catalyzes the transfer of 3-hydroxymyristic acid or 3-hydroxy-arachidic acid, depending on the organism, from the acyl carrier protein (ACP) to UDP-3-O-acyl-glucosamine to produce UDP-2; Region: LbH_LpxD; cd03352 336407003151 trimer interface [polypeptide binding]; other site 336407003152 active site 336407003153 UDP-GlcNAc binding site [chemical binding]; other site 336407003154 lipid binding site [chemical binding]; lipid-binding site 336407003155 Cytotoxic translational repressor of toxin-antitoxin stability system [Translation, ribosomal structure and biogenesis / Cell division and chromosome partitioning]; Region: RelE; COG2026 336407003156 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 336407003157 Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only]; Region: RssA; COG1752 336407003158 ExoU and VipD-like proteins; homologus to patatin, cPLA2, and iPLA2; Region: Pat_ExoU_VipD_like; cd07207 336407003159 active site 336407003160 nucleophile elbow; other site 336407003161 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 336407003162 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 336407003163 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 336407003164 Putative catalytic NodB homology domain of uncharacterized protein RC0012 from Rickettsia conorii and its bacterial homologs; Region: CE4_RC0012_like; cd10963 336407003165 NodB motif; other site 336407003166 putative active site [active] 336407003167 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 336407003168 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 336407003169 FMN binding site [chemical binding]; other site 336407003170 active site 336407003171 catalytic residues [active] 336407003172 substrate binding site [chemical binding]; other site 336407003173 Protein of unknown function (DUF3800); Region: DUF3800; pfam12686 336407003174 Protein of unknown function (DUF3800); Region: DUF3800; pfam12686 336407003175 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 336407003176 Uncharacterized conserved protein [General function prediction only]; Region: BioY; COG1268 336407003177 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 336407003178 Glutathione S-transferase (GST) family, N-terminal domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic...; Region: GST_N_family; cd00570 336407003179 GSH binding site (G-site) [chemical binding]; other site 336407003180 C-terminal domain interface [polypeptide binding]; other site 336407003181 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 336407003182 N-terminal domain interface [polypeptide binding]; other site 336407003183 dimer interface [polypeptide binding]; other site 336407003184 substrate binding pocket (H-site) [chemical binding]; other site 336407003185 pyruvate phosphate dikinase; Provisional; Region: PRK09279 336407003186 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 336407003187 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 336407003188 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 336407003189 DNA polymerase I; Provisional; Region: PRK05755 336407003190 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 336407003191 active site 336407003192 metal binding site 1 [ion binding]; metal-binding site 336407003193 putative 5' ssDNA interaction site; other site 336407003194 metal binding site 3; metal-binding site 336407003195 metal binding site 2 [ion binding]; metal-binding site 336407003196 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 336407003197 putative DNA binding site [nucleotide binding]; other site 336407003198 putative metal binding site [ion binding]; other site 336407003199 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 336407003200 active site 336407003201 DNA binding site [nucleotide binding] 336407003202 catalytic site [active] 336407003203 Transposase; Region: DEDD_Tnp_IS110; pfam01548 336407003204 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 336407003205 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 336407003206 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl17212 336407003207 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl17212 336407003208 Acetate kinase [Energy production and conversion]; Region: ackA; COG0282 336407003209 looped-hinge helix DNA binding domain, AbrB family; Region: lp_hng_hel_AbrB; TIGR01439 336407003210 PIN (PilT N terminus) domain: Superfamily; Region: PIN_SF; cl14812 336407003211 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 336407003212 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 336407003213 Domain of unknown function (DUF4375); Region: DUF4375; pfam14300 336407003214 tRNA (guanine-N(1)-)-methyltransferase; Reviewed; Region: trmD; PRK00026 336407003215 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 336407003216 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 336407003217 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 336407003218 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 336407003219 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 