-- dump date 20120504_160633 -- class Genbank::misc_feature -- table misc_feature_note -- id note 1105104000001 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 1105104000002 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl01155 1105104000003 periplasmic folding chaperone; Provisional; Region: PRK10788 1105104000004 PPIC-type PPIASE domain; Region: Rotamase; cl08278 1105104000005 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 1105104000006 Poly(3-hydroxyalkanoate) synthetase [Lipid metabolism]; Region: PhaC; COG3243 1105104000007 Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar proteins; Region: PLDc_Nuc; cd09170 1105104000008 PLD-like domain; Region: PLDc_2; pfam13091 1105104000009 putative active site [active] 1105104000010 catalytic site [active] 1105104000011 Phasin protein; Region: Phasin_2; cl11491 1105104000012 site-specific tyrosine recombinase XerC; Reviewed; Region: xerC; PRK00236 1105104000013 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 1105104000014 active site 1105104000015 DNA binding site [nucleotide binding] 1105104000016 Int/Topo IB signature motif; other site 1105104000017 Prokaryotic dksA/traR C4-type zinc finger; Region: zf-dskA_traR; cl00755 1105104000018 Maf-like protein; Region: Maf; pfam02545 1105104000019 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 1105104000020 active site 1105104000021 dimer interface [polypeptide binding]; other site 1105104000022 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 1105104000023 rRNA binding site [nucleotide binding]; other site 1105104000024 predicted 30S ribosome binding site; other site 1105104000025 potential frameshift: common BLAST hit: gi|67459682|ref|YP_247306.1| cell surface antigen-like protein Sca13 1105104000026 potential frameshift: common BLAST hit: gi|67459682|ref|YP_247306.1| cell surface antigen-like protein Sca13 1105104000027 potential frameshift: common BLAST hit: gi|91204964|ref|YP_537319.1| cell surface antigen Sca13 1105104000028 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl01155 1105104000029 BolA-like protein; Region: BolA; cl00386 1105104000030 Oligomerisation domain; Region: Oligomerisation; cl00519 1105104000031 glutathione-regulated potassium-efflux system protein KefB; Provisional; Region: PRK03659 1105104000032 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; cl10482 1105104000033 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105104000034 Bacterial SH3 domain; Region: SH3_3; cl02551 1105104000035 Bacterial SH3 domain; Region: SH3_3; cl02551 1105104000036 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105104000037 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105104000038 potential frameshift: common BLAST hit: gi|67459672|ref|YP_247296.1| nucleotidyltransferase/HEPN domain-containing protein 1105104000039 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14325 1105104000040 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 1105104000041 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; cl15377 1105104000042 TRAM domain; Region: TRAM; cl01282 1105104000043 Membrane carboxypeptidase/penicillin-binding protein [Cell envelope biogenesis, outer membrane]; Region: MrcA; COG5009 1105104000044 Transglycosylase; Region: Transgly; cl07896 1105104000045 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 1105104000046 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 1105104000047 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 1105104000048 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 1105104000049 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 1105104000050 dimerization interface [polypeptide binding]; other site 1105104000051 DPS ferroxidase diiron center [ion binding]; other site 1105104000052 ion pore; other site 1105104000053 dihydrolipoamide dehydrogenase; Reviewed; Region: PRK06416 1105104000054 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105104000055 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1105104000056 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 1105104000057 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 1105104000058 ATP synthase delta (OSCP) subunit; Region: OSCP; pfam00213 1105104000059 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 1105104000060 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 1105104000061 F1 ATP synthase alpha, central domain. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to...; Region: F1_ATPase_alpha; cd01132 1105104000062 beta subunit interaction interface [polypeptide binding]; other site 1105104000063 Walker A motif; other site 1105104000064 ATP binding site [chemical binding]; other site 1105104000065 Walker B motif; other site 1105104000066 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 1105104000067 ATP synthase; Region: ATP-synt; cl00365 1105104000068 F0F1 ATP synthase subunit gamma; Provisional; Region: PRK13422 1105104000069 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 1105104000070 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; cl15275 1105104000071 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 1105104000072 alpha subunit interaction interface [polypeptide binding]; other site 1105104000073 Walker A motif; other site 1105104000074 ATP binding site [chemical binding]; other site 1105104000075 Walker B motif; other site 1105104000076 inhibitor binding site; inhibition site 1105104000077 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 1105104000078 F0F1 ATP synthase subunit epsilon; Validated; Region: atpC; PRK01474 1105104000079 ATP synthase, Delta/Epsilon chain, beta-sandwich domain; Region: ATP-synt_DE_N; cl10033 1105104000080 aconitate hydratase; Validated; Region: PRK09277 1105104000081 Aconitase A catalytic domain; Region: AcnA_IRP; cd01586 1105104000082 substrate binding site [chemical binding]; other site 1105104000083 ligand binding site [chemical binding]; other site 1105104000084 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 1105104000085 substrate binding site [chemical binding]; other site 1105104000086 Predicted membrane protein [Function unknown]; Region: COG3671 1105104000087 NADH dehydrogenase subunit G; Validated; Region: PRK09130 1105104000088 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 1105104000089 catalytic loop [active] 1105104000090 iron binding site [ion binding]; other site 1105104000091 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; cl11210 1105104000092 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 1105104000093 Domain of unknown function (DUF1982); Region: DUF1982; pfam09326 1105104000094 NADH dehydrogenase; Region: NADHdh; cl00469 1105104000095 NADH dehydrogenase subunit I; Provisional; Region: PRK05888 1105104000096 4Fe-4S binding domain; Region: Fer4; cl02805 1105104000097 4Fe-4S binding domain; Region: Fer4; cl02805 1105104000098 cytochrome c biogenesis protein CcmA; Provisional; Region: PRK13541 1105104000099 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105104000100 Walker A/P-loop; other site 1105104000101 ATP binding site [chemical binding]; other site 1105104000102 Q-loop/lid; other site 1105104000103 ABC transporter signature motif; other site 1105104000104 Walker B; other site 1105104000105 D-loop; other site 1105104000106 H-loop/switch region; other site 1105104000107 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 1105104000108 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 1105104000109 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 1105104000110 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 1105104000111 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 1105104000112 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 1105104000113 NADH:ubiquinone oxidoreductase subunit J; Provisional; Region: PRK06638 1105104000114 NADH dehydrogenase subunit J; Provisional; Region: PRK06433; cl14634 1105104000115 Predicted transcriptional regulator [Transcription]; Region: COG2944 1105104000116 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 1105104000117 salt bridge; other site 1105104000118 non-specific DNA binding site [nucleotide binding]; other site 1105104000119 sequence-specific DNA binding site [nucleotide binding]; other site 1105104000120 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 1105104000121 S-adenosylmethionine binding site [chemical binding]; other site 1105104000122 Predicted regulatory domain of a methyltransferase [General function prediction only]; Region: COG4797 1105104000123 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl01155 1105104000124 Integral membrane protein TerC family; Region: TerC; cl10468 1105104000125 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 1105104000126 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 1105104000127 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105104000128 seryl-tRNA synthetase; Provisional; Region: PRK05431 1105104000129 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 1105104000130 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 bound...; Region: SerRS_core; cd00770 1105104000131 dimer interface [polypeptide binding]; other site 1105104000132 active site 1105104000133 motif 1; other site 1105104000134 motif 2; other site 1105104000135 motif 3; other site 1105104000136 Sec-independent protein translocase protein (TatC); Region: TatC; cl00521 1105104000137 AmpG-like permease; Region: 2A0125; TIGR00901 1105104000138 muropeptide transporter; Validated; Region: ampG; PRK11010 1105104000139 Protein of unknown function; Region: DUF3971; pfam13116 1105104000140 AsmA-like C-terminal region; Region: AsmA_2; cl15864 1105104000141 Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]; Region: Ugd; COG1004 1105104000142 UDP-glucose/GDP-mannose dehydrogenase family, central domain; Region: UDPG_MGDP_dh; pfam00984 1105104000143 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105104000144 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 1105104000145 Bacterial DNA polymerase III alpha subunit; Region: DNA_pol3_alpha; pfam07733 1105104000146 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 1105104000147 generic binding surface I; other site 1105104000148 generic binding surface II; other site 1105104000149 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 1105104000150 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 1105104000151 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 1105104000152 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 1105104000153 DNA polymerase I; Provisional; Region: PRK05755 1105104000154 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 1105104000155 active site 1105104000156 metal binding site 1 [ion binding]; metal-binding site 1105104000157 putative 5' ssDNA interaction site; other site 1105104000158 metal binding site 3; metal-binding site 1105104000159 metal binding site 2 [ion binding]; metal-binding site 1105104000160 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 1105104000161 putative DNA binding site [nucleotide binding]; other site 1105104000162 putative metal binding site [ion binding]; other site 1105104000163 DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily; Region: DnaQ_like_exo; cl10012 1105104000164 active site 1105104000165 substrate binding site [chemical binding]; other site 1105104000166 catalytic site [active] 1105104000167 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 1105104000168 active site 1105104000169 DNA binding site [nucleotide binding] 1105104000170 catalytic site [active] 1105104000171 signal recognition particle-docking protein FtsY; Provisional; Region: PRK10416 1105104000172 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 1105104000173 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 1105104000174 P loop; other site 1105104000175 GTP binding site [chemical binding]; other site 1105104000176 SmpA / OmlA family; Region: SmpA_OmlA; cl01095 1105104000177 Ribosomal L32p protein family; Region: Ribosomal_L32p; cl09115 1105104000178 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed; Region: PRK09352 1105104000179 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 1105104000180 dimer interface [polypeptide binding]; other site 1105104000181 active site 1105104000182 CoA binding pocket [chemical binding]; other site 1105104000183 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105104000184 putative outer membrane lipoprotein; Provisional; Region: PRK09967 1105104000185 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 1105104000186 ligand binding site [chemical binding]; other site 1105104000187 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 1105104000188 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 1105104000189 rod shape-determining protein MreB; Provisional; Region: PRK13927 1105104000190 Actin; An ubiquitous protein involved in the formation of filaments that are a major component of the cytoskeleton. Interaction with myosin provides the basis of muscular contraction and many aspects of cell motility. Each actin protomer binds one...; Region: ACTIN; cl11528 1105104000191 ATP binding site [chemical binding]; other site 1105104000192 profilin binding site; other site 1105104000193 rod shape-determining protein MreC; Provisional; Region: PRK13922 1105104000194 rod shape-determining protein MreC; Region: MreC; pfam04085 1105104000195 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 1105104000196 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105104000197 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 1105104000198 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 1105104000199 catalytic site [active] 1105104000200 G-X2-G-X-G-K; other site 1105104000201 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105104000202 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 1105104000203 endonuclease subunit; Provisional; Region: 46; PHA02562 1105104000204 ABC transporter ATPase component; Reviewed; Region: PRK11147 1105104000205 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 1105104000206 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 1105104000207 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK07314 1105104000208 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 1105104000209 dimer interface [polypeptide binding]; other site 1105104000210 active site 1105104000211 Phosphopantetheine attachment site; Region: PP-binding; cl09936 1105104000212 3-oxoacyl-(acyl-carrier-protein) reductase; Region: 3oxo_ACP_reduc; TIGR01830 1105104000213 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105104000214 NAD(P) binding site [chemical binding]; other site 1105104000215 active site 1105104000216 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 1105104000217 protein RecA; Region: tigrfam_recA; TIGR02012 1105104000218 hexamer interface [polypeptide binding]; other site 1105104000219 Walker A motif; other site 1105104000220 ATP binding site [chemical binding]; other site 1105104000221 Walker B motif; other site 1105104000222 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 1105104000223 tRNA modification GTPase TrmE; Reviewed; Region: trmE; PRK05291 1105104000224 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 1105104000225 trmE is a tRNA modification GTPase; Region: trmE; cd04164 1105104000226 G1 box; other site 1105104000227 GTP/Mg2+ binding site [chemical binding]; other site 1105104000228 Switch I region; other site 1105104000229 G2 box; other site 1105104000230 Switch II region; other site 1105104000231 G3 box; other site 1105104000232 G4 box; other site 1105104000233 G5 box; other site 1105104000234 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 1105104000235 NAD-specific glutamate dehydrogenase [Amino acid transport and metabolism]; Region: COG2902 1105104000236 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105104000237 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 1105104000238 glutamyl-tRNA synthetase; Provisional; Region: gltX; PRK14895 1105104000239 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105104000240 Cell division protein ZapA; Region: ZapA; cl01146 1105104000241 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 1105104000242 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105104000243 putative substrate translocation pore; other site 1105104000244 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 1105104000245 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105104000246 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 1105104000247 aspartate kinase; Reviewed; Region: PRK06635 1105104000248 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 1105104000249 putative nucleotide binding site [chemical binding]; other site 1105104000250 putative catalytic residues [active] 1105104000251 putative Mg ion binding site [ion binding]; other site 1105104000252 putative aspartate binding site [chemical binding]; other site 1105104000253 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 1105104000254 putative allosteric regulatory residue; other site 1105104000255 Ribosomal L27 protein; Region: Ribosomal_L27; cl00359 1105104000256 Ribosomal prokaryotic L21 protein; Region: Ribosomal_L21p; cl00382 1105104000257 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 1105104000258 tetramer interfaces [polypeptide binding]; other site 1105104000259 binuclear metal-binding site [ion binding]; other site 1105104000260 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 1105104000261 Periplasmic binding component of lipoprotein LppC, an immunodominant antigen; Region: PBP1_YraM_LppC_lipoprotein_like; cd06339 1105104000262 putative ligand binding site [chemical binding]; other site 1105104000263 Predicted methyltransferases [General function prediction only]; Region: COG0313 1105104000264 Precorrin-3B methylase [Coenzyme metabolism]; Region: CobJ; cl00304 1105104000265 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105104000266 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105104000267 Entericidin EcnA/B family; Region: Entericidin; cl02322 1105104000268 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 1105104000269 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 1105104000270 minor groove reading motif; other site 1105104000271 helix-hairpin-helix signature motif; other site 1105104000272 substrate binding pocket [chemical binding]; other site 1105104000273 active site 1105104000274 Iron-sulfur binding domain of endonuclease III; Region: EndIII_4Fe-2S; cl15304 1105104000275 Glutaredoxin (GRX) family, PKC-interacting cousin of TRX (PICOT)-like subfamily; composed of PICOT and GRX-PICOT-like proteins. The non-PICOT members of this family contain only the GRX-like domain, whereas PICOT contains an N-terminal TRX-like domain...; Region: GRX_PICOT_like; cd03028 1105104000276 putative GSH binding site [chemical binding]; other site 1105104000277 catalytic residues [active] 1105104000278 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 1105104000279 Phospholipase/Carboxylesterase; Region: Abhydrolase_2; pfam02230 1105104000280 serine hydroxymethyltransferase; Reviewed; Region: glyA; PRK00011 1105104000281 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 1105104000282 dimer interface [polypeptide binding]; other site 1105104000283 active site 1105104000284 glycine-pyridoxal phosphate binding site [chemical binding]; other site 1105104000285 folate binding site [chemical binding]; other site 1105104000286 lipoyl synthase; Provisional; Region: PRK05481 1105104000287 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 1105104000288 FeS/SAM binding site; other site 1105104000289 PemK-like protein; Region: PemK; cl00995 1105104000290 Uncharacterized protein family UPF0054; Region: UPF0054; cl00402 1105104000291 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 1105104000292 Transporter associated domain; Region: CorC_HlyC; cl08393 1105104000293 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 1105104000294 nudix motif; other site 1105104000295 ATP/ADP translocase [Energy production and conversion]; Region: COG3202; cl03940 1105104000296 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105104000297 Poly(3-hydroxyalkanoate) synthetase [Lipid metabolism]; Region: PhaC; COG3243 1105104000298 potential frameshift: common BLAST hit: gi|341584292|ref|YP_004764783.1| superfamily I DNA/RNA helicase 1105104000299 potential frameshift: common BLAST hit: gi|67458557|ref|YP_246181.1| superfamily I DNA/RNA helicase 1105104000300 potential frameshift: common BLAST hit: gi|67458557|ref|YP_246181.1| superfamily I DNA/RNA helicase 1105104000301 Acyl transferase domain; Region: Acyl_transf_1; cl08282 1105104000302 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 1105104000303 double-strand break repair helicase AddA, alphaproteobacterial type; Region: addA_alphas; TIGR02784 1105104000304 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105104000305 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 1105104000306 DNA polymerase III, epsilon subunit, Proteobacterial; Region: dnaQ_proteo; TIGR01406 1105104000307 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 1105104000308 active site 1105104000309 catalytic site [active] 1105104000310 substrate binding site [chemical binding]; other site 1105104000311 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 1105104000312 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 1105104000313 CoA-binding site [chemical binding]; other site 1105104000314 ATP-binding [chemical binding]; other site 1105104000315 Protein of unknown function (DUF1009); Region: DUF1009; cl09182 1105104000316 Stringent starvation protein B; Region: SspB; cl01120 1105104000317 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 1105104000318 RNA/DNA hybrid binding site [nucleotide binding]; other site 1105104000319 active site 1105104000320 NADH ubiquinone oxidoreductase subunit NDUFA12; Region: NDUFA12; cl01534 1105104000321 mce related protein; Region: MCE; pfam02470 1105104000322 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 1105104000323 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; cl00409 1105104000324 Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]; Region: Tgt; COG0343 1105104000325 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 1105104000326 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 1105104000327 nucleotide binding pocket [chemical binding]; other site 1105104000328 K-X-D-G motif; other site 1105104000329 catalytic site [active] 1105104000330 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 1105104000331 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 1105104000332 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 1105104000333 Dimer interface [polypeptide binding]; other site 1105104000334 BRCT sequence motif; other site 1105104000335 Protein of unknown function (DUF519); Region: DUF519; pfam04378 1105104000336 Peptidase family M23; Region: Peptidase_M23; pfam01551 1105104000337 Tetraacyldisaccharide-1-P 4'-kinase; Region: LpxK; cl03652 1105104000338 tetraacyldisaccharide 4'-kinase; Region: lpxK; TIGR00682 1105104000339 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 1105104000340 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 1105104000341 putative acyl-acceptor binding pocket; other site 1105104000342 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 1105104000343 catalytic triad [active] 1105104000344 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 1105104000345 IHF dimer interface [polypeptide binding]; other site 1105104000346 IHF - DNA interface [nucleotide binding]; other site 1105104000347 Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Region: HTH_MerR-SF; cl02600 1105104000348 DNA binding residues [nucleotide binding] 1105104000349 Glycosyl hydrolase family 3 N terminal domain; Region: Glyco_hydro_3; cl07971 1105104000350 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 1105104000351 synthetase active site [active] 1105104000352 NTP binding site [chemical binding]; other site 1105104000353 metal binding site [ion binding]; metal-binding site 1105104000354 Rickettsia outer membrane protein B; Region: rOmpB; pfam12334 1105104000355 outer membrane autotransporter barrel domain; Region: autotrans_barl; TIGR01414 1105104000356 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl01155 1105104000357 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 1105104000358 Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]; Region: CorB; COG4536 1105104000359 Domain of unknown function DUF21; Region: DUF21; pfam01595 1105104000360 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 1105104000361 Transporter associated domain; Region: CorC_HlyC; cl08393 1105104000362 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 1105104000363 This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE). They are clustered together...; Region: ABC_MJ0796_Lo1CDE_FtsE; cd03255 1105104000364 Walker A/P-loop; other site 1105104000365 ATP binding site [chemical binding]; other site 1105104000366 Q-loop/lid; other site 1105104000367 ABC transporter signature motif; other site 1105104000368 Walker B; other site 1105104000369 D-loop; other site 1105104000370 H-loop/switch region; other site 1105104000371 lipoprotein releasing system, transmembrane protein, LolC/E family; Region: lolCE; TIGR02212 1105104000372 MacB-like periplasmic core domain; Region: MacB_PCD; pfam12704 1105104000373 FtsX-like permease family; Region: FtsX; cl15850 1105104000374 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 1105104000375 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 1105104000376 Protein of unknown function (DUF2673); Region: DUF2673; pfam10880 1105104000377 ABC transporter, permease/ATP-binding protein; Region: MsbA_rel; TIGR02204 