336407003220 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 336407003221 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 336407003222 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 336407003223 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 336407003224 Transposase; Region: DEDD_Tnp_IS110; pfam01548 336407003225 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 336407003226 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 336407003227 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 336407003228 CoA binding domain; Region: CoA_binding; pfam02629 336407003229 CoA-ligase; Region: Ligase_CoA; pfam00549 336407003230 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 336407003231 ATP-grasp domain; Region: ATP-grasp_2; pfam08442 336407003232 CoA-ligase; Region: Ligase_CoA; pfam00549 336407003233 PIN domain of ribonucleases (toxins), VapC, FitB, and PAE0151 of bacterial and archaeal toxin/antitoxin-like operons, and other similar homologs; Region: PIN_VapC-like; cd09861 336407003234 putative active site [active] 336407003235 Regulators of stationary/sporulation gene expression [Transcription]; Region: AbrB; COG2002 336407003236 looped-hinge helix DNA binding domain, AbrB family; Region: lp_hng_hel_AbrB; TIGR01439 336407003237 Cytochrome B561 [Energy production and conversion]; Region: CybB; COG3038 336407003238 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cl00859 336407003239 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 336407003240 Prolyl oligopeptidase family; Region: Peptidase_S9; pfam00326 336407003241 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4395 336407003242 ribosome-binding factor A; Validated; Region: rbfA; PRK00521 336407003243 Predicted membrane protein [Function unknown]; Region: COG1238 336407003244 RDD family; Region: RDD; pfam06271 336407003245 Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]; Region: RecR; COG0353 336407003246 RecR protein; Region: RecR; pfam02132 336407003247 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 336407003248 putative active site [active] 336407003249 putative metal-binding site [ion binding]; other site 336407003250 tetramer interface [polypeptide binding]; other site 336407003251 Transposase; Region: DEDD_Tnp_IS110; pfam01548 336407003252 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 336407003253 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 336407003254 bifunctional N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase/tRNA (m7G46) methyltransferase; Reviewed; Region: PRK01544 336407003255 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 336407003256 S-adenosylmethionine binding site [chemical binding]; other site 336407003257 Predicted S-adenosylmethionine-dependent methyltransferase [General function prediction only]; Region: COG0220 336407003258 PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; Region: PIN_Pae0151; cd09873 336407003259 putative active site [active] 336407003260 homotetrameric interface [polypeptide binding]; other site 336407003261 metal binding site [ion binding]; metal-binding site 336407003262 Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]; Region: Phd; COG4118 336407003263 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 336407003264 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 336407003265 RNA binding surface [nucleotide binding]; other site 336407003266 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 336407003267 active site 336407003268 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 336407003269 Fe-S cluster binding site [ion binding]; other site 336407003270 active site 336407003271 Transposase; Region: DEDD_Tnp_IS110; pfam01548 336407003272 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 336407003273 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 336407003274 NAD kinase [Coenzyme metabolism]; Region: nadF; cl01255 336407003275 NAD kinase [Coenzyme metabolism]; Region: nadF; cl01255 336407003276 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 336407003277 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 336407003278 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 336407003279 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK06603 336407003280 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 336407003281 NAD binding site [chemical binding]; other site 336407003282 homotetramer interface [polypeptide binding]; other site 336407003283 homodimer interface [polypeptide binding]; other site 336407003284 substrate binding site [chemical binding]; other site 336407003285 active site 336407003286 apolipoprotein N-acyltransferase; Region: lnt; TIGR00546 336407003287 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 336407003288 putative active site [active] 336407003289 catalytic triad [active] 336407003290 putative dimer interface [polypeptide binding]; other site 336407003291 Predicted transcriptional regulators [Transcription]; Region: HipB; COG1396 336407003292 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 336407003293 non-specific DNA binding site [nucleotide binding]; other site 336407003294 salt bridge; other site 336407003295 sequence-specific DNA binding site [nucleotide binding]; other site 336407003296 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 336407003297 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 336407003298 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 336407003299 UGMP family protein; Validated; Region: PRK09604 336407003300 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 336407003301 Carbamoyltransferase; Region: CmcH_NodU; pfam02543 336407003302 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 336407003303 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 336407003304 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 336407003305 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 336407003306 Type IV secretory pathway, VirB6 components [Intracellular trafficking and secretion]; Region: VirB6; COG3704 336407003307 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 336407003308 type IV secretion system ATPase VirB4; Provisional; Region: PRK13898 336407003309 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 336407003310 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 336407003311 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 336407003312 Walker A/P-loop; other site 336407003313 ATP binding site [chemical binding]; other site 336407003314 Transposase; Region: DEDD_Tnp_IS110; pfam01548 336407003315 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 336407003316 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 336407003317 Circularly permuted YlqF-related GTPases; Region: YlqF_related_GTPase; cl17249 336407003318 50S ribosome-binding GTPase; Region: MMR_HSR1; pfam01926 336407003319 G1 box; other site 336407003320 G1 box; other site 336407003321 GTP/Mg2+ binding site [chemical binding]; other site 336407003322 GTP/Mg2+ binding site [chemical binding]; other site 336407003323 G2 box; other site 336407003324 Switch I region; other site 336407003325 G3 box; other site 336407003326 Switch II region; other site 336407003327 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 336407003328 Opacity protein and related surface antigens [Cell envelope biogenesis, outer membrane]; Region: COG3637 336407003329 Ferredoxin [Energy production and conversion]; Region: COG1146 336407003330 4Fe-4S binding domain; Region: Fer4; cl02805 336407003331 Domain of unknown function (DUF3470); Region: DUF3470; pfam11953 336407003332 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 336407003333 Transposase; Region: DEDD_Tnp_IS110; pfam01548 336407003334 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 336407003335 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 336407003336 type IV secretion system protein VirB3; Provisional; Region: PRK13899 336407003337 Acetylglutamate kinase [Amino acid transport and metabolism]; Region: ArgB; COG0548 336407003338 substrate binding site [chemical binding]; other site 336407003339 nucleotide binding site [chemical binding]; other site 336407003340 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 336407003341 G1 box; other site 336407003342 GTP/Mg2+ binding site [chemical binding]; other site 336407003343 Switch I region; other site 336407003344 G2 box; other site 336407003345 G3 box; other site 336407003346 Switch II region; other site 336407003347 G4 box; other site 336407003348 G5 box; other site 336407003349 50S ribosomal protein L31; Provisional; Region: PRK01397 336407003350 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 336407003351 Autotransporter beta-domain; Region: Autotransporter; pfam03797 336407003352 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 336407003353 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 336407003354 active site 336407003355 HIGH motif; other site 336407003356 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 336407003357 KMSKS motif; other site 336407003358 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 336407003359 tRNA binding surface [nucleotide binding]; other site 336407003360 anticodon binding site; other site 336407003361 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 336407003362 rRNA interaction site [nucleotide binding]; other site 336407003363 S8 interaction site; other site 336407003364 putative laminin-1 binding site; other site 336407003365 elongation factor Ts; Provisional; Region: tsf; PRK09377 336407003366 UBA/TS-N domain; Region: UBA; pfam00627 336407003367 Elongation factor TS; Region: EF_TS; pfam00889 336407003368 Elongation factor TS; Region: EF_TS; pfam00889 336407003369 MutS2 family protein; Region: mutS2; TIGR01069 336407003370 Predicted ATPase or kinase [General function prediction only]; Region: COG0802 336407003371 Transcriptional regulators, similar to M. xanthus CarD [Transcription]; Region: COG1329 336407003372 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 336407003373 Thioredoxin; Region: Thioredoxin_4; pfam13462 336407003374 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5336 336407003375 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 336407003376 ATP synthase subunit 6 (eukaryotes),also subunit A (prokaryotes); Region: ATP_synt_6_or_A; TIGR01131 336407003377 F0F1 ATP synthase subunit C; Validated; Region: PRK07558 336407003378 F0F1 ATP synthase subunit B'; Validated; Region: PRK06569 336407003379 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 336407003380 F0F1 ATP synthase subunit B; Validated; Region: PRK06568 336407003381 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 336407003382 7-cyano-7-deazaguanine reductase; Region: QueF; TIGR03138 336407003383 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2904 336407003384 Enzyme related to GTP cyclohydrolase I [General function prediction only]; Region: COG0780 336407003385 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 336407003386 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 336407003387 active site 336407003388 phosphorylation site [posttranslational modification] 336407003389 intermolecular recognition site; other site 336407003390 dimerization interface [polypeptide binding]; other site 336407003391 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 336407003392 DNA binding site [nucleotide binding] 336407003393 Preprotein translocase subunit SecB. SecB is a cytoplasmic component of the multisubunit membrane-bound enzyme termed Sec protein translocase, which is the main constituent of the General Secretory (type II) Pathway involved in translocation of nascent...; Region: Translocase_SecB; cd00557 336407003394 SecA binding site; other site 336407003395 Preprotein binding site; other site 336407003396 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 336407003397 trimer interface [polypeptide binding]; other site 336407003398 active site 336407003399 Gram-negative porin; Region: Porin_4; pfam13609 336407003400 Iron-sulfur cluster assembly accessory protein; Region: TIGR00049 336407003401 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria; Region: GIY-YIG_unchar_3; cd10448 336407003402 GIY-YIG motif/motif A; other site 336407003403 putative active site [active] 336407003404 putative metal binding site [ion binding]; other site 336407003405 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 336407003406 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 336407003407 Zn2+ binding site [ion binding]; other site 336407003408 Mg2+ binding site [ion binding]; other site 336407003409 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 336407003410 Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: ArgS; COG0018 336407003411 Arginyl tRNA synthetase N terminal dom; Region: Arg_tRNA_synt_N; smart01016 336407003412 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 336407003413 active site 336407003414 HIGH motif; other site 336407003415 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 336407003416 KMSK motif region; other site 336407003417 tRNA binding surface [nucleotide binding]; other site 336407003418 DALR anticodon binding domain; Region: DALR_1; smart00836 336407003419 anticodon binding site; other site 336407003420 Sporulation related domain; Region: SPOR; pfam05036 336407003421 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 336407003422 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 336407003423 CAP-like domain; other site 336407003424 active site 336407003425 primary dimer interface [polypeptide binding]; other site 336407003426 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 336407003427 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 336407003428 minor groove reading motif; other site 336407003429 helix-hairpin-helix signature motif; other site 336407003430 substrate binding pocket [chemical binding]; other site 336407003431 active site 336407003432 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 336407003433 putative hydrolase; Provisional; Region: PRK11460 336407003434 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 336407003435 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 336407003436 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 336407003437 dimer interface [polypeptide binding]; other site 336407003438 active site 336407003439 glycine-pyridoxal phosphate binding site [chemical binding]; other site 336407003440 folate binding site [chemical binding]; other site 336407003441 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 336407003442 lipoyl synthase; Provisional; Region: PRK05481 336407003443 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 336407003444 FeS/SAM binding site; other site 336407003445 metal-binding heat shock protein; Provisional; Region: PRK00016 336407003446 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 336407003447 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 336407003448 Transporter associated domain; Region: CorC_HlyC; smart01091 336407003449 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 