1105104000378 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 1105104000379 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105104000380 Walker A/P-loop; other site 1105104000381 ATP binding site [chemical binding]; other site 1105104000382 Q-loop/lid; other site 1105104000383 ABC transporter signature motif; other site 1105104000384 Walker B; other site 1105104000385 D-loop; other site 1105104000386 H-loop/switch region; other site 1105104000387 YcfA-like protein; Region: YcfA; cl00752 1105104000388 Uncharacterized protein family (UPF0150); Region: UPF0150; cl00691 1105104000389 HicB family; Region: HicB; pfam05534 1105104000390 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 1105104000391 Ligand Binding Site [chemical binding]; other site 1105104000392 Acetyltransferases, including N-acetylases of ribosomal proteins [Translation, ribosomal structure and biogenesis]; Region: RimL; COG1670 1105104000393 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 1105104000394 ATP-dependent protease ATP-binding subunit ClpX; Provisional; Region: clpX; PRK05342 1105104000395 ClpX C4-type zinc finger; Region: zf-C4_ClpX; cl05964 1105104000396 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 1105104000397 Walker A motif; other site 1105104000398 ATP binding site [chemical binding]; other site 1105104000399 Walker B motif; other site 1105104000400 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 1105104000401 DoxX-like family; Region: DoxX_3; pfam13781 1105104000402 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of...; Region: Glyco_transf_25; cl01298 1105104000403 RmuC family; Region: RmuC; pfam02646 1105104000404 potential frameshift: common BLAST hit: gi|67458618|ref|YP_246242.1| ATPase 1105104000405 LicD family; Region: LicD; cl01378 1105104000406 LicD family; Region: LicD; cl01378 1105104000407 valyl-tRNA synthetase; Reviewed; Region: valS; PRK13208 1105104000408 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105104000409 active site 1105104000410 HIGH motif; other site 1105104000411 nucleotide binding site [chemical binding]; other site 1105104000412 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 1105104000413 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105104000414 active site 1105104000415 KMSKS motif; other site 1105104000416 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 1105104000417 tRNA binding surface [nucleotide binding]; other site 1105104000418 anticodon binding site; other site 1105104000419 potential frameshift: common BLAST hit: gi|350273815|ref|YP_004885128.1| transposase 1105104000420 potential frameshift: common BLAST hit: gi|67458622|ref|YP_246246.1| transposase 1105104000421 UbiA prenyltransferase family; Region: UbiA; cl00337 1105104000422 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105104000423 thymidylate kinase; Validated; Region: tmk; PRK00698 1105104000424 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 1105104000425 TMP-binding site; other site 1105104000426 ATP-binding site [chemical binding]; other site 1105104000427 methionyl-tRNA synthetase; Reviewed; Region: PRK11893 1105104000428 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 1105104000429 HIGH motif; other site 1105104000430 active site 1105104000431 KMSKS motif; other site 1105104000432 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 1105104000433 tRNA binding surface [nucleotide binding]; other site 1105104000434 anticodon binding site; other site 1105104000435 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 1105104000436 active site 1105104000437 Protein of unknown function (DUF511); Region: DUF511; cl01114 1105104000438 Protein of unknown function (DUF511); Region: DUF511; cl01114 1105104000439 Protein of unknown function (DUF511); Region: DUF511; cl01114 1105104000440 Protein of unknown function (DUF511); Region: DUF511; cl01114 1105104000441 potential frameshift: common BLAST hit: gi|157964831|ref|YP_001499655.1| Poly-beta-hydroxyalkanoate depolymerase 1105104000442 potential frameshift: common BLAST hit: gi|15892963|ref|NP_360677.1| mannose-1-phosphate guanylyltransferase 1105104000443 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105104000444 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105104000445 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 1105104000446 active site 1105104000447 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated; Region: PRK01103 1105104000448 N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; Region: EcFpg-like_N; cd08966 1105104000449 DNA binding site [nucleotide binding] 1105104000450 catalytic residue [active] 1105104000451 H2TH interface [polypeptide binding]; other site 1105104000452 putative catalytic residues [active] 1105104000453 turnover-facilitating residue; other site 1105104000454 intercalation triad [nucleotide binding]; other site 1105104000455 8OG recognition residue [nucleotide binding]; other site 1105104000456 putative reading head residues; other site 1105104000457 Formamidopyrimidine-DNA glycosylase H2TH domain; Region: H2TH; pfam06831 1105104000458 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 1105104000459 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 1105104000460 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 1105104000461 S-adenosylmethionine binding site [chemical binding]; other site 1105104000462 Predicted unusual protein kinase [General function prediction only]; Region: AarF; COG0661 1105104000463 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 1105104000464 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 1105104000465 active site 1105104000466 ATP binding site [chemical binding]; other site 1105104000467 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 1105104000468 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105104000469 GTP-binding protein Der; Reviewed; Region: PRK00093 1105104000470 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 1105104000471 G1 box; other site 1105104000472 GTP/Mg2+ binding site [chemical binding]; other site 1105104000473 Switch I region; other site 1105104000474 G2 box; other site 1105104000475 Switch II region; other site 1105104000476 G3 box; other site 1105104000477 G4 box; other site 1105104000478 G5 box; other site 1105104000479 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 1105104000480 G1 box; other site 1105104000481 GTP/Mg2+ binding site [chemical binding]; other site 1105104000482 Switch I region; other site 1105104000483 G2 box; other site 1105104000484 G3 box; other site 1105104000485 Switch II region; other site 1105104000486 G4 box; other site 1105104000487 G5 box; other site 1105104000488 PQ loop repeat; Region: PQ-loop; cl12056 1105104000489 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 1105104000490 putative catalytic site [active] 1105104000491 putative phosphate binding site [ion binding]; other site 1105104000492 active site 1105104000493 metal binding site A [ion binding]; metal-binding site 1105104000494 DNA binding site [nucleotide binding] 1105104000495 putative AP binding site [nucleotide binding]; other site 1105104000496 putative metal binding site B [ion binding]; other site 1105104000497 exodeoxyribonuclease VII large subunit; Reviewed; Region: xseA; PRK00286 1105104000498 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 1105104000499 generic binding surface II; other site 1105104000500 generic binding surface I; other site 1105104000501 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 1105104000502 Organic solvent tolerance protein; Region: OstA_C; pfam04453 1105104000503 SurA N-terminal domain; Region: SurA_N_3; cl07813 1105104000504 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 1105104000505 S-adenosylmethionine binding site [chemical binding]; other site 1105104000506 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 protein; Region: CSP_CDS; cd04458 1105104000507 DNA-binding site [nucleotide binding]; DNA binding site 1105104000508 RNA-binding motif; other site 1105104000509 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 1105104000510 ATP-dependent RNA helicase SrmB; Provisional; Region: PRK11192 1105104000511 ATP binding site [chemical binding]; other site 1105104000512 Mg++ binding site [ion binding]; other site 1105104000513 motif III; other site 1105104000514 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 1105104000515 nucleotide binding region [chemical binding]; other site 1105104000516 ATP-binding site [chemical binding]; other site 1105104000517 muropeptide transporter; Validated; Region: ampG; PRK11010 1105104000518 Scaffold protein Nfu/NifU N terminal; Region: Nfu_N; cl07364 1105104000519 NifU-like domain; Region: NifU; cl00484 1105104000520 Protease Inhibitor Ecotin; homodimeric protease inhibitor; Region: Ecotin; cl00178 1105104000521 secondary substrate binding site; other site 1105104000522 primary substrate binding site; other site 1105104000523 inhibition loop; other site 1105104000524 cell division protein FtsZ; Validated; Region: PRK09330 1105104000525 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 1105104000526 nucleotide binding site [chemical binding]; other site 1105104000527 SulA interaction site; other site 1105104000528 PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; Region: PIN_Pae0151; cd09873 1105104000529 putative active site [active] 1105104000530 homotetrameric interface [polypeptide binding]; other site 1105104000531 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 1105104000532 fumarate hydratase; Reviewed; Region: fumC; PRK00485 1105104000533 Class II fumarases; Region: Fumarase_classII; cd01362 1105104000534 active site 1105104000535 tetramer interface [polypeptide binding]; other site 1105104000536 rRNA methylases [Translation, ribosomal structure and biogenesis]; Region: SpoU; COG0566 1105104000537 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; cl06870 1105104000538 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 1105104000539 elongation factor Tu; Reviewed; Region: PRK00049 1105104000540 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 1105104000541 G1 box; other site 1105104000542 GEF interaction site [polypeptide binding]; other site 1105104000543 GTP/Mg2+ binding site [chemical binding]; other site 1105104000544 Switch I region; other site 1105104000545 G2 box; other site 1105104000546 G3 box; other site 1105104000547 Switch II region; other site 1105104000548 G4 box; other site 1105104000549 G5 box; other site 1105104000550 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 1105104000551 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 1105104000552 Antibiotic Binding Site [chemical binding]; other site 1105104000553 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105104000554 Ribosomal protein S10p/S20e; Region: Ribosomal_S10; cl00314 1105104000555 Ribosomal protein L3; Region: Ribosomal_L3; cl00324 1105104000556 Ribosomal protein L4/L1 family; Region: Ribosomal_L4; cl00325 1105104000557 Ribosomal protein L23; Region: Ribosomal_L23; cl00326 1105104000558 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 1105104000559 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 1105104000560 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 1105104000561 Ribosomal protein S19; Region: Ribosomal_S19; cl00350 1105104000562 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 1105104000563 putative translocon binding site; other site 1105104000564 protein-rRNA interface [nucleotide binding]; other site 1105104000565 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 1105104000566 K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH...; Region: 30S_S3_KH; cd02412 1105104000567 G-X-X-G motif; other site 1105104000568 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 1105104000569 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 1105104000570 23S rRNA interface [nucleotide binding]; other site 1105104000571 5S rRNA interface [nucleotide binding]; other site 1105104000572 putative antibiotic binding site [chemical binding]; other site 1105104000573 L25 interface [polypeptide binding]; other site 1105104000574 L27 interface [polypeptide binding]; other site 1105104000575 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; cl09943 1105104000576 Ribosomal protein S17; Region: Ribosomal_S17; cl00351 1105104000577 Ribosomal protein L14p/L23e; Region: Ribosomal_L14; cl00328 1105104000578 KOW motif; Region: KOW; cl00354 1105104000579 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 1105104000580 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 1105104000581 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 1105104000582 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 1105104000583 Ribosomal protein S14p/S29e; Region: Ribosomal_S14; cl00355 1105104000584 Ribosomal protein S8; Region: Ribosomal_S8; cl00330 1105104000585 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 1105104000586 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 1105104000587 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 1105104000588 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 1105104000589 5S rRNA interface [nucleotide binding]; other site 1105104000590 23S rRNA interface [nucleotide binding]; other site 1105104000591 L5 interface [polypeptide binding]; other site 1105104000592 30S ribosomal protein S5; Validated; Region: rpsE; PRK00550 1105104000593 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 1105104000594 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 1105104000595 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 1105104000596 23S rRNA binding site [nucleotide binding]; other site 1105104000597 Ribosomal protein L18e/L15; Region: Ribosomal_L18e; cl12022 1105104000598 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 1105104000599 SecY translocase; Region: SecY; pfam00344 1105104000600 adenylate kinase; Reviewed; Region: adk; PRK00279 1105104000601 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 1105104000602 AMP-binding site [chemical binding]; other site 1105104000603 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 1105104000604 Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]; Region: RpsM; COG0099 1105104000605 Ribosomal protein S13/S18; Region: Ribosomal_S13; cl00331 1105104000606 Ribosomal protein S11; Region: Ribosomal_S11; cl00332 1105104000607 DNA-directed RNA polymerase subunit alpha; Provisional; Region: PRK05182 1105104000608 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 1105104000609 alphaNTD - beta interaction site [polypeptide binding]; other site 1105104000610 alphaNTD homodimer interface [polypeptide binding]; other site 1105104000611 alphaNTD - beta' interaction site [polypeptide binding]; other site 1105104000612 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; cl11613 1105104000613 Ribosomal protein L17; Region: Ribosomal_L17; cl00356 1105104000614 Ribosomal protein S20; Region: Ribosomal_S20p; cl00384 1105104000615 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 1105104000616 potential frameshift: common BLAST hit: gi|67458789|ref|YP_246413.1| MFS type sugar transporter 1105104000617 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105104000618 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105104000619 pheromone autoinducer 2 transporter; Reviewed; Region: tqsA; cl00465 1105104000620 Domain of unknown function DUF20; Region: UPF0118; pfam01594 1105104000621 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 1105104000622 dimer interface [polypeptide binding]; other site 1105104000623 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 1105104000624 ribonuclease PH; Reviewed; Region: rph; PRK00173 1105104000625 Ribonuclease PH; Region: RNase_PH_bact; cd11362 1105104000626 hexamer interface [polypeptide binding]; other site 1105104000627 active site 1105104000628 potential frameshift: common BLAST hit: gi|67458799|ref|YP_246423.1| glycosyltransferase 1105104000629 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 1105104000630 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 1105104000631 potential frameshift: common BLAST hit: gi|67458799|ref|YP_246423.1| glycosyltransferase 1105104000632 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 1105104000633 oligomerisation interface [polypeptide binding]; other site 1105104000634 mobile loop; other site 1105104000635 roof hairpin; other site 1105104000636 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 1105104000637 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 1105104000638 ring oligomerisation interface [polypeptide binding]; other site 1105104000639 ATP/Mg binding site [chemical binding]; other site 1105104000640 stacking interactions; other site 1105104000641 hinge regions; other site 1105104000642 Invasion associated locus B (IalB) protein; Region: IalB; cl02207 1105104000643 glutamyl-tRNA synthetase; Provisional; Region: gltX; PRK14895 1105104000644 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 1105104000645 HIGH motif; other site 1105104000646 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 1105104000647 active site 1105104000648 KMSKS motif; other site 1105104000649 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105104000650 bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase; Provisional; Region: PRK05134 1105104000651 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105104000652 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 1105104000653 S-adenosylmethionine binding site [chemical binding]; other site 1105104000654 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 1105104000655 ABC-ATPase subunit interface; other site 1105104000656 dimer interface [polypeptide binding]; other site 1105104000657 putative PBP binding regions; other site 1105104000658 TfoX N-terminal domain; Region: TfoX_N; cl01167 1105104000659 acylglycerophosphoethanolamine acyltransferase; Provisional; Region: PRK06814 1105104000660 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 1105104000661 putative substrate translocation pore; other site 1105104000662 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 1105104000663 putative acyl-acceptor binding pocket; other site 1105104000664 AMP-binding enzyme; Region: AMP-binding; cl15778 1105104000665 methylmalonyl-CoA decarboxylase alpha subunit; Region: mmdA; TIGR01117 1105104000666 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 1105104000667 Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit; Region: ACCA; cl15772 1105104000668 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]; Region: COG4770 1105104000669 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 1105104000670 ATP-grasp domain; Region: ATP-grasp_4; cl03087 1105104000671 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; cl08365 1105104000672 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 1105104000673 carboxyltransferase (CT) interaction site; other site 1105104000674 biotinylation site [posttranslational modification]; other site 1105104000675 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 1105104000676 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK06039 1105104000677 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 1105104000678 HIGH motif; other site 1105104000679 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 1105104000680 active site 1105104000681 KMSKS motif; other site 1105104000682 Anticodon-binding domain of archaeal, bacterial, and eukaryotic cytoplasmic isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_ABEc; cd07961 1105104000683 tRNA binding surface [nucleotide binding]; other site 1105104000684 anticodon binding site; other site 1105104000685 Uncharacterized conserved protein [Function unknown]; Region: COG5590 1105104000686 Helix-turn-helix domains; Region: HTH; cl00088 1105104000687 Ribosomal protein S21; Region: Ribosomal_S21; cl00529 1105104000688 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]; Region: NtrY; COG5000 1105104000689 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 1105104000690 dimerization interface [polypeptide binding]; other site 1105104000691 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 1105104000692 dimer interface [polypeptide binding]; other site 1105104000693 phosphorylation site [posttranslational modification] 1105104000694 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 1105104000695 ATP binding site [chemical binding]; other site 1105104000696 Mg2+ binding site [ion binding]; other site 1105104000697 G-X-G motif; other site 1105104000698 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 1105104000699 Protein Kinases, catalytic domain; Region: PKc_like; cl09925 1105104000700 active site 1105104000701 ATP binding site [chemical binding]; other site 1105104000702 substrate binding site [chemical binding]; other site 1105104000703 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 1105104000704 magnesium/nickel/cobalt transporter CorA; Provisional; Region: PRK11085; cl00459 1105104000705 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 1105104000706 Ribonuclease P; Region: Ribonuclease_P; cl00457 1105104000707 Ribosomal protein L34; Region: Ribosomal_L34; cl00370 1105104000708 ribosomal protein L20; Region: rpl20; CHL00068 1105104000709 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 1105104000710 23S rRNA binding site [nucleotide binding]; other site 1105104000711 L21 binding site [polypeptide binding]; other site 1105104000712 L13 binding site [polypeptide binding]; other site 1105104000713 Ribosomal protein L35; Region: Ribosomal_L35p; cl00392 1105104000714 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 1105104000715 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 1105104000716 FeS/SAM binding site; other site 1105104000717 50S ribosomal protein L25/general stress protein Ctc; Reviewed; Region: PRK05618 1105104000718 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 1105104000719 5S rRNA interface [nucleotide binding]; other site 1105104000720 CTC domain interface [polypeptide binding]; other site 1105104000721 L16 interface [polypeptide binding]; other site 1105104000722 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 1105104000723 putative active site [active] 1105104000724 catalytic residue [active] 1105104000725 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 1105104000726 GTP-binding protein YchF; Reviewed; Region: PRK09601 1105104000727 YchF GTPase; Region: YchF; cd01900 1105104000728 G1 box; other site 1105104000729 GTP/Mg2+ binding site [chemical binding]; other site 1105104000730 Switch I region; other site 1105104000731 G2 box; other site 1105104000732 Switch II region; other site 1105104000733 G3 box; other site 1105104000734 G4 box; other site 1105104000735 G5 box; other site 1105104000736 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 1105104000737 RelA- and SpoT-like ppGpp Synthetases and Hydrolases, catalytic domain; Region: Rel-Spo_like; cl11966 1105104000738 metal binding triad [ion binding]; metal-binding site 1105104000739 HEPN domain; Region: HEPN; cl00824 1105104000740 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 1105104000741 drug resistance transporter, Bcr/CflA subfamily; Region: efflux_Bcr_CflA; TIGR00710 1105104000742 Patatin-like phospholipase; includes PNPLA8, PNPLA9, and Pat17; Region: Pat17_PNPLA8_PNPLA9_like; cd07199 1105104000743 active site 1105104000744 nucleophile elbow; other site 1105104000745 chromosomal replication initiation protein; Reviewed; Region: dnaA; PRK00149 1105104000746 DnaA N-terminal domain; Region: DnaA_N; pfam11638 1105104000747 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 1105104000748 Walker A motif; other site 1105104000749 ATP binding site [chemical binding]; other site 1105104000750 Walker B motif; other site 1105104000751 arginine finger; other site 1105104000752 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 1105104000753 DnaA box-binding interface [nucleotide binding]; other site 1105104000754 Member of the Rhodanese Homology Domain superfamily, subgroup 1. This CD includes the putative rhodanese-related sulfurtransferases of several uncharacterized proteins; Region: RHOD_1; cd01522 1105104000755 active site residue [active] 1105104000756 Flavinator of succinate dehydrogenase; Region: Sdh5; cl01110 1105104000757 Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]; Region: Mfd; COG1197 1105104000758 CarD-like/TRCF domain; Region: CarD_CdnL_TRCF; cl00588 1105104000759 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 1105104000760 ATP binding site [chemical binding]; other site 1105104000761 putative Mg++ binding site [ion binding]; other site 1105104000762 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 1105104000763 nucleotide binding region [chemical binding]; other site 1105104000764 ATP-binding site [chemical binding]; other site 1105104000765 TRCF domain; Region: TRCF; cl04088 1105104000766 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 1105104000767 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1105104000768 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1105104000769 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1105104000770 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1105104000771 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Region: murF; TIGR01143 1105104000772 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1105104000773 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1105104000774 phospho-N-acetylmuramoyl-pentapeptide-transferase; Provisional; Region: mraY; PRK00108 1105104000775 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 1105104000776 Mg++ binding site [ion binding]; other site 1105104000777 putative catalytic motif [active] 1105104000778 putative substrate