336407003450 nudix motif; other site 336407003451 Predicted integral membrane protein (DUF2269); Region: DUF2269; pfam10027 336407003452 DoxX-like family; Region: DoxX_3; pfam13781 336407003453 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 336407003454 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 336407003455 NADH(P)-binding; Region: NAD_binding_10; pfam13460 336407003456 NAD(P) binding site [chemical binding]; other site 336407003457 active site 336407003458 Predicted aspartyl protease [General function prediction only]; Region: COG3577 336407003459 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 336407003460 catalytic motif [active] 336407003461 Catalytic residue [active] 336407003462 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 336407003463 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 336407003464 Walker A/P-loop; other site 336407003465 ATP binding site [chemical binding]; other site 336407003466 Q-loop/lid; other site 336407003467 ABC transporter signature motif; other site 336407003468 Walker B; other site 336407003469 D-loop; other site 336407003470 H-loop/switch region; other site 336407003471 Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]; Region: PhnP; COG1235 336407003472 putative hydrolase; Provisional; Region: PRK02113 336407003473 PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid...; Region: PAP2_like; cd01610 336407003474 active site 336407003475 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 336407003476 Predicted permeases [General function prediction only]; Region: COG0795 336407003477 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 336407003478 GTPase CgtA; Reviewed; Region: obgE; PRK12299 336407003479 GTP1/OBG; Region: GTP1_OBG; pfam01018 336407003480 Obg GTPase; Region: Obg; cd01898 336407003481 G1 box; other site 336407003482 GTP/Mg2+ binding site [chemical binding]; other site 336407003483 Switch I region; other site 336407003484 G2 box; other site 336407003485 G3 box; other site 336407003486 Switch II region; other site 336407003487 G4 box; other site 336407003488 G5 box; other site 336407003489 Escherichia coli (Ec) citrate synthase (CS) GltA_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). The overall CS...; Region: EcCS_like; cd06114 336407003490 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 336407003491 dimer interface [polypeptide binding]; other site 336407003492 active site 336407003493 citrylCoA binding site [chemical binding]; other site 336407003494 NADH binding [chemical binding]; other site 336407003495 cationic pore residues; other site 336407003496 oxalacetate/citrate binding site [chemical binding]; other site 336407003497 coenzyme A binding site [chemical binding]; other site 336407003498 catalytic triad [active] 336407003499 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]; Region: HicB; COG4226 336407003500 HicB family; Region: HicB; pfam05534 336407003501 Transposase; Region: DEDD_Tnp_IS110; pfam01548 336407003502 Transposase and inactivated derivatives [DNA replication, recombination, and repair]; Region: COG3547 336407003503 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 336407003504 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; cl01074 336407003505 Surface lipoprotein [Cell envelope biogenesis, outer membrane]; Region: VacJ; COG2853 336407003506 Tetratricopeptide repeat; Region: TPR_12; pfam13424 336407003507 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 336407003508 binding surface 336407003509 TPR motif; other site 336407003510 Methyltransferase domain; Region: Methyltransf_23; pfam13489 336407003511 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 336407003512 S-adenosylmethionine binding site [chemical binding]; other site 336407003513 aspartate aminotransferase; Provisional; Region: PRK05764 336407003514 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 336407003515 pyridoxal 5'-phosphate binding site [chemical binding]; other site 336407003516 homodimer interface [polypeptide binding]; other site 336407003517 catalytic residue [active] 336407003518 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 336407003519 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: DUF374; Region: LPLAT_DUF374-like; cd07983 336407003520 putative acyl-acceptor binding pocket; other site 336407003521 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 336407003522 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 336407003523 120 KDa Rickettsia surface antigen; Region: 120_Rick_ant; pfam12574 336407003524 Phosphoribosylpyrophosphate synthetase [Nucleotide transport and metabolism / Amino acid transport and metabolism]; Region: PrsA; COG0462 336407003525 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 336407003526 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 336407003527 active site 336407003528 Alanine racemase [Cell envelope biogenesis, outer membrane]; Region: Alr; COG0787 336407003529 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 336407003530 active site 