binding site [chemical binding]; other site 1105104000779 NADPH-dependent FMN reductase; Region: FMN_red; cl00438 1105104000780 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 1105104000781 SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; Region: SugarP_isomerase; cl00339 1105104000782 RecG-like helicase [DNA replication, recombination, and repair / Transcription]; Region: RecG; COG1200 1105104000783 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 1105104000784 ssDNA binding site; other site 1105104000785 generic binding surface II; other site 1105104000786 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 1105104000787 ATP binding site [chemical binding]; other site 1105104000788 putative Mg++ binding site [ion binding]; other site 1105104000789 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 1105104000790 nucleotide binding region [chemical binding]; other site 1105104000791 ATP-binding site [chemical binding]; other site 1105104000792 TraX protein; Region: TraX; cl05434 1105104000793 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105104000794 MviN-like protein; Region: MVIN; pfam03023 1105104000795 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 1105104000796 dimer interface [polypeptide binding]; other site 1105104000797 substrate binding site [chemical binding]; other site 1105104000798 metal binding sites [ion binding]; metal-binding site 1105104000799 CcmE; Region: CcmE; cl00994 1105104000800 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 1105104000801 Cu(I) binding site [ion binding]; other site 1105104000802 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 1105104000803 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 1105104000804 Protein export membrane protein; Region: SecD_SecF; cl14618 1105104000805 Preprotein translocase subunit; Region: YajC; cl00806 1105104000806 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105104000807 Ribbon-helix-helix protein, copG family; Region: RHH_1; cl15783 1105104000808 potential frameshift: common BLAST hit: gi|67459346|ref|YP_246970.1| proline/betaine transporter 1105104000809 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 1105104000810 Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]; Region: MgtE; COG2239 1105104000811 MgtE intracellular N domain; Region: MgtE_N; cl15244 1105104000812 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 1105104000813 Divalent cation transporter; Region: MgtE; cl00786 1105104000814 HAD-superfamily class IIA hydrolase, TIGR01459; Region: HAD-SF-IIA-hyp4 1105104000815 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 1105104000816 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 1105104000817 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 1105104000818 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 1105104000819 ATP binding site [chemical binding]; other site 1105104000820 Mg2+ binding site [ion binding]; other site 1105104000821 G-X-G motif; other site 1105104000822 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 1105104000823 anchoring element; other site 1105104000824 dimer interface [polypeptide binding]; other site 1105104000825 ATP binding site [chemical binding]; other site 1105104000826 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 1105104000827 active site 1105104000828 putative metal-binding site [ion binding]; other site 1105104000829 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 1105104000830 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 1105104000831 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 1105104000832 hinge; other site 1105104000833 active site 1105104000834 RNA polymerase Rpb6; Region: RNA_pol_Rpb6; cl14651 1105104000835 4'-phosphopantetheinyl transferase superfamily; Region: ACPS; cl00500 1105104000836 peptidylprolyl isomerase; Reviewed; Region: prsA; PRK03002 1105104000837 PPIC-type PPIASE domain; Region: Rotamase; cl08278 1105104000838 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 1105104000839 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105104000840 SecA preprotein cross-linking domain; Region: SecA_PP_bind; cl03078 1105104000841 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 1105104000842 nucleotide binding region [chemical binding]; other site 1105104000843 ATP-binding site [chemical binding]; other site 1105104000844 SEC-C motif; Region: SEC-C; pfam02810 1105104000845 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 1105104000846 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 1105104000847 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 1105104000848 DNA binding site [nucleotide binding] 1105104000849 active site 1105104000850 Metal binding domain of Ada; Region: Ada_Zn_binding; pfam02805 1105104000851 potential frameshift: common BLAST hit: gi|67459307|ref|YP_246931.1| methylated-DNA--protein-cysteine methyltransferase 1105104000852 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 1105104000853 active site 1105104000854 DNA binding site [nucleotide binding] 1105104000855 A new structural DNA glycosylase; Region: AlkD_like; cd06561 1105104000856 active site 1105104000857 Protein of unknown function (DUF461); Region: DUF461; cl01071 1105104000858 excinuclease ABC subunit C; Validated; Region: uvrC; PRK00558 1105104000859 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 1105104000860 GIY-YIG motif/motif A; other site 1105104000861 active site 1105104000862 catalytic site [active] 1105104000863 putative DNA binding site [nucleotide binding]; other site 1105104000864 metal binding site [ion binding]; metal-binding site 1105104000865 UvrB/uvrC motif; Region: UVR; pfam02151 1105104000866 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 1105104000867 Solute carrier 5 family, sodium/glucose transporters and related proteins; solute-binding domain; Region: SLC5sbd; cd10322 1105104000868 Na binding site [ion binding]; other site 1105104000869 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2001 1105104000870 MraZ protein; Region: MraZ; pfam02381 1105104000871 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG0275 1105104000872 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 1105104000873 S-adenosylmethionine binding site [chemical binding]; other site 1105104000874 Predicted secreted (periplasmic) protein [Function unknown]; Region: COG5462 1105104000875 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 1105104000876 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 1105104000877 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 1105104000878 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 1105104000879 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 1105104000880 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 1105104000881 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: COG3264 1105104000882 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1105104000883 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 1105104000884 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 1105104000885 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1105104000886 Pentapeptide repeats (9 copies); Region: Pentapeptide_4; pfam13599 1105104000887 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1105104000888 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]; Region: AtoC; COG2204 1105104000889 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 1105104000890 active site 1105104000891 phosphorylation site [posttranslational modification] 1105104000892 intermolecular recognition site; other site 1105104000893 dimerization interface [polypeptide binding]; other site 1105104000894 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 1105104000895 Walker A motif; other site 1105104000896 ATP binding site [chemical binding]; other site 1105104000897 Walker B motif; other site 1105104000898 arginine finger; other site 1105104000899 Helix-turn-helix domains; Region: HTH; cl00088 1105104000900 Multiple resistance and pH regulation protein F (MrpF / PhaF); Region: MrpF_PhaF; cl09154 1105104000901 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105104000902 2-octaprenyl-6-methoxyphenyl hydroxylase; Validated; Region: PRK06617 1105104000903 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105104000904 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 1105104000905 Transposase IS116/IS110/IS902 family; Region: Transposase_20; pfam02371 1105104000906 Protein of unknown function (DUF3680); Region: DUF3680; cl02189 1105104000907 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 1105104000908 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 1105104000909 active site 1105104000910 HIGH motif; other site 1105104000911 dimer interface [polypeptide binding]; other site 1105104000912 KMSKS motif; other site 1105104000913 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 1105104000914 RNA binding surface [nucleotide binding]; other site 1105104000915 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: COG1189 1105104000916 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cl09940 1105104000917 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; cl16911 1105104000918 Predicted transcriptional regulator [Transcription]; Region: COG1959 1105104000919 Helix-turn-helix domains; Region: HTH; cl00088 1105104000920 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 1105104000921 NAD binding pocket [chemical binding]; other site 1105104000922 ribosome maturation protein RimP; Reviewed; Region: PRK00092 1105104000923 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of...; Region: Sm_like; cl00259 1105104000924 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of...; Region: Sm_like; cl00259 1105104000925 Sm1 motif; other site 1105104000926 D1 - D2 interaction site; other site 1105104000927 D3 - B interaction site; other site 1105104000928 Hfq - Hfq interaction site; other site 1105104000929 RNA binding pocket [nucleotide binding]; other site 1105104000930 Sm2 motif; other site 1105104000931 transcription elongation factor NusA; Validated; Region: nusA; PRK09202 1105104000932 NusA N-terminal domain; Region: NusA_N; pfam08529 1105104000933 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 1105104000934 RNA binding site [nucleotide binding]; other site 1105104000935 homodimer interface [polypeptide binding]; other site 1105104000936 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 1105104000937 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 1105104000938 G-X-X-G motif; other site 1105104000939 transcription termination factor NusA, C-terminal duplication; Region: nusA_Cterm_rpt; TIGR01954 1105104000940 translation initiation factor IF-2; Validated; Region: infB; PRK05306 1105104000941 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 1105104000942 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 1105104000943 G1 box; other site 1105104000944 putative GEF interaction site [polypeptide binding]; other site 1105104000945 GTP/Mg2+ binding site [chemical binding]; other site 1105104000946 Switch I region; other site 1105104000947 G2 box; other site 1105104000948 G3 box; other site 1105104000949 Switch II region; other site 1105104000950 G4 box; other site 1105104000951 G5 box; other site 1105104000952 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 1105104000953 Translation-initiation factor 2; Region: IF-2; pfam11987 1105104000954 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 1105104000955 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 1105104000956 DNA repair protein RecO; Reviewed; Region: recO; PRK00085 1105104000957 Recombination protein O N terminal; Region: RecO_N; cl15812 1105104000958 Recombination protein O C terminal; Region: RecO_C; pfam02565 1105104000959 DNA repair protein RadA; Provisional; Region: PRK11823 1105104000960 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 1105104000961 Walker A motif/ATP binding site; other site 1105104000962 ATP binding site [chemical binding]; other site 1105104000963 Walker B motif; other site 1105104000964 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 1105104000965 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; cl16911 1105104000966 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 1105104000967 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1105104000968 Pentapeptide repeats containing protein [Function unknown]; Region: COG1357 1105104000969 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1105104000970 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1105104000971 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 1105104000972 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 1105104000973 RNA binding surface [nucleotide binding]; other site 1105104000974 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 1105104000975 active site 1105104000976 Transmembrane amino acid transporter protein; Region: Aa_trans; cl15776 1105104000977 aromatic amino acid transport protein; Region: araaP; TIGR00837 1105104000978 Transmembrane amino acid transporter protein; Region: Aa_trans; cl15776 1105104000979 replicative DNA helicase; Provisional; Region: PRK09165 1105104000980 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 1105104000981 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 1105104000982 Walker A motif; other site 1105104000983 ATP binding site [chemical binding]; other site 1105104000984 Walker B motif; other site 1105104000985 DNA binding loops [nucleotide binding] 1105104000986 aromatic acid decarboxylase; Validated; Region: PRK05920 1105104000987 Flavoprotein; Region: Flavoprotein; cl08021 1105104000988 primosome assembly protein PriA; Validated; Region: PRK05580 1105104000989 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 1105104000990 ATP binding site [chemical binding]; other site 1105104000991 putative Mg++ binding site [ion binding]; other site 1105104000992 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105104000993 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 1105104000994 dimer interface [polypeptide binding]; other site 1105104000995 allosteric magnesium binding site [ion binding]; other site 1105104000996 active site 1105104000997 aspartate-rich active site metal binding site; other site 1105104000998 Schiff base residues; other site 1105104000999 NADH dehydrogenase subunit 2; Provisional; Region: ND2; MTH00196 1105104001000 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 1105104001001 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105104001002 AAA domain; Region: AAA_18; pfam13238 1105104001003 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 1105104001004 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 1105104001005 active site 1105104001006 homodimer interface [polypeptide binding]; other site 1105104001007 putative chemical substrate binding site [chemical binding]; other site 1105104001008 metal binding site [ion binding]; metal-binding site 1105104001009 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 1105104001010 Substrate binding site; other site 1105104001011 Mg++ binding site; other site 1105104001012 Transcriptional regulator; Region: Transcrip_reg; cl00361 1105104001013 Ribosomal protein L36; Region: Ribosomal_L36; cl00380 1105104001014 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 1105104001015 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 catalyze...; Region: LT_GEWL; cd00254 1105104001016 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1105104001017 Protein of unknown function (DUF2532); Region: DUF2532; pfam10811 1105104001018 ISXO2-like transposase domain; Region: DDE_Tnp_IS1595; cl01481 1105104001019 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; cl16911 1105104001020 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; cl16911 1105104001021 dihydrolipoamide dehydrogenase; Validated; Region: PRK06327 1105104001022 glycerol-3-phosphate dehydrogenase, anaerobic, B subunit; Region: glycerol3P_GlpB; TIGR03378 1105104001023 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1105104001024 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain; Region: Pyr_redox_dim; pfam02852 1105104001025 5-formyltetrahydrofolate cyclo-ligase family; Region: 5-FTHF_cyc-lig; cl00360 1105104001026 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 1105104001027 catalytic site [active] 1105104001028 putative active site [active] 1105104001029 putative substrate binding site [chemical binding]; other site 1105104001030 HRDC domain; Region: HRDC; cl02578 1105104001031 Uncharacterized ACR, YagE family COG1723; Region: DUF155; cl00751 1105104001032 Predicted aminomethyltransferase related to GcvT [General function prediction only]; Region: COG0354 1105104001033 Rickettsial palindromic element RPE2 domain; Region: RPE2; TIGR03774 1105104001034 folate-binding protein YgfZ; Region: ygfZ_signature; TIGR03317 1105104001035 Glycine cleavage T-protein C-terminal barrel domain; Region: GCV_T_C; pfam08669 1105104001036 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 1105104001037 potential frameshift: common BLAST hit: gi|15892625|ref|NP_360339.1| sodium/pantothenate symporter 1105104001038 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 1105104001039 dimer interface [polypeptide binding]; other site 1105104001040 phosphorylation site [posttranslational modification] 1105104001041 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; cl00075 1105104001042 G-X-G motif; other site 1105104001043 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 1105104001044 dimer interface [polypeptide binding]; other site 1105104001045 catalytic triad [active] 1105104001046 porphobilinogen deaminase; Reviewed; Region: hemC; PRK00072 1105104001047 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 1105104001048 domain interfaces; other site 1105104001049 active site 1105104001050 Domain of unknown function (DUF4143); Region: DUF4143; pfam13635 1105104001051 Uncharacterized ACR, YhhQ family COG1738; Region: DUF165; cl00756 1105104001052 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 1105104001053 non-specific DNA binding site [nucleotide binding]; other site 1105104001054 salt bridge; other site 1105104001055 sequence-specific DNA binding site [nucleotide binding]; other site 1105104001056 cytidylate kinase; Provisional; Region: cmk; PRK00023 1105104001057 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 1105104001058 CMP-binding site; other site 1105104001059 The sites determining sugar specificity; other site 1105104001060 30S ribosomal protein S1; Reviewed; Region: rpsA; PRK06299 1105104001061 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists...; Region: S1_RPS1_repeat_ec1_hs1; cd05687 1105104001062 RNA binding site [nucleotide binding]; other site 1105104001063 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 consists...; Region: S1_RPS1_repeat_ec2_hs2; cd04465 1105104001064 RNA binding site [nucleotide binding]; other site 1105104001065 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 of...; Region: S1_RPS1_repeat_ec3; cd05688 1105104001066 RNA binding site [nucleotide binding]; other site 1105104001067 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 1105104001068 RNA binding site [nucleotide binding]; other site 1105104001069 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 1105104001070 RNA binding site [nucleotide binding]; other site 1105104001071 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 1105104001072 RNA binding site [nucleotide binding]; other site 1105104001073 Clp protease; Region: CLP_protease; pfam00574 1105104001074 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 1105104001075 oligomer interface [polypeptide binding]; other site 1105104001076 active site residues [active] 1105104001077 isopentenyl pyrophosphate isomerase; Provisional; Region: PRK05437 1105104001078 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 1105104001079 homotetramer interface [polypeptide binding]; other site 1105104001080 FMN binding site [chemical binding]; other site 1105104001081 homodimer contacts [polypeptide binding]; other site 1105104001082 putative active site [active] 1105104001083 putative substrate binding site [chemical binding]; other site 1105104001084 N-Acyltransferase superfamily: Various enyzmes that characteristicly catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl00357 1105104001085 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 1105104001086 Coenzyme A binding pocket [chemical binding]; other site 1105104001087 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 1105104001088 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 1105104001089 Predicted transcriptional regulator [Transcription]; Region: COG1959 1105104001090 Helix-turn-helix domains; Region: HTH; cl00088 1105104001091 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 1105104001092 cysteine desulfurase DndA; Region: DNA_S_dndA; TIGR03235 1105104001093 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1105104001094 catalytic residue [active] 1105104001095 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 1105104001096 cysteine desulfurase DndA; Region: DNA_S_dndA; TIGR03235 1105104001097 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 1105104001098 catalytic residue [active] 1105104001099 NifU homolog involved in Fe-S cluster formation [Energy production and conversion]; Region: IscU; COG0822 1105104001100 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 1105104001101 trimerization site [polypeptide binding]; other site 1105104001102 active site 1105104001103 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 1105104001104 Spore germination protein; Region: Spore_permease; cl15802 1105104001105 arginine:agmatin antiporter; Provisional; Region: PRK10644 1105104001106 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 1105104001107 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 1105104001108 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 1105104001109 active site 1105104001110 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 1105104001111 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 1105104001112 substrate binding pocket [chemical binding]; other site 1105104001113 chain length determination region; other site 1105104001114 substrate-Mg2+ binding site; other site 1105104001115 catalytic residues [active] 1105104001116 aspartate-rich region 1; other site 1105104001117 active site lid residues [active] 1105104001118 aspartate-rich region 2; other site 1105104001119 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105104001120 ATP/ADP translocase [Energy production and conversion]; Region: COG3202; cl03940 1105104001121 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 1105104001122 Putative transposase, YhgA-like; Region: Transposase_31; pfam04754 1105104001123 muropeptide transporter; Validated; Region: ampG; PRK11010 1105104001124 AmpG-like permease; Region: 2A0125; TIGR00901 1105104001125 muropeptide transporter; Validated; Region: ampG; PRK11010 1105104001126 LysE type translocator; Region: LysE; cl00565 1105104001127 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 1105104001128 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 1105104001129 active site 1105104001130 Rickettsial palindromic element RPE2 domain; Region: RPE2; TIGR03774 1105104001131 Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]; Region: HemY; COG3071 1105104001132 HemY protein N-terminus; Region: HemY_N; pfam07219 1105104001133 Predicted hydrolase of the alpha/beta superfamily [General function prediction only]; Region: COG2945 1105104001134 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 1105104001135 RelB antitoxin; Region: RelB; cl01171 1105104001136 Protein required for attachment to host cells; Region: Host_attach; cl02398 1105104001137 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 1105104001138 putative acyl-acceptor binding pocket; other site 1105104001139 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 1105104001140 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 1105104001141 active site 1105104001142 HIGH motif; other site 1105104001143 dimer interface [polypeptide binding]; other site 1105104001144 KMSKS motif; other site 1105104001145 Bacteriophage head to tail connecting protein; Region: Head-tail_con; cl10251 1105104001146 Bacteriophage head to tail connecting protein; Region: Head-tail_con; cl10251 1105104001147 Protein of unknown function (DUF328); Region: DUF328; cl01143 1105104001148 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 1105104001149 IHF - DNA interface [nucleotide binding]; other site 1105104001150 IHF dimer interface [polypeptide binding]; other site 1105104001151 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 1105104001152 tandem repeat interface [polypeptide binding]; other site 1105104001153 oligomer interface [polypeptide binding]; other site 1105104001154 active site residues [active] 1105104001155 transcription termination factor Rho; Provisional; Region: rho; PRK09376 1105104001156 Rho termination factor, N-terminal domain; Region: Rho_N; cl06505 1105104001157 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 1105104001158 RNA binding site [nucleotide binding]; other site 1105104001159 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 1105104001160 multimer interface [polypeptide binding]; other site 1105104001161 Walker A motif; other site 1105104001162 ATP binding site [chemical binding]; other site 1105104001163 Walker B motif; other site 1105104001164 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1, 4-benzoquinol methylase [Coenzyme metabolism]; Region: UbiG; COG2227 1105104001165 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 1105104001166 S-adenosylmethionine binding site [chemical binding]; other site 1105104001167 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 1105104001168 DHH family; Region: DHH; pfam01368 1105104001169 DHHA1 domain; Region: DHHA1; pfam02272 1105104001170 peptide chain release factor 1; Validated; Region: prfA; PRK00591 1105104001171 RF-1 domain; Region: RF-1; cl02875 1105104001172 RF-1 domain; Region: RF-1; cl02875 1105104001173 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 1105104001174 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; Region: PDHac_trf_mito; TIGR01349 1105104001175 E3 interaction surface; other site 1105104001176 lipoyl attachment site [posttranslational modification]; other site 1105104001177 e3 binding domain; Region: E3_binding; pfam02817 1105104001178 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 1105104001179 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 1105104001180 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 1105104001181 Predicted membrane protein (DUF2335); Region: DUF2335; cl02210 1105104001182 Phage conserved hypothetical protein BR0599; Region: Phage_BR0599; pfam09356 1105104001183 Uncharacterized conserved protein (DUF2163); Region: DUF2163; pfam09931 1105104001184 Conserved hypothetical protein 2217 (DUF2460); Region: DUF2460; cl02268 1105104001185 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]; Region: BirA; COG0340 1105104001186 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 1105104001187 Biotin protein ligase C terminal domain; Region: BPL_C; pfam02237 1105104001188 potential frameshift: common BLAST hit: gi|157964571|ref|YP_001499395.1| putative esterase of the alpha/beta hydrolase superfamily protein 1105104001189 potential frameshift: common BLAST hit: gi|157964571|ref|YP_001499395.1| putative esterase of the alpha/beta hydrolase superfamily protein 1105104001190 potential frameshift: common BLAST hit: gi|157964571|ref|YP_001499395.1| putative esterase of the alpha/beta hydrolase superfamily protein 1105104001191 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 1105104001192 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 1105104001193 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 1105104001194 folylpolyglutamate synthase/dihydrofolate synthase; Region: folC; TIGR01499 1105104001195 ECF-type riboflavin transporter, S component; Region: ECF-ribofla_trS; cl01942 1105104001196 Uncharacterized conserved protein [Function unknown]; Region: COG4285 1105104001197 Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Saccharomyces cerevisiae biotin-apoprotein ligase (ScBLP); Region: GATase1_ScBLP_like; cd03144 1105104001198 conserved cys residue [active] 1105104001199 Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]; Region: Gst; COG0625 1105104001200 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 1105104001201 GSH binding site (G-site) [chemical binding]; other site 1105104001202 C-terminal domain interface [polypeptide binding]; other site 1105104001203 C-terminal, alpha helical domain of the Glutathione S-transferase family; Region: GST_C_family; cd00299 1105104001204 N-terminal domain interface [polypeptide binding]; other site 1105104001205 dimer interface [polypeptide binding]; other site 1105104001206 substrate binding pocket (H-site) [chemical binding]; other site 1105104001207 pyruvate phosphate dikinase; Provisional; Region: PRK09279 1105104001208 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 1105104001209 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; cl01586 1105104001210 Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low...; Region: Pyruvate_Kinase; cl09155 1105104001211 Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II); Region: Aldolase_II; cl00214 1105104001212 intersubunit interface [polypeptide binding]; other site 1105104001213 active site 1105104001214 Zn2+ binding site [ion binding]; other site 1105104001215 PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs; Region: PIN_Pae0151; cd09873 1105104001216 putative active site [active] 1105104001217 homotetrameric interface [polypeptide binding]; other site 1105104001218 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105104001219 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; cl00234 1105104001220 catalytic residues [active] 1105104001221 Multicopper polyphenol oxidase (laccase) [Secondary metabolites biosynthesis, transport and catabolism]; Region: yfiH; COG1496 1105104001222 Multi-copper polyphenol oxidoreductase laccase; Region: Cu-oxidase_4; cl00650 1105104001223 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 1105104001224 Virulence factor BrkB; Region: Virul_fac_BrkB; cl07918 1105104001225 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 1105104001226 non-specific DNA binding site [nucleotide binding]; other site 1105104001227 salt bridge; other site 1105104001228 sequence-specific DNA binding site [nucleotide binding]; other site 1105104001229 120 KDa Rickettsia surface antigen; Region: 120_Rick_ant; pfam12574 1105104001230 ATP/ADP translocase [Energy production and conversion]; Region: COG3202; cl03940 1105104001231 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105104001232 tRNA pseudouridine synthase B; Provisional; Region: truB; PRK14846 1105104001233 Pseudouridine synthase, Escherichia coli TruB like; Region: PseudoU_synth_EcTruB; cd02573 1105104001234 RNA binding site [nucleotide binding]; other site 1105104001235 active site 1105104001236 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105104001237 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 1105104001238 16S/18S rRNA binding site [nucleotide binding]; other site 1105104001239 S13e-L30e interaction site [polypeptide binding]; other site 1105104001240 25S rRNA binding site [nucleotide binding]; other site 1105104001241 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 1105104001242 Polyribonucleotide nucleotidyltransferase, repeat 1; Region: RNase_PH_PNPase_1; cd11363 1105104001243 RNase E interface [polypeptide binding]; other site 1105104001244 trimer interface [polypeptide binding]; other site 1105104001245 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 1105104001246 Polyribonucleotide nucleotidyltransferase, repeat 2; Region: RNase_PH_PNPase_2; cd11364 1105104001247 RNase E interface [polypeptide binding]; other site 1105104001248 trimer interface [polypeptide binding]; other site 1105104001249 active site 1105104001250 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 1105104001251 putative nucleic acid binding region [nucleotide binding]; other site 1105104001252 G-X-X-G motif; other site 1105104001253 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 1105104001254 RNA binding site [nucleotide binding]; other site 1105104001255 domain interface; other site 1105104001256 D-arabinose 5-phosphate isomerase; Provisional; Region: PRK10892 1105104001257 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 1105104001258 putative active site [active] 1105104001259 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 1105104001260 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5375 1105104001261 OstA-like protein; Region: OstA; cl00844 1105104001262 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 1105104001263 The ABC transporters belonging to the YhbG family are similar to members of the Mj1267_LivG family, which is involved in the transport of branched-chain amino acids. The genes yhbG and yhbN are located in a single operon and may function together in...; Region: ABC_YhbG; cd03218 1105104001264 Walker A/P-loop; other site 1105104001265 ATP binding site [chemical binding]; other site 1105104001266 Q-loop/lid; other site 1105104001267 ABC transporter signature motif; other site 1105104001268 Walker B; other site 1105104001269 D-loop; other site 1105104001270 H-loop/switch region; other site 1105104001271 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 1105104001272 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 1105104001273 active site 1105104001274 substrate binding site [chemical binding]; other site 1105104001275 metal binding site [ion binding]; metal-binding site 1105104001276 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105104001277 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 1105104001278 Pentapeptide repeats (8 copies); Region: Pentapeptide; pfam00805 1105104001279 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 1105104001280 dimer interface [polypeptide binding]; other site 1105104001281 putative radical transfer pathway; other site 1105104001282 diiron center [ion binding]; other site 1105104001283 tyrosyl radical; other site 1105104001284 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK09102 1105104001285 Class I ribonucleotide reductase; Region: RNR_I; cd01679 1105104001286 active site 1105104001287 dimer interface [polypeptide binding]; other site 1105104001288 catalytic residues [active] 1105104001289 effector binding site; other site 1105104001290 R2 peptide binding site; other site 1105104001291 Spore Coat Protein U domain; Region: SCPU; cl02253 1105104001292 potential frameshift: common BLAST hit: gi|67459098|ref|YP_246722.1| P pilus assembly protein FimD 1105104001293 potential frameshift: common BLAST hit: gi|67459098|ref|YP_246722.1| P pilus assembly protein FimD 1105104001294 potential frameshift: common BLAST hit: gi|91205792|ref|YP_538147.1| P pilus assembly, fimbrial usher protein 1105104001295 P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FimC; COG3121 1105104001296 potential frameshift: common BLAST hit: gi|165933233|ref|YP_001650022.1| protein U 1105104001297 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 1105104001298 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105104001299 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1105104001300 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14171 1105104001301 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 1105104001302 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 1105104001303 homodimer interface [polypeptide binding]; other site 1105104001304 NADP binding site [chemical binding]; other site 1105104001305 substrate binding site [chemical binding]; other site 1105104001306 potential frameshift: common BLAST hit: gi|229586740|ref|YP_002845241.1| Carbonic anhydrases/acetyltransferase, isoleucine patch superfamily 1105104001307 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 A site; Region: RaiA; cd00552 1105104001308 30S subunit binding site; other site 1105104001309 ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]; Region: Lon; COG0466 1105104001310 Found in ATP-dependent protease La (LON); Region: LON; smart00464 1105104001311 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 1105104001312 Walker A motif; other site 1105104001313 ATP binding site [chemical binding]; other site 1105104001314 Walker B motif; other site 1105104001315 arginine finger; other site 1105104001316 Subunit ChlI of Mg-chelatase; Region: ChlI; cl12214 1105104001317 Threonine dehydratase [Amino acid transport and metabolism]; Region: IlvA; COG1171 1105104001318 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 1105104001319 tetramer interface [polypeptide binding]; other site 1105104001320 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1105104001321 catalytic residue [active] 1105104001322 Alanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: AlaS; COG0013 1105104001323 ATP-dependent DNA helicase PcrA; Region: pcrA; TIGR01073 1105104001324 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105104001325 Family description; Region: UvrD_C_2; cl15862 1105104001326 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 1105104001327 active site 1105104001328 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 1105104001329 Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like; Region: ALDH_F5_SSADH_GabD; cd07103 1105104001330 tetramerization interface [polypeptide binding]; other site 1105104001331 NAD(P) binding site [chemical binding]; other site 1105104001332 catalytic residues [active] 1105104001333 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 1105104001334 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 1105104001335 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 1105104001336 Membrane transport protein; Region: Mem_trans; cl09117 1105104001337 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 1105104001338 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105104001339 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 1105104001340 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 1105104001341 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 1105104001342 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 1105104001343 Diacylglycerol kinase catalytic domain; Region: DAGK_cat; cl01255 1105104001344 recombination protein RecR; Reviewed; Region: recR; PRK00076 1105104001345 RecR protein; Region: RecR; pfam02132 1105104001346 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 1105104001347 putative active site [active] 1105104001348 putative metal-binding site [ion binding]; other site 1105104001349 tetramer interface [polypeptide binding]; other site 1105104001350 RDD family; Region: RDD; cl00746 1105104001351 SNARE associated Golgi protein; Region: SNARE_assoc; cl00429 1105104001352 Ribosome-binding factor A; Region: RBFA; cl00542 1105104001353 OpgC protein; Region: OpgC_C; cl00792 1105104001354 Tim44-like domain; Region: Tim44; cl09208 1105104001355 Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]; Region: DAP2; COG1506 1105104001356 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 1105104001357 substrate binding pocket [chemical binding]; other site 1105104001358 catalytic triad [active] 1105104001359 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 1105104001360 Regulators of stationary/sporulation gene expression [Transcription]; Region: AbrB; COG2002 1105104001361 Antidote-toxin recognition MazE; Region: Antitoxin-MazE; cl00877 1105104001362 succinyl-CoA synthetase subunit beta; Provisional; Region: sucC; PRK00696 1105104001363 ATP-grasp domain; Region: ATP-grasp_4; cl03087 1105104001364 CoA-ligase; Region: Ligase_CoA; cl02894 1105104001365 succinyl-CoA synthetase subunit alpha; Validated; Region: PRK05678 1105104001366 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105104001367 CoA-ligase; Region: Ligase_CoA; cl02894 1105104001368 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 1105104001369 DSBA-like thioredoxin domain; Region: DSBA; pfam01323 1105104001370 catalytic residues [active] 1105104001371 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 1105104001372 SmpB-tmRNA interface; other site 1105104001373 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 1105104001374 dihydrodipicolinate synthase; Region: dapA; TIGR00674 1105104001375 dimer interface [polypeptide binding]; other site 1105104001376 active site 1105104001377 catalytic residue [active] 1105104001378 BCAT_beta_family: Branched-chain aminotransferase catalyses the transamination of the branched-chain amino acids leusine, isoleucine and valine to their respective alpha-keto acids, alpha-ketoisocaproate, alpha-keto-beta-methylvalerate and...; Region: BCAT_beta_family; cd01557 1105104001379 homodimer interface [polypeptide binding]; other site 1105104001380 substrate-cofactor binding pocket; other site 1105104001381 catalytic residue [active] 1105104001382 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1105104001383 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 1105104001384 active site 1105104001385 phosphorylation site [posttranslational modification] 1105104001386 intermolecular recognition site; other site 1105104001387 dimerization interface [polypeptide binding]; other site 1105104001388 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 1105104001389 DNA binding site [nucleotide binding] 1105104001390 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105104001391 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cl01054 1105104001392 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cl00080 1105104001393 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 1105104001394 ATP binding site [chemical binding]; other site 1105104001395 Mg2+ binding site [ion binding]; other site 1105104001396 G-X-G motif; other site 1105104001397 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 1105104001398 Putative undecaprenyl diphosphate synthase; Region: Prenyltransf; pfam01255 1105104001399 catalytic residue [active] 1105104001400 putative FPP diphosphate binding site; other site 1105104001401 putative FPP binding hydrophobic cleft; other site 1105104001402 dimer interface [polypeptide binding]; other site 1105104001403 putative IPP diphosphate binding site; other site 1105104001404 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 1105104001405 Septum formation initiator; Region: DivIC; cl11433 1105104001406 DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Region: RNaseD_exo; cd06142 1105104001407 catalytic site [active] 1105104001408 putative active site [active] 1105104001409 putative substrate binding site [chemical binding]; other site 1105104001410 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 1105104001411 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 1105104001412 HIGH motif; other site 1105104001413 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 1105104001414 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105104001415 active site 1105104001416 KMSKS motif; other site 1105104001417 Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases; Region: Anticodon_Ia_Leu_BEm; cd07958 1105104001418 tRNA binding surface [nucleotide binding]; other site 1105104001419 Domain of unknown function (DUF3576); Region: DUF3576; pfam12100 1105104001420 Protein of unknown function (DUF1653); Region: DUF1653; cl01949 1105104001421 Protein of unknown function (DUF1653); Region: DUF1653; cl01949 1105104001422 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 1105104001423 DNA polymerase III subunit beta; Validated; Region: PRK05643 1105104001424 putative DNA binding surface [nucleotide binding]; other site 1105104001425 dimer interface [polypeptide binding]; other site 1105104001426 beta-clamp/clamp loader binding surface; other site 1105104001427 beta-clamp/translesion DNA polymerase binding surface; other site 1105104001428 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 1105104001429 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 1105104001430 putative tRNA-binding site [nucleotide binding]; other site 1105104001431 B3/4 domain; Region: B3_4; cl11458 1105104001432 tRNA synthetase B5 domain; Region: B5; cl08394 1105104001433 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 1105104001434 dimer interface [polypeptide binding]; other site 1105104001435 motif 1; other site 1105104001436 motif 3; other site 1105104001437 motif 2; other site 1105104001438 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; cl08386 1105104001439 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 1105104001440 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 1105104001441 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 1105104001442 dimer interface [polypeptide binding]; other site 1105104001443 motif 1; other site 1105104001444 active site 1105104001445 motif 2; other site 1105104001446 motif 3; other site 1105104001447 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 1105104001448 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 1105104001449 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 1105104001450 FeS/SAM binding site; other site 1105104001451 diaminopimelate epimerase; Region: DapF; TIGR00652 1105104001452 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 1105104001453 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 1105104001454 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105104001455 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105104001456 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105104001457 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 1105104001458 potential frameshift: common BLAST hit: gi|67459035|ref|YP_246659.1| RND efflux system, outer membrane protein 1105104001459 potential frameshift: common BLAST hit: gi|67459034|ref|YP_246658.1| RND family transporter membrane-fusion protein 1105104001460 AcrB/AcrD/AcrF family; Region: ACR_tran; pfam00873 1105104001461 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 1105104001462 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 1105104001463 multidrug efflux system subunit MdtB; Provisional; Region: PRK10503 1105104001464 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 1105104001465 undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional; Region: murG; PRK00726 1105104001466 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 1105104001467 active site 1105104001468 homodimer interface [polypeptide binding]; other site 1105104001469 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 1105104001470 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK01368 1105104001471 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1105104001472 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105104001473 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1105104001474 Protein of unknown function (DUF3035); Region: DUF3035; pfam11233 1105104001475 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 1105104001476 putative peptidase; Provisional; Region: PRK11649 1105104001477 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105104001478 Cytochrome C oxidase subunit II, transmembrane domain; Region: COX2_TM; pfam02790 1105104001479 cytochrome c oxidase subunit II; Provisional; Region: COX2; MTH00154 1105104001480 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 1105104001481 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 1105104001482 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 1105104001483 cytochrome c oxidase subunit I; Validated; Region: COX1; MTH00007 1105104001484 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 1105104001485 Subunit I/III interface [polypeptide binding]; other site 1105104001486 D-pathway; other site 1105104001487 Subunit I/VIIc interface [polypeptide binding]; other site 1105104001488 Subunit I/IV interface [polypeptide binding]; other site 1105104001489 Subunit I/II interface [polypeptide binding]; other site 1105104001490 Low-spin heme (heme a) binding site [chemical binding]; other site 1105104001491 Subunit I/VIIa interface [polypeptide binding]; other site 1105104001492 Subunit I/VIa interface [polypeptide binding]; other site 1105104001493 Dimer interface; other site 1105104001494 Putative water exit pathway; other site 1105104001495 Binuclear center (heme a3/CuB) [ion binding]; other site 1105104001496 K-pathway; other site 1105104001497 Subunit I/Vb interface [polypeptide binding]; other site 1105104001498 Putative proton exit pathway; other site 1105104001499 Subunit I/VIb interface; other site 1105104001500 Subunit I/VIc interface [polypeptide binding]; other site 1105104001501 Electron transfer pathway; other site 1105104001502 Subunit I/VIIIb interface [polypeptide binding]; other site 1105104001503 Subunit I/VIIb interface [polypeptide binding]; other site 1105104001504 Predicted glutamine amidotransferases [General function prediction only]; Region: COG2071 1105104001505 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain; Region: GATase1_2; cd01745 1105104001506 catalytic triad [active] 1105104001507 Rickettsial palindromic element RPE4 domain; Region: RPE4; TIGR03777 1105104001508 CRISPR/Cas system-associated protein Cas4; Region: Cas4_I-A_I-B_I-C_I-D_II-B; cl00641 1105104001509 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein; Region: Peptidase_S66; cd07025 1105104001510 dimer interface [polypeptide binding]; other site 1105104001511 catalytic triad [active] 1105104001512 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 1105104001513 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 catalyze...; Region: LT_GEWL; cd00254 1105104001514 N-acetyl-D-glucosamine binding site [chemical binding]; other site 1105104001515 catalytic residue [active] 1105104001516 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 1105104001517 trimer interface [polypeptide binding]; other site 1105104001518 active site 1105104001519 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 1105104001520 tandem repeat interface [polypeptide binding]; other site 1105104001521 oligomer interface [polypeptide binding]; other site 1105104001522 active site residues [active] 1105104001523 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 1105104001524 catalytic residues [active] 1105104001525 Protocatechuate 3,4-dioxygenase beta subunit [Secondary metabolites biosynthesis, transport, and catabolism]; Region: PcaH; COG3485 1105104001526 Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain; Region: Peptidase_M14NE-CP-C_like; cl01383 1105104001527 active site 1105104001528 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 1105104001529 Cytochrome C oxidase subunit II, periplasmic domain; Region: COX2; cl11412 1105104001530 Iron permease FTR1 family; Region: FTR1; cl00475 1105104001531 Intracellular septation protein A; Region: IspA; cl01098 1105104001532 Predicted periplasmic or secreted lipoprotein [General function prediction only]; Region: OsmY; COG2823 1105104001533 BON domain; Region: BON; cl02771 1105104001534 BON domain; Region: BON; cl02771 1105104001535 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105104001536 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105104001537 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; cl04011 1105104001538 