336407003531 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 336407003532 dimer interface [polypeptide binding]; other site 336407003533 substrate binding site [chemical binding]; other site 336407003534 catalytic residues [active] 336407003535 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 336407003536 Permease; Region: Permease; pfam02405 336407003537 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 336407003538 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 336407003539 Walker A/P-loop; other site 336407003540 ATP binding site [chemical binding]; other site 336407003541 Q-loop/lid; other site 336407003542 ABC transporter signature motif; other site 336407003543 Walker B; other site 336407003544 D-loop; other site 336407003545 H-loop/switch region; other site 336407003546 tRNA-binding-domain-containing CsaA-like proteins. CsaA is a molecular chaperone with export related activities. CsaA has a putative tRNA binding activity. The functional unit of CsaA is a homodimer and this domain acts as a dimerization domain; Region: tRNA_bind_CsaA; cd02798 336407003547 dimer interface [polypeptide binding]; other site 336407003548 putative tRNA-binding site [nucleotide binding]; other site 336407003549 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 336407003550 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 336407003551 Protein of unknown function (DUF2672); Region: DUF2672; pfam10878 336407003552 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 336407003553 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 336407003554 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 336407003555 ABC transporter; Region: ABC_tran_2; pfam12848 336407003556 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 336407003557 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 336407003558 ParB-like nuclease domain; Region: ParBc; pfam02195 336407003559 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 336407003560 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 336407003561 Magnesium ion binding site [ion binding]; other site 336407003562 Predicted S-adenosylmethionine-dependent methyltransferase involved in bacterial cell division [Cell envelope biogenesis, outer membrane]; Region: GidB; COG0357 336407003563 16S rRNA methyltransferase GidB; Reviewed; Region: gidB; PRK00107 336407003564 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 336407003565 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 336407003566 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 336407003567 Nucleoside diphosphate kinase Group I (NDPk_I)-like: NDP kinase domains are present in a large family of structurally and functionally conserved proteins from bacteria to humans that generally catalyze the transfer of gamma-phosphates of a nucleoside...; Region: NDPk_I; cd04413 336407003568 active site 336407003569 multimer interface [polypeptide binding]; other site 336407003570 Sugar phosphate permease [Carbohydrate transport and metabolism]; Region: UhpC; COG2271 336407003571 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 336407003572 putative substrate translocation pore; other site 336407003573 TLC ATP/ADP transporter; Region: TLC; pfam03219 336407003574 Methyltransferase domain; Region: Methyltransf_31; pfam13847 336407003575 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 336407003576 S-adenosylmethionine binding site [chemical binding]; other site 336407003577 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]; Region: SUA5; COG0009 336407003578 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 336407003579 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 336407003580 DALR anticodon binding domain; Region: DALR_1; pfam05746 336407003581 glycyl-tRNA synthetase subunit alpha; Validated; Region: glyQ; PRK09348 336407003582 motif 1; other site 336407003583 dimer interface [polypeptide binding]; other site 336407003584 active site 336407003585 motif 2; other site 336407003586 motif 3; other site 336407003587 PIN domain of ribonucleases (toxins), VapC and FitB, of prokaryotic toxin/antitoxin operons, Pyrococcus horikoshii protein PH0500, and other similar bacterial and archaeal homologs; Region: PIN_VapC-FitB; cd09881 336407003588 oligomeric interface; other site 336407003589 putative active site [active] 336407003590 homodimer interface [polypeptide binding]; other site 336407003591 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; pfam02604 336407003592 trigger factor; Provisional; Region: tig; PRK01490 336407003593 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 336407003594 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 336407003595 AAA ATPase domain; Region: AAA_16; pfam13191 336407003596 NACHT domain; Region: NACHT; pfam05729 336407003597 putative transposase; Provisional; Region: PRK09857 336407003598 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 336407003599 Protein of unknown function (DUF2748); Region: DUF2748; pfam10871 336407003600 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 