D-alanyl-D-alanine carboxypeptidase; Region: Peptidase_S11; pfam00768 1105104001539 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 1105104001540 muropeptide transporter; Validated; Region: ampG; PRK11010 1105104001541 muropeptide transporter; Reviewed; Region: ampG; PRK11902 1105104001542 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 1105104001543 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 1105104001544 MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic...; Region: ABCC_MsbA; cd03251 1105104001545 Walker A/P-loop; other site 1105104001546 ATP binding site [chemical binding]; other site 1105104001547 Q-loop/lid; other site 1105104001548 ABC transporter signature motif; other site 1105104001549 Walker B; other site 1105104001550 D-loop; other site 1105104001551 H-loop/switch region; other site 1105104001552 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 1105104001553 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 1105104001554 Walker A motif; other site 1105104001555 ATP binding site [chemical binding]; other site 1105104001556 Walker B motif; other site 1105104001557 arginine finger; other site 1105104001558 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 1105104001559 Holliday junction DNA helicase RuvA; Reviewed; Region: ruvA; PRK00116 1105104001560 RuvA N terminal domain; Region: RuvA_N; pfam01330 1105104001561 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 1105104001562 Fic family protein [Function unknown]; Region: COG3177 1105104001563 Fic/DOC family; Region: Fic; cl00960 1105104001564 prolyl-tRNA synthetase; Provisional; Region: PRK12325 1105104001565 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 formation of...; Region: ProRS_core_prok; cd00779 1105104001566 dimer interface [polypeptide binding]; other site 1105104001567 motif 1; other site 1105104001568 active site 1105104001569 motif 2; other site 1105104001570 motif 3; other site 1105104001571 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 1105104001572 anticodon binding site; other site 1105104001573 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 1105104001574 GTP cyclohydrolase I; Provisional; Region: PLN03044 1105104001575 active site 1105104001576 Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+...; Region: Nudix_Hydrolase; cl00447 1105104001577 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 1105104001578 Ligand binding site; other site 1105104001579 oligomer interface; other site 1105104001580 CTP synthetase; Validated; Region: pyrG; PRK05380 1105104001581 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 1105104001582 Catalytic site [active] 1105104001583 active site 1105104001584 UTP binding site [chemical binding]; other site 1105104001585 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 1105104001586 active site 1105104001587 putative oxyanion hole; other site 1105104001588 catalytic triad [active] 1105104001589 ATP/ADP translocase [Energy production and conversion]; Region: COG3202; cl03940 1105104001590 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105104001591 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 1105104001592 malate dehydrogenase; Reviewed; Region: PRK06223 1105104001593 L-lactate dehydrogenase-like malate dehydrogenase proteins; Region: LDH-like_MDH; cd01339 1105104001594 NAD(P) binding site [chemical binding]; other site 1105104001595 dimer interface [polypeptide binding]; other site 1105104001596 tetramer (dimer of dimers) interface [polypeptide binding]; other site 1105104001597 substrate binding site [chemical binding]; other site 1105104001598 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105104001599 Antidote-toxin recognition MazE; Region: Antitoxin-MazE; cl00877 1105104001600 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 1105104001601 putative active site [active] 1105104001602 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed; Region: PRK07232 1105104001603 Malic enzyme, N-terminal domain; Region: malic; pfam00390 1105104001604 NAD(P) binding domain of malic enzyme (ME), subgroup 2; Region: NAD_bind_2_malic_enz; cd05311 1105104001605 putative NAD(P) binding site [chemical binding]; other site 1105104001606 Phosphate acetyl/butaryl transferase; Region: PTA_PTB; cl00390 1105104001607 Membrane transport protein; Region: Mem_trans; cl09117 1105104001608 lysyl-tRNA synthetase; Reviewed; Region: lysK; PRK00750 1105104001609 catalytic core domain of class I lysyl tRNA synthetase; Region: LysRS_core_class_I; cd00674 1105104001610 active site 1105104001611 HIGH motif; other site 1105104001612 KMSKS motif; other site 1105104001613 Disulfide bond formation protein DsbB; Region: DsbB; cl00649 1105104001614 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 1105104001615 ABC-type uncharacterized transport system, ATPase component [General function prediction only]; Region: PhnK; COG1101 1105104001616 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC...; Region: ABC_cobalt_CbiO_domain1; cd03225 1105104001617 Walker A/P-loop; other site 1105104001618 ATP binding site [chemical binding]; other site 1105104001619 Q-loop/lid; other site 1105104001620 ABC transporter signature motif; other site 1105104001621 Walker B; other site 1105104001622 D-loop; other site 1105104001623 H-loop/switch region; other site 1105104001624 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 1105104001625 TM-ABC transporter signature motif; other site 1105104001626 Type 1 periplasmic binding fold superfamily; Region: Periplasmic_Binding_Protein_Type_1; cl10011 1105104001627 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 1105104001628 Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20...; Region: PGRP; cd06583 1105104001629 amidase catalytic site [active] 1105104001630 Zn binding residues [ion binding]; other site 1105104001631 substrate binding site [chemical binding]; other site 1105104001632 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 1105104001633 apolipoprotein N-acyltransferase; Reviewed; Region: lnt; PRK00302 1105104001634 Apolipoprotein N-acyl transferase (class 9 nitrilases); Region: ALP_N-acyl_transferase; cd07571 1105104001635 putative active site [active] 1105104001636 catalytic triad [active] 1105104001637 putative dimer interface [polypeptide binding]; other site 1105104001638 Enoyl-[acyl-carrier-protein]; Region: FabI; COG0623 1105104001639 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 1105104001640 NAD binding site [chemical binding]; other site 1105104001641 homotetramer interface [polypeptide binding]; other site 1105104001642 homodimer interface [polypeptide binding]; other site 1105104001643 substrate binding site [chemical binding]; other site 1105104001644 active site 1105104001645 site-specific tyrosine recombinase XerD; Reviewed; Region: xerD; PRK00283 1105104001646 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 1105104001647 active site 1105104001648 DNA binding site [nucleotide binding] 1105104001649 Int/Topo IB signature motif; other site 1105104001650 potential frameshift: common BLAST hit: gi|67458962|ref|YP_246586.1| phage protein 1105104001651 potential frameshift: common BLAST hit: gi|67458962|ref|YP_246586.1| phage protein 1105104001652 Uncharacterized protein conserved in bacteria (DUF2155); Region: DUF2155; cl01970 1105104001653 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 1105104001654 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3; Region: Oxidored_q4; cl00535 1105104001655 NADH dehydrogenase subunit B; Provisional; Region: PRK14816 1105104001656 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; cl15792 1105104001657 NADH dehydrogenase subunit C; Provisional; Region: PRK06074 1105104001658 Respiratory-chain NADH dehydrogenase, 30 Kd subunit; Region: Complex1_30kDa; cl16917 1105104001659 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; cl00417 1105104001660 Respiratory-chain NADH dehydrogenase, 49 Kd subunit; Region: Complex1_49kDa; pfam00346 1105104001661 Respiratory-chain NADH dehydrogenase 24 Kd subunit; Region: Complex1_24kDa; pfam01257 1105104001662 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 1105104001663 putative dimer interface [polypeptide binding]; other site 1105104001664 [2Fe-2S] cluster binding site [ion binding]; other site 1105104001665 Haemolytic domain; Region: Haemolytic; cl00506 1105104001666 YCII-related domain; Region: YCII; cl00999 1105104001667 Alkyladenine DNA glycosylase catalyzes the first step in base excision repair; Region: AAG; cd00540 1105104001668 active site 1105104001669 DNA binding site [nucleotide binding] 1105104001670 Protein of unknown function (DUF3680); Region: DUF3680; cl02189 1105104001671 Exonuclease VII small subunit; Region: Exonuc_VII_S; cl00750 1105104001672 AsmA-like C-terminal region; Region: AsmA_2; cl15864 1105104001673 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK00122 1105104001674 RimM N-terminal domain; Region: RimM; pfam01782 1105104001675 Photosynthetic reaction center (RC) complex, subunit H; RC is an integral membrane protein-pigment complex which catalyzes light-induced reduction of ubiquinone to ubiquinol, generating a transmembrane electrochemical gradient of protons used to produce...; Region: PRCH; cl09959 1105104001676 Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]; Region: AsmA; COG2982 1105104001677 AsmA-like C-terminal region; Region: AsmA_2; cl15864 1105104001678 TPR repeat; Region: TPR_11; pfam13414 1105104001679 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 1105104001680 TPR motif; other site 1105104001681 binding surface 1105104001682 Domain of unknown function (DUF4385); Region: DUF4385; pfam14328 1105104001683 spore photoproduct lyase; Region: photo_TT_lyase; cl15393 1105104001684 UbiA prenyltransferase family; Region: UbiA; cl00337 1105104001685 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 1105104001686 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 1105104001687 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 1105104001688 RNA binding surface [nucleotide binding]; other site 1105104001689 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105104001690 Walker A/P-loop; other site 1105104001691 ATP binding site [chemical binding]; other site 1105104001692 Q-loop/lid; other site 1105104001693 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 1105104001694 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 1105104001695 putative ADP-binding pocket [chemical binding]; other site 1105104001696 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 1105104001697 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 1105104001698 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 1105104001699 RND family efflux transporter, MFP subunit; Region: RND_mfp; TIGR01730 1105104001700 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 1105104001701 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 1105104001702 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 1105104001703 active site 1105104001704 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 1105104001705 active site 1105104001706 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 1105104001707 S-adenosylmethionine binding site [chemical binding]; other site 1105104001708 UDP-N-acetylglucosamine 2-epimerase [Cell envelope biogenesis, outer membrane]; Region: WecB; COG0381 1105104001709 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 1105104001710 active site 1105104001711 homodimer interface [polypeptide binding]; other site 1105104001712 UDP-N-acetylglucosamine 4,6-dehydratase/5-epimerase; Region: FnlA; TIGR04130 1105104001713 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 1105104001714 NAD(P) binding site [chemical binding]; other site 1105104001715 homodimer interface [polypeptide binding]; other site 1105104001716 substrate binding site [chemical binding]; other site 1105104001717 active site 1105104001718 Polysaccharide biosynthesis protein C-terminal; Region: Polysacc_syn_2C; pfam08485 1105104001719 dTDP-4-dehydrorhamnose reductase [Cell envelope biogenesis, outer membrane]; Region: RfbD; COG1091 1105104001720 dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs; Region: dTDP_HR_like_SDR_e; cd05254 1105104001721 NADP binding site [chemical binding]; other site 1105104001722 active site 1105104001723 putative substrate binding site [chemical binding]; other site 1105104001724 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 1105104001725 sequence-specific DNA binding site [nucleotide binding]; other site 1105104001726 salt bridge; other site 1105104001727 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 includes...; Region: RuvC_resolvase; cl00243 1105104001728 Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; Region: COG2194 1105104001729 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 1105104001730 Sulfatase; Region: Sulfatase; cl10460 1105104001731 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 1105104001732 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 1105104001733 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 1105104001734 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 1105104001735 dimer interface [polypeptide binding]; other site 1105104001736 decamer (pentamer of dimers) interface [polypeptide binding]; other site 1105104001737 catalytic triad [active] 1105104001738 peroxidatic and resolving cysteines [active] 1105104001739 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 1105104001740 Possible lysine decarboxylase; Region: Lysine_decarbox; cl00695 1105104001741 DNA topoisomerase I; Validated; Region: PRK06599 1105104001742 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 1105104001743 active site 1105104001744 interdomain interaction site; other site 1105104001745 putative metal-binding site [ion binding]; other site 1105104001746 nucleotide binding site [chemical binding]; other site 1105104001747 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 1105104001748 domain I; other site 1105104001749 DNA binding groove [nucleotide binding] 1105104001750 phosphate binding site [ion binding]; other site 1105104001751 domain II; other site 1105104001752 domain III; other site 1105104001753 nucleotide binding site [chemical binding]; other site 1105104001754 catalytic site [active] 1105104001755 domain IV; other site 1105104001756 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 1105104001757 Uncharacterized C-terminal domain of topoisomerase IA [General function prediction only]; Region: COG1754 1105104001758 Topoisomerase C-terminal repeat; Region: Toprim_C_rpt; pfam13368 1105104001759 glutamyl-tRNA synthetase; Provisional; Region: PRK12558 1105104001760 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 1105104001761 HIGH motif; other site 1105104001762 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 1105104001763 active site 1105104001764 KMSKS motif; other site 1105104001765 Frataxin is a nuclear-encoded mitochondrial protein implicated in Friedreich's ataxia (FRDA), an human autosomal recessive neurodegenerative disease; Frataxin is found in eukaryotes and in purple bacteria; lack of frataxin causes iron to accumulate in...; Region: Frataxin; cd00503 1105104001766 putative iron binding site [ion binding]; other site 1105104001767 YceG-like family; Region: YceG; pfam02618 1105104001768 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 1105104001769 dimerization interface [polypeptide binding]; other site 1105104001770 lipid-A-disaccharide synthase; Reviewed; Region: lpxB; PRK00025 1105104001771 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 1105104001772 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105104001773 Uncharacterized conserved protein [Function unknown]; Region: COG5464 1105104001774 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105104001775 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105104001776 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105104001777 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 1105104001778 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105104001779 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 1105104001780 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 1105104001781 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 1105104001782 Walker A motif; other site 1105104001783 ATP binding site [chemical binding]; other site 1105104001784 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105104001785 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 1105104001786 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 1105104001787 active site 1105104001788 HslU subunit interaction site [polypeptide binding]; other site 1105104001789 Rickettsial palindromic element RPE5 domain; Region: RPE5; TIGR03776 1105104001790 Protein of unknown function (DUF2628); Region: DUF2628; pfam10947 1105104001791 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 1105104001792 nucleotide binding site/active site [active] 1105104001793 HIT family signature motif; other site 1105104001794 catalytic residue [active] 1105104001795 aspartate-semialdehyde dehydrogenase; Provisional; Region: PRK14874 1105104001796 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105104001797 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; cl15856 1105104001798 type I secretion system ABC transporter, PrtD family; Region: type_I_sec_PrtD; TIGR01842 1105104001799 This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain. They export...; Region: ABCC_Protease_Secretion; cd03246 1105104001800 Walker A/P-loop; other site 1105104001801 ATP binding site [chemical binding]; other site 1105104001802 Q-loop/lid; other site 1105104001803 ABC transporter signature motif; other site 1105104001804 Walker B; other site 1105104001805 D-loop; other site 1105104001806 H-loop/switch region; other site 1105104001807 type I secretion membrane fusion protein, HlyD family; Region: type_I_hlyD; TIGR01843 1105104001808 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 1105104001809 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 1105104001810 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 1105104001811 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105104001812 putative substrate translocation pore; other site 1105104001813 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 1105104001814 Gram-negative bacterial tonB protein; Region: TonB; cl10048 1105104001815 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 1105104001816 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; cl00568 1105104001817 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 1105104001818 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 1105104001819 histidyl-tRNA synthetase; Reviewed; Region: hisS; PRK00037 1105104001820 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 ATP-dependent...; Region: HisRS-like_core; cd00773 1105104001821 dimer interface [polypeptide binding]; other site 1105104001822 motif 1; other site 1105104001823 active site 1105104001824 motif 2; other site 1105104001825 motif 3; other site 1105104001826 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 1105104001827 anticodon binding site; other site 1105104001828 amino acid transporter; Region: 2A0306; TIGR00909 1105104001829 Spore germination protein; Region: Spore_permease; cl15802 1105104001830 tRNA methyl transferase; Region: tRNA_Me_trans; pfam03054 1105104001831 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 1105104001832 Ligand Binding Site [chemical binding]; other site 1105104001833 Cytochrome c oxidase assembly protein CtaG/Cox11; Region: CtaG_Cox11; cl01240 1105104001834 RNA polymerase factor sigma-32; Reviewed; Region: PRK06596 1105104001835 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 1105104001836 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1105104001837 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 1105104001838 translocation protein TolB; Provisional; Region: tolB; PRK05137 1105104001839 TolB amino-terminal domain; Region: TolB_N; cl00639 1105104001840 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 1105104001841 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 1105104001842 Thymidylate synthase complementing protein; Region: Thy1; cl03630 1105104001843 Protein of unknown function DUF45; Region: DUF45; cl00636 1105104001844 Peptidase family M23; Region: Peptidase_M23; pfam01551 1105104001845 Ribose/Galactose Isomerase; Region: LacAB_rpiB; cl00485 1105104001846 DNA mismatch repair protein MutS; Provisional; Region: PRK05399 1105104001847 MutS domain I; Region: MutS_I; pfam01624 1105104001848 MutS domain II; Region: MutS_II; pfam05188 1105104001849 MutS family domain IV; Region: MutS_IV; pfam05190 1105104001850 MutS1 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal...; Region: ABC_MutS1; cd03284 1105104001851 Walker A/P-loop; other site 1105104001852 ATP binding site [chemical binding]; other site 1105104001853 Q-loop/lid; other site 1105104001854 ABC transporter signature motif; other site 1105104001855 Walker B; other site 1105104001856 D-loop; other site 1105104001857 H-loop/switch region; other site 1105104001858 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 cysteine...; Region: CysQ; cd01638 1105104001859 active site 1105104001860 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 1105104001861 Haloacid Dehalogenase-like Hydrolases; Region: HAD_like; cl11391 1105104001862 Phage portal protein; Region: Phage_portal; pfam04860 1105104001863 Phage portal protein; Region: Phage_portal; pfam04860 1105104001864 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 1105104001865 Ppx/GppA phosphatase family; Region: Ppx-GppA; cl15449 1105104001866 type IV secretion system component VirD4; Provisional; Region: PRK13897 1105104001867 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 1105104001868 Walker A motif; other site 1105104001869 ATP binding site [chemical binding]; other site 1105104001870 Walker B motif; other site 1105104001871 P-type DNA transfer ATPase VirB11; Region: VirB11; TIGR02788 1105104001872 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 1105104001873 Walker A motif; other site 1105104001874 hexamer interface [polypeptide binding]; other site 1105104001875 ATP binding site [chemical binding]; other site 1105104001876 Walker B motif; other site 1105104001877 Bacterial conjugation TrbI-like protein; Region: TrbI; cl04242 1105104001878 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cl11423 1105104001879 VirB8 protein; Region: VirB8; cl01500 1105104001880 Protein of unknown function (DUF2706); Region: DUF2706; pfam10913 1105104001881 VirB8 protein; Region: VirB8; cl01500 1105104001882 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 1105104001883 VirB7 interaction site; other site 1105104001884 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Region: Oxidored_q2; cl00492 1105104001885 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06591 1105104001886 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 1105104001887 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06589 1105104001888 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 1105104001889 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 1105104001890 oligomeric interface; other site 1105104001891 putative active site [active] 1105104001892 homodimer interface [polypeptide binding]; other site 1105104001893 putative monovalent cation/H+ antiporter subunit D; Reviewed; Region: PRK06588 1105104001894 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; cl14187 1105104001895 Protease II [Amino acid transport and metabolism]; Region: PtrB; COG1770 1105104001896 Rickettsial palindromic element RPE3 domain; Region: RPE3; TIGR03775 1105104001897 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 1105104001898 Cell cycle protein; Region: FTSW_RODA_SPOVE; cl00511 1105104001899 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105104001900 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 1105104001901 potential frameshift: common BLAST hit: gi|67459245|ref|YP_246869.1| NTPase 1105104001902 potential frameshift: common BLAST hit: gi|15892293|ref|NP_360007.1| ATP-dependent protease subunit C (ClpC) 1105104001903 Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators; Region: HTH_XRE; cl15761 1105104001904 GTP-binding protein LepA; Provisional; Region: PRK05433 1105104001905 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 1105104001906 G1 box; other site 1105104001907 putative GEF interaction site [polypeptide binding]; other site 1105104001908 GTP/Mg2+ binding site [chemical binding]; other site 1105104001909 Switch I region; other site 1105104001910 G2 box; other site 1105104001911 G3 box; other site 1105104001912 Switch II region; other site 1105104001913 G4 box; other site 1105104001914 G5 box; other site 1105104001915 lepA_II: This subfamily represents the domain II of LepA, a GTP-binding protein localized in the cytoplasmic membrane. The N-terminal domain of LepA shares regions of homology to translation factors. In terms of interaction with the ribosome, EF-G, EF-Tu...; Region: lepA_II; cd03699 1105104001916 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 1105104001917 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 1105104001918 RF-1 domain; Region: RF-1; cl02875 1105104001919 Protein chain release factor B [Translation, ribosomal structure and biogenesis]; Region: PrfB; COG1186 1105104001920 RF-1 domain; Region: RF-1; cl02875 1105104001921 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]; Region: COG4804 1105104001922 Protein of unknown function (DUF1016); Region: DUF1016; pfam06250 1105104001923 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 1105104001924 putative dimer interface [polypeptide