336407003601 NAD(P) binding site [chemical binding]; other site 336407003602 active site 336407003603 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 336407003604 Clp amino terminal domain; Region: Clp_N; pfam02861 336407003605 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 336407003606 Walker A motif; other site 336407003607 ATP binding site [chemical binding]; other site 336407003608 Walker B motif; other site 336407003609 arginine finger; other site 336407003610 Protein of unknown function (DUF1640); Region: DUF1640; pfam07798 336407003611 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 336407003612 Walker A motif; other site 336407003613 ATP binding site [chemical binding]; other site 336407003614 Walker B motif; other site 336407003615 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 336407003616 PemK-like protein; Region: PemK; pfam02452 336407003617 Cytotoxic translational repressor of toxin-antitoxin stability system [Translation, ribosomal structure and biogenesis / Cell division and chromosome partitioning]; Region: RelE; COG2026 336407003618 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 336407003619 non-specific DNA binding site [nucleotide binding]; other site 336407003620 salt bridge; other site 336407003621 sequence-specific DNA binding site [nucleotide binding]; other site 336407003622 Methyltransferase domain; Region: Methyltransf_31; pfam13847 336407003623 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 336407003624 S-adenosylmethionine binding site [chemical binding]; other site 336407003625 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 336407003626 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 336407003627 coproporphyrinogen III oxidase; Provisional; Region: PRK05330 336407003628 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; pfam01218 336407003629 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 336407003630 metabolite-proton symporter; Region: 2A0106; TIGR00883 336407003631 putative substrate translocation pore; other site 336407003632 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 336407003633 3-hydroxybutyrate dehydrogenase; Region: PHB_DH; TIGR01963 336407003634 NAD(P) binding site [chemical binding]; other site 336407003635 active site 336407003636 Zinc-finger domain; Region: zf-CHCC; cl01821 336407003637 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 336407003638 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 336407003639 ATP binding site [chemical binding]; other site 336407003640 Mg2+ binding site [ion binding]; other site 336407003641 G-X-G motif; other site 336407003642 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 336407003643 ATP binding site [chemical binding]; other site 336407003644 MutL C terminal dimerisation domain; Region: MutL_C; pfam08676 336407003645 Antitoxin of toxin-antitoxin stability system N-terminal; Region: RelB_N; pfam12910 336407003646 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 336407003647 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 336407003648 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 336407003649 C-5 cytosine-specific DNA methylase; Region: DNA_methylase; pfam00145 336407003650 cofactor binding site; other site 336407003651 DNA binding site [nucleotide binding] 336407003652 substrate interaction site [chemical binding]; other site 336407003653 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 336407003654 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 336407003655 Walker A motif; other site 336407003656 ATP binding site [chemical binding]; other site 336407003657 Walker B motif; other site 336407003658 arginine finger; other site 336407003659 Peptidase family M41; Region: Peptidase_M41; pfam01434 336407003660 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 336407003661 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 336407003662 Ligand Binding Site [chemical binding]; other site 336407003663 Cytotoxic translational repressor of toxin-antitoxin stability system [Translation, ribosomal structure and biogenesis / Cell division and chromosome partitioning]; Region: RelE; COG2026 336407003664 Possible hemagglutinin (DUF637); Region: DUF637; pfam04830 336407003665 Possible hemagglutinin (DUF637); Region: DUF637; pfam04830 336407003666 Possible hemagglutinin (DUF637); Region: DUF637; pfam04830 336407003667 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 336407003668 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 336407003669 Beta-lactamase superfamily domain; Region: Lactamase_B_2; pfam12706 336407003670 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]; Region: COG2220 336407003671 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 336407003672 aspartate kinase; Reviewed; Region: PRK06635 336407003673 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 336407003674 putative nucleotide binding site [chemical binding]; other site 336407003675 putative catalytic residues [active] 336407003676 putative Mg ion binding site [ion binding]; other site 336407003677 putative aspartate binding site [chemical binding]; other site 336407003678 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 336407003679 putative allosteric regulatory residue; other site 336407003680 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 336407003681 50S ribosomal protein L21/unknown domain fusion protein; Provisional; Region: PRK12278 336407003682 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 336407003683 PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by...; Region: PCD_DCoH_subfamily_a; cd00913 336407003684 aromatic arch; other site 336407003685 DCoH dimer interaction site [polypeptide binding]; other site 336407003686 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 336407003687 DCoH tetramer interaction site [polypeptide binding]; other site 336407003688 substrate binding site [chemical binding]; other site 336407003689 Prokaryotic phenylalanine-4-hydroxylase (pro_PheOH); a member of the biopterin-dependent aromatic amino acid hydroxylase family of non-heme, iron(II)-dependent enzymes that also includes the eukaryotic proteins, phenylalanine-4-hydroxylase (eu_PheOH); Region: pro_PheOH; cd03348 336407003690 cofactor binding site; other site 336407003691 metal binding site [ion binding]; metal-binding site 336407003692 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 336407003693 tetramer interfaces [polypeptide binding]; other site 336407003694 binuclear metal-binding site [ion binding]; other site 336407003695 twin arginine translocase protein A; Provisional; Region: tatA; PRK01470 336407003696 Ankyrin repeats (many copies); Region: Ank_5; pfam13857 336407003697 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 336407003698 Ankyrin repeats (many copies); Region: Ank_5; pfam13857 336407003699 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 336407003700 Receptor family ligand binding region; Region: ANF_receptor; pfam01094 336407003701 putative ligand binding site [chemical binding]; other site 336407003702 Predicted methyltransferases [General function prediction only]; Region: COG0313 336407003703 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 336407003704 putative SAM binding site [chemical binding]; other site 336407003705 putative homodimer interface [polypeptide binding]; other site 336407003706 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 336407003707 conserved hypothetical protein (putative transposase or invertase); Region: T_den_put_tspse; TIGR01784 336407003708 Predicted small secreted protein [Function unknown]; Region: COG5510 336407003709 Na+/H+ antiporter [Inorganic ion transport and metabolism]; Region: NhaA; COG3004 336407003710 Na+/H+ antiporter [Inorganic ion transport and metabolism]; Region: NhaA; COG3004 336407003711 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; cl14958 336407003712 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 336407003713 Methyltransferase domain; Region: Methyltransf_26; pfam13659 336407003714 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 336407003715 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 336407003716 metal binding site [ion binding]; metal-binding site 336407003717 dimer interface [polypeptide binding]; other site 336407003718 DNA polymerase III subunit chi; Provisional; Region: PRK06646 336407003719 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 336407003720 ATP-binding cassette domain of the metal-type transporters; Region: ABC_Metallic_Cations; cd03235 336407003721 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 336407003722 substrate binding site [chemical binding]; other site 336407003723 Surface antigen [Cell envelope biogenesis, outer membrane]; Region: LipA; COG4520 336407003724 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 336407003725 Cation efflux family; Region: Cation_efflux; cl00316 336407003726 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 336407003727 nucleoside/Zn binding site; other site 336407003728 dimer interface [polypeptide binding]; other site 336407003729 catalytic motif [active] 336407003730 Uncharacterized protein family (UPF0093); Region: UPF0093; cl00863 336407003731 ferrochelatase; Reviewed; Region: hemH; PRK00035 336407003732 Ferrochelatase, N-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is...; Region: Ferrochelatase_N; cd03411 336407003733 C-terminal domain interface [polypeptide binding]; other site 336407003734 active site 336407003735 Ferrochelatase, C-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is...; Region: Ferrochelatase_C; cd00419 336407003736 active site 336407003737 N-terminal domain interface [polypeptide binding]; other site 336407003738 Uroporphyrinogen decarboxylase (URO-D) is a dimeric cytosolic enzyme that decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, without requiring any prosthetic groups or cofactors. This reaction...; Region: URO-D; cd00717 336407003739 substrate binding site [chemical binding]; other site 336407003740 active site