binding]; other site 1105104001925 Cytochrome C1 family; Region: Cytochrom_C1; pfam02167 1105104001926 Cytochrome c; Region: Cytochrom_C; cl11414 1105104001927 GIY-YIG nuclease domain superfamily; Region: GIY-YIG_SF; cl15257 1105104001928 catalytic site [active] 1105104001929 metal binding site [ion binding]; metal-binding site 1105104001930 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 1105104001931 Qi binding site; other site 1105104001932 cytochrome b; Provisional; Region: CYTB; MTH00191 1105104001933 intrachain domain interface; other site 1105104001934 interchain domain interface [polypeptide binding]; other site 1105104001935 heme bH binding site [chemical binding]; other site 1105104001936 heme bL binding site [chemical binding]; other site 1105104001937 Qo binding site; other site 1105104001938 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 1105104001939 interchain domain interface [polypeptide binding]; other site 1105104001940 intrachain domain interface; other site 1105104001941 Qi binding site; other site 1105104001942 Qo binding site; other site 1105104001943 Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; Region: UCR_Fe-S_N; pfam10399 1105104001944 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 1105104001945 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 1105104001946 [2Fe-2S] cluster binding site [ion binding]; other site 1105104001947 Protein of unknown function (DUF2670); Region: DUF2670; pfam10875 1105104001948 putative monovalent cation/H+ antiporter subunit B; Reviewed; Region: PRK12507 1105104001949 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 1105104001950 Domain of unknown function (DUF4040); Region: DUF4040; cl00676 1105104001951 Na+/H+ antiporter subunit; Region: PhaG_MnhG_YufB; cl00583 1105104001952 isocitrate dehydrogenase; Validated; Region: PRK09222 1105104001953 Isocitrate/isopropylmalate dehydrogenase; Region: Iso_dh; cl00445 1105104001954 Outer membrane protein [Cell envelope biogenesis, outer membrane]; Region: HlpA; COG2825 1105104001955 haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED; Region: HAD-SF-IA-v3; TIGR01509 1105104001956 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 1105104001957 GTP-binding protein TypA/BipA; Region: TypA_BipA; TIGR01394 1105104001958 G1 box; other site 1105104001959 putative GEF interaction site [polypeptide binding]; other site 1105104001960 GTP/Mg2+ binding site [chemical binding]; other site 1105104001961 Switch I region; other site 1105104001962 G2 box; other site 1105104001963 G3 box; other site 1105104001964 Switch II region; other site 1105104001965 G4 box; other site 1105104001966 G5 box; other site 1105104001967 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 1105104001968 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 1105104001969 pyruvate dehydrogenase subunit beta; Validated; Region: PRK09212 1105104001970 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 1105104001971 alpha subunit interface [polypeptide binding]; other site 1105104001972 TPP binding site [chemical binding]; other site 1105104001973 heterodimer interface [polypeptide binding]; other site 1105104001974 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 1105104001975 pyruvate dehydrogenase E1 component, alpha subunit; Region: PDH_E1_alph_y; TIGR03182 1105104001976 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 1105104001977 tetramer interface [polypeptide binding]; other site 1105104001978 TPP-binding site [chemical binding]; other site 1105104001979 heterodimer interface [polypeptide binding]; other site 1105104001980 phosphorylation loop region [posttranslational modification] 1105104001981 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 1105104001982 putative catalytic site [active] 1105104001983 putative phosphate binding site [ion binding]; other site 1105104001984 active site 1105104001985 metal binding site A [ion binding]; metal-binding site 1105104001986 DNA binding site [nucleotide binding] 1105104001987 putative AP binding site [nucleotide binding]; other site 1105104001988 putative metal binding site B [ion binding]; other site 1105104001989 potential frameshift: common BLAST hit: gi|15892268|ref|NP_359982.1| penicillin-binding protein 4* 1105104001990 potential frameshift: common BLAST hit: gi|15892268|ref|NP_359982.1| penicillin-binding protein 4* 1105104001991 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 1105104001992 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 1105104001993 RNA binding surface [nucleotide binding]; other site 1105104001994 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 1105104001995 active site 1105104001996 Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]; Region: CtaA; COG1612 1105104001997 Cytochrome oxidase assembly protein; Region: COX15-CtaA; cl15852 1105104001998 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 1105104001999 RNA binding site [nucleotide binding]; other site 1105104002000 ribonuclease, Rne/Rng family; Region: RNaseEG; TIGR00757 1105104002001 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 1105104002002 UDP-3-O-acyl-N-acetylglucosamine deacetylase [Cell envelope biogenesis, outer membrane]; Region: LpxC; cl00512 1105104002003 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 1105104002004 Cytochrome c; Region: Cytochrom_C; cl11414 1105104002005 NfeD-like C-terminal, partner-binding; Region: NfeD; cl00686 1105104002006 cell division protein FtsA; Region: ftsA; TIGR01174 1105104002007 Cell division protein FtsA; Region: FtsA; cl11496 1105104002008 Cell division protein FtsA; Region: FtsA; cl11496 1105104002009 POTRA domain, FtsQ-type; Region: POTRA_1; pfam08478 1105104002010 Cell division protein FtsQ; Region: FtsQ; pfam03799 1105104002011 D-alanine--D-alanine ligase; Reviewed; Region: ddl; PRK01372 1105104002012 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 1105104002013 ATP-grasp domain; Region: ATP-grasp_4; cl03087 1105104002014 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13905 1105104002015 FAD binding domain; Region: FAD_binding_4; pfam01565 1105104002016 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 1105104002017 UDP-N-acetylmuramate--L-alanine ligase; Provisional; Region: murC; PRK00421 1105104002018 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 1105104002019 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 1105104002020 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 1105104002021 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 1105104002022 BolA-like protein; Region: BolA; cl00386 1105104002023 PD-(D/E)XK nuclease family transposase; Region: PDDEXK_2; pfam12784 1105104002024 Multidrug resistance efflux pump [Defense mechanisms]; Region: EmrA; COG1566 1105104002025 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 1105104002026 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 1105104002027 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 1105104002028 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 1105104002029 Phosphatidylserine decarboxylase; Region: PS_Dcarbxylase; cl03656 1105104002030 Domain of unknown function (DUF2610); Region: DUF2610; pfam11020 1105104002031 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 1105104002032 active site 1105104002033 elongation factor P; Validated; Region: PRK00529 1105104002034 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 1105104002035 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 1105104002036 RNA binding site [nucleotide binding]; other site 1105104002037 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 1105104002038 RNA binding site [nucleotide binding]; other site 1105104002039 response regulator PleD; Reviewed; Region: pleD; PRK09581 1105104002040 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 1105104002041 active site 1105104002042 phosphorylation site [posttranslational modification] 1105104002043 intermolecular recognition site; other site 1105104002044 dimerization interface [polypeptide binding]; other site 1105104002045 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 1105104002046 active site 1105104002047 phosphorylation site [posttranslational modification] 1105104002048 intermolecular recognition site; other site 1105104002049 dimerization interface [polypeptide binding]; other site 1105104002050 Diguanylate-cyclase (DGC) or GGDEF domain; Region: GGDEF; cd01949 1105104002051 metal binding site [ion binding]; metal-binding site 1105104002052 active site 1105104002053 I-site; other site 1105104002054 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 1105104002055 putative active site [active] 1105104002056 Ap4A binding site [chemical binding]; other site 1105104002057 nudix motif; other site 1105104002058 putative metal binding site [ion binding]; other site 1105104002059 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; cl00942 1105104002060 DCoH /HNF-1 dimer interaction site [polypeptide binding]; other site 1105104002061 DCoH tetramer interaction site [polypeptide binding]; other site 1105104002062 Ribosomal protein S9/S16; Region: Ribosomal_S9; cl00334 1105104002063 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 1105104002064 23S rRNA interface [nucleotide binding]; other site 1105104002065 L3 interface [polypeptide binding]; other site 1105104002066 FOG: WD40-like repeat [Function unknown]; Region: COG1520 1105104002067 Beta-barrel assembly machinery (Bam) complex component B and related proteins; Region: BamB_YfgL; cd10276 1105104002068 Trp docking motif [polypeptide binding]; other site 1105104002069 Protein of unknown function (DUF2659); Region: DUF2659; pfam10858 1105104002070 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1729 1105104002071 Tetratricopeptide repeat; Region: TPR_6; pfam13174 1105104002072 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 1105104002073 dimer interface [polypeptide binding]; other site 1105104002074 phosphorylation site [posttranslational modification] 1105104002075 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 1105104002076 ATP binding site [chemical binding]; other site 1105104002077 Mg2+ binding site [ion binding]; other site 1105104002078 G-X-G motif; other site 1105104002079 Periplasmic protease [Cell envelope biogenesis, outer membrane]; Region: Prc; COG0793 1105104002080 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 1105104002081 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 1105104002082 protein binding site [polypeptide binding]; other site 1105104002083 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 1105104002084 Catalytic dyad [active] 1105104002085 DNA topoisomerase IV, B subunit, proteobacterial; Region: parE_Gneg; TIGR01055 1105104002086 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 1105104002087 ATP binding site [chemical binding]; other site 1105104002088 Mg2+ binding site [ion binding]; other site 1105104002089 G-X-G motif; other site 1105104002090 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 1105104002091 anchoring element; other site 1105104002092 dimer interface [polypeptide binding]; other site 1105104002093 ATP binding site [chemical binding]; other site 1105104002094 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 1105104002095 active site 1105104002096 metal binding site [ion binding]; metal-binding site 1105104002097 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 1105104002098 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 1105104002099 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 1105104002100 Protein of unknown function (DUF2497); Region: DUF2497; cl11534 1105104002101 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 1105104002102 glutamyl-tRNA(Gln) amidotransferase subunit E; Validated; Region: PRK04028 1105104002103 Protein of unknown function (DUF2660); Region: DUF2660; pfam10859 1105104002104 Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); Region: DUF2310; cl02380 1105104002105 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105104002106 H-loop/switch region; other site 1105104002107 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105104002108 ABC transporter signature motif; other site 1105104002109 Walker B; other site 1105104002110 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105104002111 Walker A/P-loop; other site 1105104002112 ATP binding site [chemical binding]; other site 1105104002113 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK00413 1105104002114 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 1105104002115 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 1105104002116 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 1105104002117 active site 1105104002118 dimer interface [polypeptide binding]; other site 1105104002119 motif 1; other site 1105104002120 motif 2; other site 1105104002121 motif 3; other site 1105104002122 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 1105104002123 anticodon binding site; other site 1105104002124 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed; Region: PRK09362 1105104002125 bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase; Region: SAICAR_synt_PurC; cd01415 1105104002126 ATP binding site [chemical binding]; other site 1105104002127 active site 1105104002128 substrate binding site [chemical binding]; other site 1105104002129 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 1105104002130 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 1105104002131 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 1105104002132 UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide; Region: Beta4Glucosyltransferase; cd02511 1105104002133 putative metal binding site; other site 1105104002134 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 1105104002135 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 1105104002136 cytochrome d ubiquinol oxidase subunit 2; Provisional; Region: PRK15003; cl12219 1105104002137 Cytochrome oxidase subunit II; Region: Cyto_ox_2; pfam02322 1105104002138 Bacterial Cytochrome Ubiquinol Oxidase; Region: Bac_Ubq_Cox; cl00562 1105104002139 Protein of unknown function (DUF2671); Region: DUF2671; pfam10877 1105104002140 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 1105104002141 ABC transporter transmembrane region; Region: ABC_membrane; cl00549 1105104002142 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105104002143 Walker A/P-loop; other site 1105104002144 ATP binding site [chemical binding]; other site 1105104002145 Q-loop/lid; other site 1105104002146 ABC transporter signature motif; other site 1105104002147 Walker B; other site 1105104002148 D-loop; other site 1105104002149 H-loop/switch region; other site 1105104002150 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 1105104002151 Ankyrin repeats (many copies); Region: Ank_4; pfam13637 1105104002152 Queuosine biosynthesis protein; Region: Queuosine_synth; cl00523 1105104002153 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 1105104002154 Predicted ATPase [General function prediction only]; Region: COG1485 1105104002155 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 1105104002156 Walker A motif; other site 1105104002157 ATP binding site [chemical binding]; other site 1105104002158 Walker B motif; other site 1105104002159 Protein of unknown function (DUF563); Region: DUF563; cl15705 1105104002160 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 1105104002161 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 1105104002162 putative active site [active] 1105104002163 substrate binding site [chemical binding]; other site 1105104002164 putative cosubstrate binding site; other site 1105104002165 catalytic site [active] 1105104002166 C-terminal domain of Formyltransferase and other enzymes; Region: Met_tRNA_FMT_C; cd08704 1105104002167 substrate binding site [chemical binding]; other site 1105104002168 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 1105104002169 active site 1105104002170 catalytic residues [active] 1105104002171 metal binding site [ion binding]; metal-binding site 1105104002172 Iron-sulphur cluster assembly; Region: Fe-S_assembly; cl01123 1105104002173 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 1105104002174 DNA gyrase subunit A; Validated; Region: PRK05560 1105104002175 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 in DNA...; Region: TOP4c; cd00187 1105104002176 CAP-like domain; other site 1105104002177 active site 1105104002178 primary dimer interface [polypeptide binding]; other site 1105104002179 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105104002180 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105104002181 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105104002182 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105104002183 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 1105104002184 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]; Region: ATM1; COG5265 1105104002185 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105104002186 Walker A/P-loop; other site 1105104002187 ATP binding site [chemical binding]; other site 1105104002188 Q-loop/lid; other site 1105104002189 potential frameshift: common BLAST hit: gi|157964270|ref|YP_001499094.1| multidrug resistance protein Atm1 1105104002190 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 1105104002191 GSH binding site [chemical binding]; other site 1105104002192 catalytic residues [active] 1105104002193 excinuclease ABC subunit B; Provisional; Region: PRK05298 1105104002194 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 1105104002195 ATP binding site [chemical binding]; other site 1105104002196 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 1105104002197 nucleotide binding region [chemical binding]; other site 1105104002198 ATP-binding site [chemical binding]; other site 1105104002199 Ultra-violet resistance protein B; Region: UvrB; pfam12344 1105104002200 UvrB/uvrC motif; Region: UVR; pfam02151 1105104002201 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 1105104002202 RNA/DNA hybrid binding site [nucleotide binding]; other site 1105104002203 active site 1105104002204 co-chaperone HscB; Provisional; Region: hscB; PRK01356 1105104002205 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 1105104002206 HSP70 interaction site [polypeptide binding]; other site 1105104002207 chaperone protein HscA; Provisional; Region: hscA; PRK01433 1105104002208 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 1105104002209 catalytic loop [active] 1105104002210 iron binding site [ion binding]; other site 1105104002211 TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]; Region: Imp; COG2358 1105104002212 NMT1-like family; Region: NMT1_2; cl15260 1105104002213 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 1105104002214 Ligand Binding Site [chemical binding]; other site 1105104002215 potential frameshift: common BLAST hit: gi|67459460|ref|YP_247084.1| cell surface antigen-like protein Sca8 1105104002216 potential frameshift: common BLAST hit: gi|67459460|ref|YP_247084.1| cell surface antigen-like protein Sca8 1105104002217 potential frameshift: common BLAST hit: gi|15892172|ref|NP_359886.1| bifunctional penicillin-binding protein 1C 1105104002218 potential frameshift: common BLAST hit: gi|229586439|ref|YP_002844940.1| Bifunctional penicillin-binding protein 1C 1105104002219 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional; Region: dapD; PRK11830 1105104002220 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 1105104002221 trimer interface [polypeptide binding]; other site 1105104002222 active site 1105104002223 substrate binding site [chemical binding]; other site 1105104002224 CoA binding site [chemical binding]; other site 1105104002225 zinc-ribbon domain; Region: zinc_ribbon_5; cl11777 1105104002226 TrbC/VIRB2 family; Region: TrbC; cl01583 1105104002227 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 1105104002228 Subunit III/VIIa interface [polypeptide binding]; other site 1105104002229 Phospholipid binding site [chemical binding]; other site 1105104002230 Subunit I/III interface [polypeptide binding]; other site 1105104002231 Subunit III/VIb interface [polypeptide binding]; other site 1105104002232 Subunit III/VIa interface; other site 1105104002233 Subunit III/Vb interface [polypeptide binding]; other site 1105104002234 Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain; Region: DMQH; cd01042 1105104002235 diiron binding motif [ion binding]; other site 1105104002236 DNA polymerase III subunit delta; Reviewed; Region: holA; PRK06585 1105104002237 Lipopolysaccharide-assembly; Region: LptE; cl01125 1105104002238 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad...; Region: Tryp_SPc; cl00149 1105104002239 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 1105104002240 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 1105104002241 FGGY family of carbohydrate kinases; Region: FGGY; cl08364 1105104002242 chaperone protein DnaJ; Provisional; Region: PRK14300 1105104002243 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 1105104002244 HSP70 interaction site [polypeptide binding]; other site 1105104002245 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 1105104002246 substrate binding site [polypeptide binding]; other site 1105104002247 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 1105104002248 Zn binding sites [ion binding]; other site 1105104002249 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 1105104002250 dimer interface [polypeptide binding]; other site 1105104002251 ChaB; Region: ChaB; cl01887 1105104002252 ChaB; Region: ChaB; cl01887 1105104002253 DNA uptake lipoprotein [General function prediction only]; Region: ComL; COG4105 1105104002254 Tetratricopeptide repeat; Region: TPR_6; pfam13174 1105104002255 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 1105104002256 RecN ATPase involved in DNA repair; ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and...; Region: ABC_RecN; cd03241 1105104002257 Walker A/P-loop; other site 1105104002258 ATP binding site [chemical binding]; other site 1105104002259 Q-loop/lid; other site 1105104002260 Allexivirus 40kDa protein; Region: Allexi_40kDa; pfam05549 1105104002261 RecN ATPase involved in DNA repair; ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and...; Region: ABC_RecN; cd03241 1105104002262 ABC transporter signature motif; other site 1105104002263 Walker B; other site 1105104002264 D-loop; other site 1105104002265 H-loop/switch region; other site 1105104002266 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]; Region: COG2317 1105104002267 Peptidase family M32 includes thermostable carboxypeptidases TaqCP and PfuCP; Region: M32_Taq; cd06460 1105104002268 active site 1105104002269 Zn binding site [ion binding]; other site 1105104002270 2-oxoglutarate dehydrogenase E1 component; Reviewed; Region: sucA; PRK09404 1105104002271 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 1105104002272 TPP-binding site [chemical binding]; other site 1105104002273 Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes; Region: TPP_enzyme_PYR; cl11410 1105104002274 dihydrolipoamide succinyltransferase; Validated; Region: PRK05704 1105104002275 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 1105104002276 E3 interaction surface; other site 1105104002277 lipoyl attachment site [posttranslational modification]; other site 1105104002278 e3 binding domain; Region: E3_binding; pfam02817 1105104002279 2-oxoacid dehydrogenases acyltransferase (catalytic domain); Region: 2-oxoacid_dh; cl02008 1105104002280 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 1105104002281 active site 1105104002282 CutA1 divalent ion tolerance protein; Region: CutA1; cl00584 1105104002283 Na+/H+-dicarboxylate symporters [Energy production and conversion]; Region: GltP; COG1301 1105104002284 Sodium:dicarboxylate symporter family; Region: SDF; cl00573 1105104002285 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; cl16911 1105104002286 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 1105104002287 Ankyrin repeats (3 copies); Region: Ank_2; pfam12796 1105104002288 coproporphyrinogen III oxidase; Provisional; Region: PRK06582 1105104002289 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 1105104002290 FeS/SAM binding site; other site 1105104002291 HemN C-terminal domain; Region: HemN_C; pfam06969 1105104002292 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 1105104002293 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 1105104002294 Serine proteases of the peptidase family S9A [Amino acid transport and metabolism]; Region: COG1505 1105104002295 Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These...; Region: Esterase_lipase; cl12031 1105104002296 signal recognition particle protein; Provisional; Region: PRK10867 1105104002297 SRP54-type protein, helical bundle domain; Region: SRP54_N; cl03758 1105104002298 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 1105104002299 P loop; other site 1105104002300 GTP binding site [chemical binding]; other site 1105104002301 Signal peptide binding domain; Region: SRP_SPB; pfam02978 1105104002302 DNA polymerase III subunit delta'; Validated; Region: PRK06581 1105104002303 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 1105104002304 IHF dimer interface [polypeptide binding]; other site 1105104002305 IHF - DNA interface [nucleotide binding]; other site 1105104002306 Cation/multidrug efflux pump [Defense mechanisms]; Region: AcrB; COG0841 1105104002307 Protein export membrane protein; Region: SecD_SecF; cl14618 1105104002308 Domain of unknown function (DUF378); Region: DUF378; cl00943 1105104002309 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385; cl00611 1105104002310 RNA methyltransferase; Region: Methyltrans_RNA; pfam04452 1105104002311 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105104002312 Uncharacterized conserved small protein [Function unknown]; Region: COG5508 1105104002313 Protein of unknown function (DUF1674); Region: DUF1674; pfam07896 1105104002314 Coenzyme Q-binding protein COQ10p and similar proteins; Region: COQ10p_like; cd07813 1105104002315 putative coenzyme Q binding site [chemical binding]; other site 1105104002316 23S rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: FtsJ; COG0293 1105104002317 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; cl16911 1105104002318 RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the...; Region: NusB_Sun; cl00223 1105104002319 putative RNA binding site [nucleotide binding]; other site 1105104002320 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]; Region: COG0750 1105104002321 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 1105104002322 active site 1105104002323 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 1105104002324 protein binding site [polypeptide binding]; other site 1105104002325 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 1105104002326 putative substrate binding region [chemical binding]; other site 1105104002327 outer membrane protein assembly complex, YaeT protein; Region: OM_YaeT; TIGR03303 1105104002328 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 1105104002329 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 1105104002330 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 1105104002331 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 1105104002332 Surface antigen variable number repeat; Region: Surf_Ag_VNR; cl10520 1105104002333 Surface antigen; Region: Bac_surface_Ag; cl03097 1105104002334 Protein of unknown function (DUF2674); Region: DUF2674; pfam10879 1105104002335 drug resistance transporter, EmrB/QacA subfamily; Region: efflux_EmrB; TIGR00711 1105104002336 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 1105104002337 putative substrate translocation pore; other site 1105104002338 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 1105104002339 Na+/H+ ion antiporter subunit; Region: MNHE; cl00807 1105104002340 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 1105104002341 putative nucleotide binding site [chemical binding]; other site 1105104002342 uridine monophosphate binding site [chemical binding]; other site 1105104002343 homohexameric interface [polypeptide binding]; other site 1105104002344 ribosome recycling factor; Reviewed; Region: frr; PRK00083 1105104002345 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 round of...; Region: RRF; cd00520 1105104002346 hinge region; other site 1105104002347 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain superfamily; Region: NTP-PPase; cl16941 1105104002348 Glu-tRNAGln amidotransferase C subunit; Region: Glu-tRNAGln; cl00495 1105104002349 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases [Translation, ribosomal structure and biogenesis]; Region: GatA; COG0154 1105104002350 Amidase; Region: Amidase; cl11426 1105104002351 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 1105104002352 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 1105104002353 GatB domain; Region: GatB_Yqey; cl11497 1105104002354 Bacterial extracellular solute-binding proteins, family 3; Region: SBP_bac_3; pfam00497 1105104002355 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 1105104002356 substrate binding pocket [chemical binding]; other site 1105104002357 membrane-bound complex binding site; other site 1105104002358 hinge residues; other site 1105104002359 Flavin Reductases; Region: FlaRed; cl00801 1105104002360 dihydrodipicolinate reductase; Provisional; Region: PRK00048 1105104002361 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105104002362 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 1105104002363 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 1105104002364 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 1105104002365 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 1105104002366 dimer interface [polypeptide binding]; other site 1105104002367 anticodon binding site; other site 1105104002368 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 the...; Region: AspRS_core; cd00777 1105104002369 homodimer interface [polypeptide binding]; other site 1105104002370 motif 1; other site 1105104002371 active site 1105104002372 motif 2; other site 1105104002373 GAD domain; Region: GAD; pfam02938 1105104002374 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 attaches...; Region: class_II_aaRS-like_core; cl00268 1105104002375 active site 1105104002376 motif 3; other site 1105104002377 ATPase MipZ; Region: MipZ; pfam09140 1105104002378 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 1105104002379 P-loop; other site 1105104002380 Magnesium ion binding site [ion binding]; other site 1105104002381 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 1105104002382 Magnesium ion binding site [ion binding]; other site 1105104002383 multifunctional aminopeptidase A; Provisional; Region: PRK00913 1105104002384 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 1105104002385 interface (dimer of trimers) [polypeptide binding]; other site 1105104002386 Substrate-binding/catalytic site; other site 1105104002387 Zn-binding sites [ion binding]; other site 1105104002388 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105104002389 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 1105104002390 DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; Region: RpoC; COG0086 1105104002391 RNA polymerase Rpb1, domain 2; Region: RNA_pol_Rpb1_2; cl11591 1105104002392 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 1105104002393 DNA-directed RNA polymerase subunit beta'; Provisional; Region: rpoC2; PRK02597 1105104002394 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 1105104002395 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 1105104002396 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 1105104002397 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed; Region: PRK09603 1105104002398 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 1105104002399 DNA binding site [nucleotide binding] 1105104002400 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 1105104002401 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; cl04593 1105104002402 DNA-directed RNA polymerase subunit beta'; Provisional; Region: PRK00566 1105104002403 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 1105104002404 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 1105104002405 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; cl04593 1105104002406 RPB10 interaction site [polypeptide binding]; other site 1105104002407 RPB11 interaction site [polypeptide binding]; other site 1105104002408 RPB3 interaction site [polypeptide binding]; other site 1105104002409 RPB12 interaction site [polypeptide binding]; other site 1105104002410 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 1105104002411 RPB3 interaction site [polypeptide binding]; other site 1105104002412 RPB1 interaction site [polypeptide binding]; other site 1105104002413 RPB11 interaction site [polypeptide binding]; other site 1105104002414 RPB10 interaction site [polypeptide binding]; other site 1105104002415 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 1105104002416 core dimer interface [polypeptide binding]; other site 1105104002417 peripheral dimer interface [polypeptide binding]; other site 1105104002418 L10 interface [polypeptide binding]; other site 1105104002419 L11 interface [polypeptide binding]; other site 1105104002420 putative EF-Tu interaction site [polypeptide binding]; other site 1105104002421 putative EF-G interaction site [polypeptide binding]; other site 1105104002422 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 1105104002423 23S rRNA interface [nucleotide binding]; other site 1105104002424 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 1105104002425 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 1105104002426 mRNA/rRNA interface [nucleotide binding]; other site 1105104002427 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 1105104002428 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 1105104002429 23S rRNA interface [nucleotide binding]; other site 1105104002430 putative thiostrepton binding site; other site 1105104002431 L7/L12 interface [polypeptide binding]; other site 1105104002432 L25 interface [polypeptide binding]; other site 1105104002433 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 1105104002434 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 1105104002435 putative homodimer interface [polypeptide binding]; other site 1105104002436 KOW motif; Region: KOW; cl00354 1105104002437 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 1105104002438 elongation factor G; Reviewed; Region: PRK00007 1105104002439 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 1105104002440 G1 box; other site 1105104002441 putative GEF interaction site [polypeptide binding]; other site 1105104002442 GTP/Mg2+ binding site [chemical binding]; other site 1105104002443 Switch I region; other site 1105104002444 G2 box; other site 1105104002445 G3 box; other site 1105104002446 Switch II region; other site 1105104002447 G4 box; other site 1105104002448 G5 box; other site 1105104002449 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 1105104002450 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 1105104002451 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 1105104002452 Ribosomal protein S7p/S5e; Region: Ribosomal_S7; cl00313 1105104002453 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 1105104002454 S17 interaction site [polypeptide binding]; other site 1105104002455 S8 interaction site; other site 1105104002456 16S rRNA interaction site [nucleotide binding]; other site 1105104002457 streptomycin interaction site [chemical binding]; other site 1105104002458 23S rRNA interaction site [nucleotide binding]; other site 1105104002459 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 1105104002460 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 1105104002461 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 1105104002462 dimer interface [polypeptide binding]; other site 1105104002463 conserved gate region; other site 1105104002464 putative PBP binding loops; other site 1105104002465 ABC-ATPase subunit interface; other site 1105104002466 succinate dehydrogenase flavoprotein subunit; Reviewed; Region: sdhA; PRK09078 1105104002467 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105104002468 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 1105104002469 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 1105104002470 putative SdhC subunit interface [polypeptide binding]; other site 1105104002471 putative proximal heme binding site [chemical binding]; other site 1105104002472 putative Iron-sulfur protein interface [polypeptide binding]; other site 1105104002473 putative proximal quinone binding site; other site 1105104002474 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 1105104002475 Iron-sulfur protein interface; other site 1105104002476 proximal quinone binding site [chemical binding]; other site 1105104002477 SdhD (CybS) interface [polypeptide binding]; other site 1105104002478 proximal heme binding site [chemical binding]; other site 1105104002479 hypothetical protein; Validated; Region: PRK01415 1105104002480 Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins; Region: RHOD_YceA; cd01518 1105104002481 active site residue [active] 1105104002482 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 1105104002483 Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad...; Region: Tryp_SPc; cl00149 1105104002484 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 1105104002485 protein binding site [polypeptide binding]; other site 1105104002486 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 1105104002487 protein binding site [polypeptide binding]; other site 1105104002488 FtsH protease regulator HflC; Provisional; Region: PRK11029 1105104002489 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 1105104002490 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 1105104002491 HflK protein; Region: hflK; TIGR01933 1105104002492 AAA domain; Region: AAA_31; pfam13614 1105104002493 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 1105104002494 Walker A motif; other site 1105104002495 Predicted nucleoside-diphosphate-sugar epimerase [Cell envelope biogenesis, outer membrane]; Region: COG3660 1105104002496 Mitochondrial fission ELM1; Region: Mito_fiss_Elm1; pfam06258 1105104002497 Nucleotidyltransferase substrate binding protein like; Region: NTase_sub_bind; cl08495 1105104002498 Nucleotidyltransferase substrate binding protein like; Region: NTase_sub_bind; cl08495 1105104002499 rRNA methylase [Translation, ribosomal structure and biogenesis]; Region: LasT; COG0565 1105104002500 SpoU rRNA Methylase family; Region: SpoU_methylase; cl00362 1105104002501 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 includes...; Region: RuvC_resolvase; cd00529 1105104002502 active site 1105104002503 putative DNA-binding cleft [nucleotide binding]; other site 1105104002504 dimer interface [polypeptide binding]; other site 1105104002505 GTPase Era; Provisional; Region: era; PRK15494 1105104002506 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105104002507 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 1105104002508 G1 box; other site 1105104002509 GTP/Mg2+ binding site [chemical binding]; other site 1105104002510 Switch I region; other site 1105104002511 G2 box; other site 1105104002512 Switch II region; other site 1105104002513 G3 box; other site 1105104002514 G4 box; other site 1105104002515 G5 box; other site 1105104002516 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 1105104002517 ribonuclease III; Reviewed; Region: rnc; PRK00102 1105104002518 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 1105104002519 dimerization interface [polypeptide binding]; other site 1105104002520 active site 1105104002521 metal binding site [ion binding]; metal-binding site 1105104002522 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 1105104002523 dsRNA binding site [nucleotide binding]; other site 1105104002524 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 1105104002525 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 1105104002526 Catalytic site [active] 1105104002527 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 1105104002528 NADH dehydrogenase I subunit F; Provisional; Region: PRK13596 1105104002529 SLBB domain; Region: SLBB; pfam10531 1105104002530 NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; Region: NADH_4Fe-4S; cl11211 1105104002531 preprotein translocase subunit SecF; Reviewed; Region: secF; PRK13022 1105104002532 SecD/SecF GG Motif; Region: Sec_GG; pfam07549 1105104002533 Protein export membrane protein; Region: SecD_SecF; cl14618 1105104002534 Uncharacterized protein conserved in bacteria (DUF2312); Region: DUF2312; cl11480 1105104002535 Ribosomal protein L19; Region: Ribosomal_L19; cl00406 1105104002536 tRNA (Guanine-1)-methyltransferase; Region: tRNA_m1G_MT; cl00407 1105104002537 potential frameshift: common BLAST hit: gi|67458489|ref|YP_246113.1| acetate kinase 1105104002538 potential frameshift: common BLAST hit: gi|67458488|ref|YP_246112.1| phosphate acetyltransferase 1105104002539 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 1105104002540 aspartyl-tRNA synthetase; Provisional; Region: PTZ00401 1105104002541 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 1105104002542 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 1105104002543 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 1105104002544 TrbL/VirB6 plasmid conjugal transfer protein; Region: TrbL; cl01503 1105104002545 type IV secretion system ATPase VirB4; Provisional; Region: PRK13898 1105104002546 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 1105104002547 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105104002548 Walker A motif; other site 1105104002549 ATP binding site [chemical binding]; other site 1105104002550 Type IV secretory pathway, VirB3-like protein; Region: VirB3; cl01501 1105104002551 Amino Acid Kinases (AAK) superfamily, catalytic domain; present in such enzymes like N-acetylglutamate kinase (NAGK), carbamate kinase (CK), aspartokinase (AK), glutamate-5-kinase (G5K) and UMP kinase (UMPK). The AAK superfamily includes kinases that...; Region: AAK; cl00452 1105104002552 nucleotide binding site [chemical binding]; other site 1105104002553 substrate binding site [chemical binding]; other site 1105104002554 Predicted GTPase [General function prediction only]; Region: COG0218 1105104002555 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 1105104002556 G1 box; other site 1105104002557 GTP/Mg2+ binding site [chemical binding]; other site 1105104002558 Switch I region; other site 1105104002559 G2 box; other site 1105104002560 G3 box; other site 1105104002561 Switch II region; other site 1105104002562 G4 box; other site 1105104002563 G5 box; other site 1105104002564 Ribosomal protein L31; Region: Ribosomal_L31; cl00377 1105104002565 Ribosomal L28 family; Region: Ribosomal_L28; cl00367 1105104002566 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 1105104002567 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105104002568 Walker A/P-loop; other site 1105104002569 ATP binding site [chemical binding]; other site 1105104002570 Q-loop/lid; other site 1105104002571 ABC transporter signature motif; other site 1105104002572 Walker B; other site 1105104002573 D-loop; other site 1105104002574 H-loop/switch region; other site 1105104002575 Permease; Region: Permease; cl00510 1105104002576 alanine racemase; Reviewed; Region: alr; PRK00053 1105104002577 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 1105104002578 active site 1105104002579 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 1105104002580 dimer interface [polypeptide binding]; other site 1105104002581 substrate binding site [chemical binding]; other site 1105104002582 catalytic residues [active] 1105104002583 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105104002584 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 1105104002585 active site 1105104002586 Phosphoribosylpyrophosphate synthetase [Nucleotide transport and metabolism / Amino acid transport and metabolism]; Region: PrsA; COG0462 1105104002587 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 1105104002588 Toluene tolerance, Ttg2; Region: Tol_Tol_Ttg2; cl01074 1105104002589 VacJ like lipoprotein; Region: VacJ; cl01073 1105104002590 Tetratricopeptide repeat; Region: TPR_16; pfam13432 1105104002591 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; cl16911 1105104002592 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 1105104002593 aspartate aminotransferase; Provisional; Region: PRK05764 1105104002594 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 1105104002595 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1105104002596 homodimer interface [polypeptide binding]; other site 1105104002597 catalytic residue [active] 1105104002598 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: DUF374; Region: LPLAT_DUF374-like; cd07983 1105104002599 putative acyl-acceptor binding pocket; other site 1105104002600 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 1105104002601 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105104002602 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 1105104002603 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 1105104002604 elongation factor Ts; Provisional; Region: tsf; PRK09377 1105104002605 Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been...; Region: UBA; cl00153 1105104002606 Elongation factor TS; Region: EF_TS; pfam00889 1105104002607 Elongation factor TS; Region: EF_TS; pfam00889 1105104002608 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 1105104002609 rRNA interaction site [nucleotide binding]; other site 1105104002610 S8 interaction site; other site 1105104002611 putative laminin-1 binding site; other site 1105104002612 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 1105104002613 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 1105104002614 active site 1105104002615 HIGH motif; other site 1105104002616 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 1105104002617 KMSKS motif; other site 1105104002618 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 1105104002619 tRNA binding surface [nucleotide binding]; other site 1105104002620 anticodon binding site; other site 1105104002621 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl01155 1105104002622 Preprotein translocase SecG subunit; Region: SecG; cl09123 1105104002623 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 1105104002624 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105104002625 putative substrate translocation pore; other site 1105104002626 EamA-like transporter family; Region: EamA; cl01037 1105104002627 Carboxylate/Amino Acid/Amine Transporter; Region: 2A78; TIGR00950 1105104002628 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl01155 1105104002629 NAD/NADP transhydrogenase beta subunit [Energy production and conversion]; Region: PntB; cl00566 1105104002630 NAD(P) transhydrogenase beta subunit; Region: PNTB; pfam02233 1105104002631 Protein of unknown function (DUF1013); Region: DUF1013; cl11533 1105104002632 7-cyano-7-deazaguanine reductase; Provisional; Region: queF; PRK11792 1105104002633 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 1105104002634 Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl...; Region: TFold; cl00263 1105104002635 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 1105104002636 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 1105104002637 active site 1105104002638 phosphorylation site [posttranslational modification] 1105104002639 intermolecular recognition site; other site 1105104002640 dimerization interface [polypeptide binding]; other site 1105104002641 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 1105104002642 DNA binding site [nucleotide binding] 1105104002643 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 1105104002644 SecA binding site; other site 1105104002645 Preprotein binding site; other site 1105104002646 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 1105104002647 trimer interface [polypeptide binding]; other site 1105104002648 active site 1105104002649 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl01155 1105104002650 DNA topoisomerase IV subunit A; Validated; Region: PRK05561 1105104002651 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 in DNA...; Region: TOP4c; cd00187 1105104002652 CAP-like domain; other site 1105104002653 active site 1105104002654 primary dimer interface [polypeptide binding]; other site 1105104002655 Sporulation related domain; Region: SPOR; cl10051 1105104002656 arginyl-tRNA synthetase; Reviewed; Region: argS; PRK01611 1105104002657 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; cl04104 1105104002658 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 1105104002659 active site 1105104002660 HIGH motif; other site 1105104002661 KMSK motif region; other site 1105104002662 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 1105104002663 tRNA binding surface [nucleotide binding]; other site 1105104002664 anticodon binding site; other site 1105104002665 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional; Region: PRK01286 1105104002666 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cl00076 1105104002667 Phosphohydrolase-associated domain; Region: HD_assoc; pfam13286 1105104002668 Iron-sulphur cluster biosynthesis; Region: Fe-S_biosyn; cl00400 1105104002669 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 1105104002670 NeuB family; Region: NeuB; cl00496 1105104002671 Protein of unknown function (DUF2672); Region: DUF2672; pfam10878 1105104002672 putative ABC transporter ATP-binding protein; Reviewed; Region: PRK11819 1105104002673 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 1105104002674 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 1105104002675 ABC transporter; Region: ABC_tran_2; pfam12848 1105104002676 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated...; Region: ABCF_EF-3; cd03221 1105104002677 Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]; Region: Spo0J; COG1475 1105104002678 ParB-like nuclease domain; Region: ParBc; cl02129 1105104002679 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 1105104002680 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 1105104002681 P-loop; other site 1105104002682 Magnesium ion binding site [ion binding]; other site 1105104002683 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 1105104002684 Magnesium ion binding site [ion binding]; other site 1105104002685 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; cl16911 1105104002686 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated; Region: PRK05192 1105104002687 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105104002688 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 1105104002689 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 1105104002690 active site 1105104002691 multimer interface [polypeptide binding]; other site 1105104002692 Sugar phosphate permease [Carbohydrate transport and metabolism]; Region: UhpC; COG2271 1105104002693 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 1105104002694 putative substrate translocation pore; other site 1105104002695 TLC ATP/ADP transporter; Region: TLC; pfam03219 1105104002696 ATP/ADP translocase [Energy production and conversion]; Region: COG3202; cl03940 1105104002697 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 1105104002698 active site 1105104002699 catalytic residues [active] 1105104002700 metal binding site [ion binding]; metal-binding site 1105104002701 Predicted periplasmic protein (DUF2233); Region: DUF2233; pfam09992 1105104002702 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; cl16911 1105104002703 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; cl00453 1105104002704 membrane protein insertase; Provisional; Region: PRK01318 1105104002705 60Kd inner membrane protein; Region: 60KD_IMP; cl00489 1105104002706 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: COG3264 1105104002707 Mechanosensitive ion channel; Region: MS_channel; pfam00924 1105104002708 Prolipoprotein diacylglyceryl transferase; Region: LGT; cl00478 1105104002709 Uncharacterized conserved protein [Function unknown]; Region: COG1565 1105104002710 Putative S-adenosyl-L-methionine-dependent methyltransferase; Region: Methyltransf_28; pfam02636 1105104002711 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105104002712 succinate dehydrogenase iron-sulfur subunit; Reviewed; Region: sdhB; PRK05950 1105104002713 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; cl00159 1105104002714 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; cl16911 1105104002715 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; cl16911 1105104002716 cofactor binding site; other site 1105104002717 FtsH Extracellular; Region: FtsH_ext; pfam06480 1105104002718 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 1105104002719 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 1105104002720 Walker A motif; other site 1105104002721 ATP binding site [chemical binding]; other site 1105104002722 Walker B motif; other site 1105104002723 arginine finger; other site 1105104002724 Peptidase family M41; Region: Peptidase_M41; pfam01434 1105104002725 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 1105104002726 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 1105104002727 Ligand Binding Site [chemical binding]; other site 1105104002728 Rickettsial palindromic element RPE1 domain; Region: RPE1; TIGR01045 1105104002729 50S ribosomal protein L9; Reviewed; Region: rplI; PRK00137 1105104002730 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 1105104002731 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 1105104002732 Ribosomal protein S18; Region: Ribosomal_S18; cl00373 1105104002733 Ribosomal protein S6; Region: Ribosomal_S6; cl00414 1105104002734 Helix-turn-helix domains; Region: HTH; cl00088 1105104002735 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 1105104002736 Fatty acid desaturase; Region: FA_desaturase; pfam00487 1105104002737 Di-iron ligands [ion binding]; other site 1105104002738 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 1105104002739 UGMP family protein; Validated; Region: PRK09604 1105104002740 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl14000 1105104002741 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 1105104002742 Clp amino terminal domain; Region: Clp_N; pfam02861 1105104002743 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 1105104002744 Walker A motif; other site 1105104002745 ATP binding site [chemical binding]; other site 1105104002746 Walker B motif; other site 1105104002747 arginine finger; other site 1105104002748 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 1105104002749 Walker A motif; other site 1105104002750 ATP binding site [chemical binding]; other site 1105104002751 Walker B motif; other site 1105104002752 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; cl11083 1105104002753 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105104002754 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105104002755 active site 1105104002756 Protein of unknown function (DUF2748); Region: DUF2748; pfam10871 1105104002757 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl01155 1105104002758 Colicin V production protein; Region: Colicin_V; cl00567 1105104002759 Uncharacterized ACR, COG1678; Region: DUF179; cl00731 1105104002760 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]; Region: COG1999 1105104002761 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 1105104002762 Cu(I) binding site [ion binding]; other site 1105104002763 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 1105104002764 catalytic center binding site [active] 1105104002765 ATP binding site [chemical binding]; other site 1105104002766 Pterin binding enzymes. This family includes dihydropteroate synthase (DHPS) and cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). DHPS, a...; Region: Pterin_binding; cl00219 1105104002767 substrate binding pocket [chemical binding]; other site 1105104002768 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 1105104002769 folate binding site [chemical binding]; other site 1105104002770 NADP+ binding site [chemical binding]; other site 1105104002771 Heme oxygenase catalyzes the rate limiting step in the degradation of heme to bilirubin, it is essential for recycling of iron from heme. Heme is used as a substrate and cofactor for its own degradation to biliverdin, iron, and carbon monoxide. This...; Region: HemeO; cl15243 1105104002772 recombination protein F; Reviewed; Region: recF; PRK00064 1105104002773 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105104002774 Walker A/P-loop; other site 1105104002775 ATP binding site [chemical binding]; other site 1105104002776 Q-loop/lid; other site 1105104002777 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105104002778 ABC transporter signature motif; other site 1105104002779 Walker B; other site 1105104002780 D-loop; other site 1105104002781 H-loop/switch region; other site 1105104002782 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 1105104002783 S-adenosylmethionine binding site [chemical binding]; other site 1105104002784 Predicted regulatory domain of a methyltransferase [General function prediction only]; Region: COG4797 1105104002785 CarD-like/TRCF domain; Region: CarD_CdnL_TRCF; cl00588 1105104002786 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 1105104002787 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 1105104002788 Putative F0F1-ATPase subunit (ATPase_gene1); Region: ATPase_gene1; cl09754 1105104002789 ATP synthase A chain; Region: ATP-synt_A; cl00413 1105104002790 ATP synthase subunit C; Region: ATP-synt_C; cl00466 1105104002791 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 1105104002792 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 1105104002793 ATP synthase B/B' CF(0); Region: ATP-synt_B; cl07975 1105104002794 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 1105104002795 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 1105104002796 AAA domain; Region: AAA_22; pfam13401 1105104002797 bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase precursor protein; Reviewed; Region: PRK11907 1105104002798 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl01155 1105104002799 Competence protein; Region: Competence; cl00471 1105104002800 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 1105104002801 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 1105104002802 active site 1105104002803 NTP binding site [chemical binding]; other site 1105104002804 metal binding triad [ion binding]; metal-binding site 1105104002805 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 1105104002806 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 1105104002807 intersubunit interface [polypeptide binding]; other site 1105104002808 Uncharacterized P-loop hydrolase UPF0079; Region: UPF0079; cl00520 1105104002809 Putative catalytic NodB homology domain of uncharacterized protein RC0012 from Rickettsia conorii and its bacterial homologs; Region: CE4_RC0012_like; cd10963 1105104002810 NodB motif; other site 1105104002811 putative active site [active] 1105104002812 putative TIM-barrel protein, nifR3 family; Region: nifR3_yhdG; TIGR00737 1105104002813 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 1105104002814 FMN binding site [chemical binding]; other site 1105104002815 active site 1105104002816 catalytic residues [active] 1105104002817 substrate binding site [chemical binding]; other site 1105104002818 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 1105104002819 Patatins and Phospholipases; Region: Patatin_and_cPLA2; cl11396 1105104002820 active site 1105104002821 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional; Region: lpxD; PRK00892 1105104002822 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 1105104002823 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 1105104002824 trimer interface [polypeptide binding]; other site 1105104002825 active site 1105104002826 UDP-GlcNAc binding site [chemical binding]; other site 1105104002827 lipid binding site [chemical binding]; lipid-binding site 1105104002828 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 1105104002829 UDP-N-acetylglucosamine acyltransferase; Provisional; Region: PRK05289 1105104002830 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 1105104002831 active site 1105104002832 PemK-like protein; Region: PemK; cl00995 1105104002833 putative bifunctional glutamate synthase subunit beta/2-polyprenylphenol hydroxylase; Validated; Region: PRK06567 1105104002834 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 1105104002835 FAD binding pocket [chemical binding]; other site 1105104002836 FAD binding motif [chemical binding]; other site 1105104002837 phosphate binding motif [ion binding]; other site 1105104002838 beta-alpha-beta structure motif; other site 1105104002839 NAD binding pocket [chemical binding]; other site 1105104002840 Iron coordination center [ion binding]; other site 1105104002841 ABC-2 type transporter; Region: ABC2_membrane; cl11417 1105104002842 ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]; Region: TagH; COG1134 1105104002843 ABC_KpsT_Wzt The KpsT/Wzt ABC transporter subfamily is involved in extracellular polysaccharide export. Among the variety of membrane-linked or extracellular polysaccharides excreted by bacteria, only capsular polysaccharides, lipopolysaccharides, and...; Region: ABC_KpsT_Wzt; cd03220 1105104002844 Walker A/P-loop; other site 1105104002845 ATP binding site [chemical binding]; other site 1105104002846 Q-loop/lid; other site 1105104002847 ABC transporter signature motif; other site 1105104002848 Walker B; other site 1105104002849 D-loop; other site 1105104002850 H-loop/switch region; other site 1105104002851 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 1105104002852 catalytic residues [active] 1105104002853 Kinase/pyrophosphorylase; Region: Kinase-PPPase; cl00780 1105104002854 methylcobalamin:coenzyme M methyltransferase; Validated; Region: PRK06252 1105104002855 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 1105104002856 substrate binding site [chemical binding]; other site 1105104002857 active site 1105104002858 ferrochelatase; Reviewed; Region: hemH; PRK00035 1105104002859 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 1105104002860 C-terminal domain interface [polypeptide binding]; other site 1105104002861 active site 1105104002862 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 1105104002863 active site 1105104002864 N-terminal domain interface [polypeptide binding]; other site 1105104002865 Uncharacterized protein family (UPF0093); Region: UPF0093; cl00863 1105104002866 potential frameshift: common BLAST hit: gi|67459789|ref|YP_247413.1| prophage antirepressor 1105104002867 Coproporphyrinogen III oxidase; Region: Coprogen_oxidas; cl00433 1105104002868 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 1105104002869 metabolite-proton symporter; Region: 2A0106; TIGR00883 1105104002870 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 1105104002871 Tetratricopeptide repeat; Region: TPR_12; pfam13424 1105104002872 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 1105104002873 TPR motif; other site 1105104002874 TPR repeat; Region: TPR_11; pfam13414 1105104002875 binding surface 1105104002876 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 1105104002877 DNA mismatch repair protein; Reviewed; Region: mutL; PRK00095 1105104002878 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 1105104002879 ATP binding site [chemical binding]; other site 1105104002880 Mg2+ binding site [ion binding]; other site 1105104002881 G-X-G motif; other site 1105104002882 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 1105104002883 ATP binding site [chemical binding]; other site 1105104002884 MutL C terminal dimerisation domain; Region: MutL_C; cl07336 1105104002885 Ribosomal protein L33; Region: Ribosomal_L33; cl00383 1105104002886 Ribosomal protein S16; Region: Ribosomal_S16; cl00368 1105104002887 N-acetyl-anhydromuramyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: ampD; COG3023 1105104002888 Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20...; Region: PGRP; cd06583 1105104002889 amidase catalytic site [active] 1105104002890 Zn binding residues [ion binding]; other site 1105104002891 substrate binding site [chemical binding]; other site 1105104002892 Putative peptidoglycan binding domain; Region: PG_binding_1; cl15437 1105104002893 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; cl14057 1105104002894 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 1105104002895 putative active site [active] 1105104002896 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 1105104002897 Na+/H+ antiporter 1; Region: Na_H_antiport_1; cl01133 1105104002898 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 1105104002899 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 1105104002900 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 1105104002901 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 1105104002902 metal binding site [ion binding]; metal-binding site 1105104002903 dimer interface [polypeptide binding]; other site 1105104002904 DNA polymerase III chi subunit, HolC; Region: DNA_pol3_chi; cl01106 1105104002905 Predicted permeases [General function prediction only]; Region: COG0795; cl12074 1105104002906 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 1105104002907 Plasmid stabilisation system protein; Region: Plasmid_stabil; cl11422 1105104002908 RelB antitoxin; Region: RelB; cl01171 1105104002909 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 1105104002910 active site 1105104002911 Metallo-beta-lactamase superfamily; Region: Lactamase_B; cl00446 1105104002912 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 1105104002913 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105104002914 Walker A/P-loop; other site 1105104002915 ATP binding site [chemical binding]; other site 1105104002916 Q-loop/lid; other site 1105104002917 ABC transporter signature motif; other site 1105104002918 Walker B; other site 1105104002919 D-loop; other site 1105104002920 H-loop/switch region; other site 1105104002921 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 1105104002922 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl01009 1105104002923 Predicted aspartyl protease [General function prediction only]; Region: COG3577 1105104002924 Bacterial aspartate proteases, retropepsin-like protease family; Region: retropepsin_like_bacteria; cd05483 1105104002925 catalytic motif [active] 1105104002926 Catalytic residue [active] 1105104002927 YbaB/EbfC DNA-binding family; Region: YbaB_DNA_bd; cl00494 1105104002928 DNA polymerase III subunits gamma and tau; Validated; Region: PRK06645 1105104002929 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 1105104002930 Walker A motif; other site 1105104002931 ATP binding site [chemical binding]; other site 1105104002932 Walker B motif; other site 1105104002933 arginine finger; other site 1105104002934 DNA polymerase III subunits gamma and tau domain III; Region: DNA_pol3_gamma3; pfam12169 1105104002935 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 1105104002936 Outer membrane lipoprotein carrier protein LolA; Region: LolA; cl01065 1105104002937 NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]; Region: PntA; COG3288 1105104002938 Alanine dehydrogenase/PNT, N-terminal domain; Region: AlaDh_PNT_N; cl15379 1105104002939 Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; Region: MDR; cl16912 1105104002940 NAD(P) binding site [chemical binding]; other site 1105104002941 Domain of unknown function (DUF3814); Region: DUF3814; pfam12769 1105104002942 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 1105104002943 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 1105104002944 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 1105104002945 Cytidylyltransferase family; Region: CTP_transf_1; cl00347 1105104002946 DNA primase, catalytic core; Region: dnaG; TIGR01391 1105104002947 CHC2 zinc finger; Region: zf-CHC2; cl15369 1105104002948 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 1105104002949 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 1105104002950 active site 1105104002951 metal binding site [ion binding]; metal-binding site 1105104002952 interdomain interaction site; other site 1105104002953 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 1105104002954 Sigma-70 factor, region 1.1; Region: Sigma70_r1_1; pfam03979 1105104002955 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 1105104002956 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 1105104002957 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 1105104002958 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 1105104002959 DNA binding residues [nucleotide binding] 1105104002960 tRNA pseudouridine synthase A; Validated; Region: truA; PRK00021 1105104002961 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 1105104002962 dimerization interface 3.5A [polypeptide binding]; other site 1105104002963 active site 1105104002964 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 1105104002965 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 formation of...; Region: AlaRS_core; cd00673 1105104002966 motif 1; other site 1105104002967 active site 1105104002968 motif 2; other site 1105104002969 motif 3; other site 1105104002970 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; cl08469 1105104002971 potential frameshift: common BLAST hit: gi|341584467|ref|YP_004764958.1| proline/betaine transporter 1105104002972 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases, ATP sulphurylases Universal Stress Response protein and electron transfer flavoprotein (ETF). The domain forms a apha/beta/apha fold which binds to Adenosine nucleotide; Region: AANH_like; cl00292 1105104002973 Antitoxin Phd_YefM, type II toxin-antitoxin system; Region: PhdYeFM_antitox; cl09153 1105104002974 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 1105104002975 oligomeric interface; other site 1105104002976 putative active site [active] 1105104002977 homodimer interface [polypeptide binding]; other site 1105104002978 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 attaches...; Region: class_II_aaRS-like_core; cl00268 1105104002979 motif 1; other site 1105104002980 dimer interface [polypeptide binding]; other site 1105104002981 active site 1105104002982 motif 2; other site 1105104002983 motif 3; other site 1105104002984 glycyl-tRNA synthetase subunit beta; Validated; Region: glyS; PRK01233 1105104002985 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 1105104002986 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 1105104002987 Putative GTP-binding controlling metal-binding; Region: SUA5; pfam03481 1105104002988 bifunctional N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase/tRNA (m7G46) methyltransferase; Reviewed; Region: PRK01544 1105104002989 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 1105104002990 S-adenosylmethionine binding site [chemical binding]; other site 1105104002991 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; cl16911 1105104002992 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 1105104002993 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 1105104002994 RNA binding surface [nucleotide binding]; other site 1105104002995 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 1105104002996 active site 1105104002997 Family 4 Uracil-DNA glycosylase (UDG), found exclusively in thermophilic organisms; Region: UDG_F4_TTUDGA_like; cd10030 1105104002998 Fe-S cluster binding site [ion binding]; other site 1105104002999 active site 1105104003000 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 1105104003001 dimer interface [polypeptide binding]; other site 1105104003002 Citrate synthase; Region: Citrate_synt; pfam00285 1105104003003 active site 1105104003004 citrylCoA binding site [chemical binding]; other site 1105104003005 NADH binding [chemical binding]; other site 1105104003006 cationic pore residues; other site 1105104003007 oxalacetate/citrate binding site [chemical binding]; other site 1105104003008 coenzyme A binding site [chemical binding]; other site 1105104003009 catalytic triad [active] 1105104003010 GTPase CgtA; Reviewed; Region: obgE; PRK12299 1105104003011 GTP1/OBG; Region: GTP1_OBG; pfam01018 1105104003012 Obg GTPase; Region: Obg; cd01898 1105104003013 G1 box; other site 1105104003014 GTP/Mg2+ binding site [chemical binding]; other site 1105104003015 Switch I region; other site 1105104003016 G2 box; other site 1105104003017 G3 box; other site 1105104003018 Switch II region; other site 1105104003019 G4 box; other site 1105104003020 G5 box; other site 1105104003021 trigger factor; Provisional; Region: tig; PRK01490 1105104003022 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; cl11587 1105104003023 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 1105104003024 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 1105104003025 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 1105104003026 substrate-cofactor binding pocket; other site 1105104003027 pyridoxal 5'-phosphate binding site [chemical binding]; other site 1105104003028 catalytic residue [active] 1105104003029 heat shock protein 90; Provisional; Region: PRK05218 1105104003030 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 1105104003031 ATP binding site [chemical binding]; other site 1105104003032 Mg2+ binding site [ion binding]; other site 1105104003033 G-X-G motif; other site 1105104003034 Uncharacterized ACR, YggU family COG1872; Region: DUF167; cl00811 1105104003035 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 1105104003036 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 1105104003037 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 1105104003038 dimer interface [polypeptide binding]; other site 1105104003039 ssDNA binding site [nucleotide binding]; other site 1105104003040 tetramer (dimer of dimers) interface [polypeptide binding]; other site 1105104003041 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 1105104003042 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 1105104003043 The excision repair protein UvrA domain I; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_I; cd03270 1105104003044 The excision repair protein UvrA domain II; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep...; Region: ABC_UvrA_II; cd03271 1105104003045 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 1105104003046 ABC component of the metal-type transporters. This family includes transporters involved in the uptake of various metallic cations such as iron, manganese, and zinc. The ATPases of this group of transporters are very similar to members of...; Region: ABC_Metallic_Cations; cd03235 1105104003047 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 1105104003048 Surface antigen [Cell envelope biogenesis, outer membrane]; Region: LipA; COG4520 1105104003049 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]; Region: MMT1; COG0053 1105104003050 Cation efflux family; Region: Cation_efflux; cl00316 1105104003051 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 1105104003052 nucleoside/Zn binding site; other site 1105104003053 dimer interface [polypeptide binding]; other site 1105104003054 catalytic motif [active] 1105104003055 Cytochrome C assembly protein; Region: Cytochrom_C_asm; cl00504 1105104003056 Ferredoxin [Energy production and conversion]; Region: COG1146 1105104003057 4Fe-4S binding domain; Region: Fer4; cl02805 1105104003058 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl01155 1105104003059 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl01155 1105104003060 Protein of unknown function (DUF721); Region: DUF721; cl02324 1105104003061 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 1105104003062 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 1105104003063 Mg++ binding site [ion binding]; other site 1105104003064 putative catalytic motif [active] 1105104003065 putative substrate binding site [chemical binding]; other site 1105104003066 Mov34/MPN/PAD-1 family; Region: MPN_DUF2466; cd08071 1105104003067 MPN+ (JAMM) motif; other site 1105104003068 Zinc-binding site [ion binding]; other site 1105104003069 DNA repair proteins [DNA replication, recombination, and repair]; Region: RadC; COG2003 1105104003070 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 1105104003071 active site 1105104003072 OpgC protein; Region: OpgC_C; cl00792 1105104003073 Domain of unknown function (DUF4117); Region: DUF4117; pfam13491 1105104003074 P-loop containing Nucleoside Triphosphate Hydrolases; Region: P-loop_NTPase; cl09099 1105104003075 Ftsk gamma domain; Region: Ftsk_gamma; cl09645 1105104003076 potential frameshift: common BLAST hit: gi|157964970|ref|YP_001499794.1| ankyrin repeat-containing protein